Cactvs Toolkit Standard Property Definition Summary

Name Datatype Description Literature Enumerations Fields Parameters Computation Dependencies Invalidation CompModule
A_3D_BONDING_VECTOR floatvector 3D bonding vector (i.e. next open ligand shell position in VSEPR model to attach a ligand to). The length of this vector is always 1.0 regardless of the elements involved - this value is only to be used for directions, not as a bond length. Currently, the implementatiion is limited to s/sp/sp2/sp3 geometries.
Compiled C module A_XYZ atomchange bondchange merge 3drelative 3dabsolute hadd mod_a_3d_bonding_vector.so
A_ALCHEMY_TYPE shortstring Atom type as used in the Alchemy program
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC atomchange bondchange a_alchemy_type.xpd
A_ALIHETERO_SUBSTITUENT_COUNT int Count the number of hetero (not C or H) ligands around a central atom which are not part of an aroamtic system
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ISAROMATIC atomchange bondchange mod_a_alihetero_substituent_count.so
A_ALIRING_COUNT short Number of aliphatic rings the atom is member of
countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
Compiled C module R_AROMATIC R_TYPE atomchange bondchange ring mod_a_aliring_count.so
A_ALLENE byte Flag for atoms in allenic system
no:terminal:odd:even
(builtin) A_VALENCE B_TYPE B_ORDER atomchange bondchange
A_ALLYLIC boolean An allylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to a carbon-carbon double bond. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER B_ARORING_COUNT atomchange bondchange atom bond mod_a_allylic.so
A_ALPHA_ARO_COUNT int Number of aromatic systems in alpha position, without the atom being a member of these.
Compiled C module A_ISAROMATIC B_TYPE atomchange bondchange mod_a_alpha_aro_count.so
A_ALPHA_UNSAT_COUNT int Number of vinyl, aliphatic systems in alpha position, without the atom being a member of these. This corresponds to the Lilly SMARTS extension "AG>0" and is used to implement the /IWVy extension.
Compiled C module A_ARORING_COUNT A_UNSATURATION B_TYPE B_ORDER atomchange bondchange mod_a_alpha_unsat_count.so
A_ANNOTATION string Atom annotation string for 2D rendering, containing, for example, charge and radical information
chargerepeatlimit: { value: 2 datatype: string}
stereogroups: { value: 1 datatype: string}
stereo: { value: 7 datatype: string}
isotope: { value: 1 datatype: string}
radical: { value: 1 datatype: string}
mapping: { value: 1 datatype: string}
query: { value: 1 datatype: string}
flags: { value: 1 datatype: string}
nostereo: { value: 0 datatype: string}
auxproperty: { value: {} datatype: string}
auxfilter: { value: {} datatype: string}
(builtin) A_TYPE A_ISOTOPE A_FORMAL_CHARGE A_FREE_ELECTRONS A_ELEMENT A_LABEL_STEREO A_CIP_STEREO A_FLAGS A_DL_STEREO A_QUERY A_HASH_STEREO A_MAP_STEREO A_RADICAL A_STEREO_GROUP atomchange bondchange stereochange
A_AROBOND_COUNT byte Number of aromatic bonds atom participates in
Compiled C module B_ISAROMATIC atomchange bondchange mod_a_arobond_count.so
A_AROCONDENSED boolean Flags for atoms in condensed aromatic ring systems (i.e. atoms which are member in two or more aromatic rings that are connected by an overlapping ring portion, or share an annealed aromatic bond)
Compiled C module R_TYPE R_AROMATIC atomchange bondchange mod_a_arocondensed.so
A_ARORING_COUNT short Number of aromatic rings the atom is member of
countenvelopes: { value: 0 datatype: string}
(builtin) R_AROMATIC R_TYPE atomchange bondchange ring
A_ARORING_SIZE_BITS bitset Bit mask for aromatic ring sizes the atom participates in
ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
Compiled C module R_SIZE R_TYPE B_TYPE A_ARORING_COUNT R_AROMATIC bondchange ring mod_a_aroring_size_bits.so
A_AUTODOCK4_TYPE shortstring Atom type as used in the Autodock 4 program
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC atomchange bondchange a_autodock4_type.xpd
A_BENZYLIC boolean A benzylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to an aromatic carbon atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER A_ARORING_COUNT atomchange bondchange atom bond mod_a_benzylic.so
A_BONDORDER_COUNT bytevector Count of different bond orders around an atom (array).
(builtin) B_ORDER atomchange bondchange
A_BOND_RANGE intpair Ids of first and last bond atom is bonded to
(builtin) B_SEQUENCE_NUMBER atomchange bondchange merge shuffle hadd mol
A_BRICS_LINKER_TYPE short BRICS fragmentation scheme linker type ChemMedChem 2008, 3, 1503-1507
none:C-R1:N-R2:O-R3:C-R4:N-R5:C-R6:C-R7:C-R8:n-R9:N-R10:S-R11:S-R12:C-R13:C-R14:C-R15:C-R16
never
A_BRIDGEHEAD boolean Flag indicating atom is a ring system bridgehead
Compiled C module A_RING_COUNT atomchange bondchange mod_a_bridgehead.so
A_C13SHIFT float C13 NMR spectrum chemical shift., as computed by a simple QSAR function. This is defined only for simple alkanes and more a demo property than of practical use. Osawa, FMC wo mochiita 13C-NMR kagakushifto no yosoku ni kan suru kenkyuu; master thesis; TUT 1993
Tcl script A_FMC0 A_FMC1 A_FMC2 A_FMC3 A_FMC4 A_FMC5 atomchange bondchange a_c13shift.xpd
A_CARBOCYCLE boolean Flag indicating an atom in a carbocycle ESSSR ring
Compiled C module R_TYPE R_HETEROATOM_COUNT atomchange bondchange atom bond mod_a_carbocycle.so
A_CARBON_FRAGMENT_SIZE int Size of the carbon skeleton the atom looked at is member of
Compiled C module B_TYPE A_ELEMENT A_TYPE atomchange bondchange mod_a_carbon_fragment_size.so
A_CENTRALITY double Centrality rating of the atom (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN)
Compiled C module A_TOPO_DISTANCE M_SPAN atomchange bondchange atom bond mod_a_centrality.so
A_CH2_CHAIN_LENGTH int The length of the unbranched CH2/CH3 chain the atom is a member of. Hetero or carbon atoms that do not have 2 or more hydrogen neighbors have a 0 value. Hydrogen atoms are assigned the value of their bonding partner.
Compiled C module A_TYPE A_ELEMENT B_TYPE A_RING_COUNT A_HEAVY_SUBSTITUENT_COUNT atomchange bondchange atom bond mod_a_ch2_chain_length.so
A_CHAIN_LENGTH int The size of the chain-heavy-atoms-only fragment the atom is a member of. Ring atoms have value 0. Hydrogen atoms inherit the value of their bond partner.
Compiled C module A_TYPE A_RING_COUNT B_TYPE atomchange bondchange atom bond mod_a_chain_length.so
A_CIP_STEREO byte Stereo descriptor for atoms, based on CIP (R/S) rules
@SS:S:undef:R:RR
(builtin) atomchange bondchange
A_CL_COUNT int Count the number of chlorine substituents around the atoms
Tcl script A_ELEMENT A_TYPE atomchange bondchange a_cl_count.xpd
A_COLOR color Atom rendering color
mode: { value: light datatype: string}
labellist: { value: 1 datatype: string}
colorlist: { value: green datatype: string}
defaultcolor: { value: gray20 datatype: string}
(builtin) A_ELEMENT A_TYPE never
A_COLOR_SCALE color Get color values in different coloration models useing some atom property as data
property: { value: A_SIGMA_CHARGE datatype: string constraints: property}
maxintensity: { value: 255 datatype: int}
minintensity: { value: 0 datatype: int}
maxvalue: { value: auto datatype: string}
minvalue: { value: auto datatype: string}
colorspace: { value: rgb enumeration: red:green:blue:grey,gray:rgb:fixed datatype: int}
invert: { value: 0 datatype: boolean}
rootscale: { value: 0 datatype: boolean}
zerobalance: { value: 0 datatype: boolean}
filter: { value: {} datatype: string constraints: filterlist}
rangecolors: { value: red 1 green 0 blue datatype: string}
Tcl script atomchange bondchange a_color_scale.xpd
A_COMMENT string free-form atom comment. This is used for exampole in reading PubChem ASN.1 structure data.
never
A_CONFORMER xyzvector Conformers of the ensemble, created by various methods
maxconformers: { value: 10 description: Maximum number of conformers to generate or store minvalue: 1 maxvalue: 99999 datatype: int}
Tcl script A_ELEMENT A_MOL_NUMBER A_TYPE B_TYPE A_FREE_ELECTRONS A_LABEL_STEREO B_LABEL_STEREO B_ORDER A_FLAGS A_FORMAL_CHARGE atomchange bondchange merge a_conformer.xpd
A_CONJUGATED boolean A conjugated atom according to the Lhasa definition. Conjugated atoms are those alpha to a multiply bonded atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
Compiled C module A_TYPE B_TYPE A_FG_PARTICIPATION B_ORDER atomchange bondchange atom bond mod_a_conjugated.so
A_CONJUGATED_SYSTEM_SIZE int The size of the conjugated system the atom participates in according to the Shoichet definition (see literature reference). Atoms not in such a system get value 0. J. Med. Chem. 2003, 46, 4477-4486
Compiled C module A_TYPE A_SP2 A_INAMIDE A_ARORING_COUNT B_TYPE atomchange bondchange atom bond mod_a_conjugated_system_size.so
A_COVALENCY_RADIUS float Default covalence radius
(builtin) A_ELEMENT A_TYPE atomchange
A_CSP2_0H boolean Flag for carbon atoms with sp2 hybridization and no hydrogen substituents
Tcl script A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp2_0h.xpd
A_CSP2_1H boolean Flag for carbon atoms with sp2 hybridization and one hydrogen substituent
Tcl script A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp2_1h.xpd
A_CSP2_2H boolean Flag for carbon atoms with sp2 hybridization and two hydrogen substituents
Tcl script A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp2_2h.xpd
A_CSPECIAL boolean Flag for carbon atoms plotted with symbols by common agreement
triplebond: { value: 1 datatype: string}
allene: { value: 1 datatype: string}
charged: { value: 1 datatype: string}
isotope: { value: 1 datatype: string}
specialbonds: { value: 1 datatype: string}
onlyhligands: { value: 1 datatype: string}
onlyterminalxligands: { value: 1 datatype: string}
never: { value: 0 datatype: string}
(builtin) B_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER A_TERMINAL_DISTANCE A_ISOTOPE A_TEXTLABEL atomchange bondchange merge hadd
A_CSP_0H boolean Flag for carbon atoms with sp hybridization and no hydrogen substituents
Tcl script A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp_0h.xpd
A_CSP_1H boolean Flag for carbon atoms with sp hybridization and one hydrogen substituent
Tcl script A_HCOUNT A_VB_NEIGHBOR_COUNT atomchange bondchange a_csp_1h.xpd
A_DAYLIGHT_ALIRING_COUNT short Number of aliphatic rings the atom is member of, with Daylight definition of aromaticity
countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE atomchange bondchange ring mod_a_daylight_aliring_count.so
A_DAYLIGHT_ARORING_COUNT short Number of aromatic rings the atom is member of, using Daylight aromaticity from R_DAYLIGHT_AROMATIC instead of globally configurable R_AROMATIC
countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE atomchange bondchange ring mod_a_daylight_aroring_count.so
A_DAYLIGHT_ARORING_SIZE_BITS bitset Bit mask for aromatic ring sizes the atom participates in, using always Daylight aromaticity
ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
Compiled C module R_SIZE R_TYPE B_TYPE A_DAYLIGHT_ARORING_COUNT R_DAYLIGHT_AROMATIC bondchange ring mod_a_daylight_aroring_size_bits.so
A_DEGREE byte Number of explicit valences around atom. This corresponds to the absurdly impractical and dangerous 'D' attribute in SMILES and should be avoided to be used for anything else.
ignorequeryatoms: { value: 0 description: If set, query atoms are not counted to the degree value in the atom neighbor sphere datatype: boolean}
ignorestereoh: { value: 1 description: If set, non-implicit H at stereo centers is treated as implicit, assuming it was only added for stereochemistry encoding, not to make a structural statement datatype: boolean}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT A_LABEL_STEREO atomchange bondchange mod_a_degree.so
A_DISTANCE floatvector Interatomic 3D distances
(builtin) A_XYZ atomchange bondchange stereochange 3drelative shuffle hadd
A_DL_STEREO byte Stereo descriptor for atoms, based on D/L nomenclature rules
@L:undef:D
(builtin) atomchange bondchange
A_EC_FRAGMENTS dataset Structure fragments associated with the different spheres of the EC hashcode Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction)
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int}
debug: { value: 0 description: If set, print debug info datatype: boolean}
usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean}
includehydrogens: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean}
lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange atom bond mod_a_ec_fragments.so
A_EC_HASH uint64vector Base atoms hashcodes for ECFP-style fingerprints. Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction)
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int}
debug: { value: 0 description: If set, print debug info datatype: boolean}
usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean}
includeh: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean}
properties: { value: A_ELEMENT A_SUBSTITUENT_COUNT A_HCOUNT description: List of properties to use in the atom seed, values cast to integer datatype: string constraints: propertylist}
boolproperties: { value: A_RING_COUNT description: List of properties to use in the atom seed, values cast to boolean datatype: string constraints: propertylist}
exprproperties: { value: A_EQUILIBRATED_CHARGE*10 description: List of property expressions to use in the atom seed, values cast to int datatype: string constraints: list}
lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange atom bond mod_a_ec_hash.so
A_ELEMENT byte Atomic number (periodic table of elements index, H=1)
(builtin) A_SYMBOL never
A_ENOLIZABLE boolean An enolizable atom by the Lhasa definition. An enolizable atom must be saturated, non-bridgehead, have at least one hydrogen and be activated by a withdrawing bond. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 48
Compiled C module A_TYPE A_ELEMENT A_BRIDGEHEAD A_HCOUNT B_TYPE B_ORDER A_FG_SUBSTITUENTS atomchange bondchange atom bond mod_a_enolizable.so
A_EQUILIBRATED_CHARGE float Equilibrated nominal charge
fixnoxides: { value: 1 datatype: string}
(builtin) B_TYPE A_FORMAL_CHARGE A_PICENTER atomchange bondchange hadd
A_EXPLICIT_VALENCE byte Sum of bond orders of bonds which do not lead to implicit atoms (property A_IMPLICIT). Use with extreme caution, this is not a generally useful property. This maps to the "nbonds" property in Bruns/Watson query processing.
ignoreallh: { value: 1 description: If set, all hydrogens are assumed to be implicit datatype: boolean}
Compiled C module B_TYPE B_ORDER A_IMPLICIT A_TYPE A_ELEMENT atomchange bondchange atom bond mod_a_explicit_valence.so
A_EXTENDED_GROUPHASH uint64 Perturbed group hashcode
usebondorder: { value: aro description: Whether to mix in bond orders within group: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string}
usesubstitution: { value: none description: none: pure group, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string}
Compiled C module A_TYPE A_FRAMEWORK A_ELEMENT atomchange bondchange groupchange hadd group mod_a_extended_grouphash.so
A_EXTENDED_GROUPHASH_GROUP index Hash group id index for atom group hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *group* indexing, the ensemble part is used as in A_HASHGROUP for global grouping.
Compiled C module A_GROUP_NUMBER A_EXTENDED_GROUPHASH atomchange bondchange groupchange merge hadd group mod_a_extended_grouphash_group.so
A_EXTENDED_RINGHASH uint64 Perturbed ringsystem hashcode
usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string}
usesubstitution: { value: none description: none: pure ring system, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string}
Compiled C module A_TYPE A_FRAMEWORK A_ELEMENT atomchange bondchange hadd ring mod_a_extended_ringhash.so
A_EXTENDED_RINGHASH_GROUP index Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping.
Compiled C module A_RINGSYSTEM_NUMBER A_EXTENDED_RINGHASH atomchange bondchange merge hadd ring mod_a_extended_ringhash_group.so
A_FG_CHECK bitvector Functional group test (for example, in Patran FGS/FGNOT clauses) of atoms as per the LHASA definition, If the atom is a carbon atom and the FG is carbon-centric, this is the A_FG_PARTICIPATION flag, otherwise a test for A_FG_SUBSTITUIENTS>1
none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide 1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving
ketone boolean
aldehyde boolean
acid boolean
thioacid boolean
ester boolean
amide*1 boolean
amide*2 boolean
amide*3 boolean
sulfonamide*1 boolean
sulfonamide*2 boolean
sulfonamide*3 boolean
carbonium boolean
isocyanate boolean
acid*halide boolean
thioester boolean
amine*3 boolean
aziridine boolean
amine*2 boolean
amine*1 boolean
nitroso boolean
diazo boolean
haloamine boolean
hydrazone boolean
oxime boolean
imine boolean
thiocyanate boolean
isocyanide boolean
nitrile boolean
azo boolean
hydroxylamine boolean
nitro boolean
enamine boolean
amine*oxide boolean
thiol boolean
episulfide boolean
sulfide boolean
sulfoxide boolean
sulfone boolean
c*sulfonate boolean
anhydride boolean
lactam boolean
phosphine boolean
phosphonate boolean
epoxide boolean
ether boolean
peroxide boolean
alcohol boolean
enol*ether boolean
nitrite boolean
o*sulfonate boolean
fluoride boolean
chloride boolean
bromide boolean
iodide boolean
gem*dihalide boolean
trihalide boolean
acetylene boolean
olefin boolean
vic*dihalide boolean
halohydrin boolean
glycol boolean
hydrate boolean
hemiketal boolean
ketal boolean
hemiacetal boolean
acetal boolean
azide boolean
disulfide boolean
allene boolean
vinylsilane boolean
lactone boolean
vinylw boolean
vinyld boolean
esterx boolean
amidz boolean
methylene boolean
carbonyl boolean
carboxyl boolean
halide boolean
amine boolean
amide boolean
sulfonamide boolean
selenide boolean
trialkylsilyl boolean
trialkylsiloxy boolean
silylenolether boolean
n*urea*h boolean
n*urea*c boolean
carbamate*h boolean
carbamate*c boolean
o*carbamate boolean
n*carbamate boolean
o*carbonate boolean
dithioacetal boolean
dithioketal boolean
requested boolean
withdrawing boolean
expandable*withdrawing boolean
nonexpandable*withdrawing boolean
donating boolean
leaving boolean
good*leaving boolean
Compiled C module A_FG_PARTICIPATION A_FG_SUBSTITUENTS A_ELEMENT A_TYPE atomchange bondchange atom bond mod_a_fg_check.so
A_FG_PARTICIPATION bitvector Functional group participation of atoms as per the LHASA definition
none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide,sulphonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving:origin
ketone boolean
aldehyde boolean
acid boolean
thioacid boolean
ester boolean
amide*1 boolean
amide*2 boolean
amide*3 boolean
sulfonamide*1 boolean
sulfonamide*2 boolean
sulfonamide*3 boolean
carbonium boolean
isocyanate boolean
acid*halide boolean
thioester boolean
amine*3 boolean
aziridine boolean
amine*2 boolean
amine*1 boolean
nitroso boolean
diazo boolean
haloamine boolean
hydrazone boolean
oxime boolean
imine boolean
thiocyanate boolean
isocyanide boolean
nitrile boolean
azo boolean
hydroxylamine boolean
nitro boolean
enamine boolean
amine*oxide boolean
thiol boolean
episulfide boolean
sulfide boolean
sulfoxide boolean
sulfone boolean
c*sulfonate boolean
anhydride boolean
lactam boolean
phosphine boolean
phosphonate boolean
epoxide boolean
ether boolean
peroxide boolean
alcohol boolean
enol*ether boolean
nitrite boolean
o*sulfonate boolean
fluoride boolean
chloride boolean
bromide boolean
iodide boolean
gem*dihalide boolean
trihalide boolean
acetylene boolean
olefin boolean
vic*dihalide boolean
halohydrin boolean
glycol boolean
hydrate boolean
hemiketal boolean
ketal boolean
hemiacetal boolean
acetal boolean
azide boolean
disulfide boolean
allene boolean
vinylsilane boolean
lactone boolean
vinylw boolean
vinyld boolean
esterx boolean
amidz boolean
methylene boolean
carbonyl boolean
carboxyl boolean
halide boolean
amine boolean
amide boolean
sulfonamide boolean
selenide boolean
trialkylsilyl boolean
trialkylsiloxy boolean
silylenolether boolean
n*urea*h boolean
n*urea*c boolean
carbamate*h boolean
carbamate*c boolean
o*carbamate boolean
n*carbamate boolean
o*carbonate boolean
dithioacetal boolean
dithioketal boolean
requested boolean
withdrawing boolean
expandable*withdrawing boolean
nonexpandable*withdrawing boolean
donating boolean
leaving boolean
good*leaving boolean
origin boolean
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER A_FORMAL_CHARGE atomchange bondchange atom bond mod_a_fg_participation.so
A_FG_SUBSTITUENTS shortvector Functional group substituents on carbon as per the LHASA definition
ketone short
aldehyde short
acid short
thioacid boolean
ester short
amide*1 short
amide*2 short
amide*3 short
sulfonamide*1 boolean
sulfonamide*2 boolean
sulfonamide*3 boolean
carbonium short
isocyanate short
acid*halide short
thioester short
amine*3 short
aziridine short
amine*2 short
amine*1 short
nitroso short
diazo short
haloamine short
hydrazone short
oxime short
imine short
thiocyanate short
isocyanide short
nitrile short
azo short
hydroxylamine short
nitro short
enamine short
amine*oxide short
thiol short
episulfide short
sulfide short
sulfoxide short
sulfone short
c*sulfonate short
anhydride short
lactam short
phosphine short
phosphonate short
epoxide short
ether short
peroxide short
alcohol short
enol*ether short
nitrite short
o*sulfonate short
fluoride short
chloride short
bromide short
iodide short
gem*dihalide short
trihalide short
acetylene short
olefin short
vic*dihalide short
halohydrin short
glycol short
hydrate short
hemiketal short
ketal short
hemiacetal short
acetal short
azide short
disulfide short
allene short
vinylsilane short
lactone short
vinylw short
vinyld short
esterx short
amidz short
methylene short
carbonyl short
carboxyl short
halide short
amine short
amide short
sulfonamide boolean
selenide short
trialkylsilyl short
trialkylsiloxy short
silylenolether short
n*urea*h short
n*urea*c short
carbamate*h short
carbamate*c short
o*carbamate short
n*carbamate short
o*carbonate short
dithioacetal short
dithioketal short
requested short
withdrawing short
expandable*withdrawing short
nonexpandable*withdrawing short
donating short
leaving short
good*leaving short
Compiled C module A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE atomchange bondchange atom bond mod_a_fg_substituents.so
A_FLAGS bitset Display attributes for atom like boxing, marks, Fisher center
^none:starred,star:inverted,inverse,invert:boxed:groupbox1,gbox1:groupbox2,gbox2:invisible,invis:secondary:bold,dgrey,dgray,dark:greyed,mgrey,mgray,medium:italic,light,lgrey,lgray:fischer,fischercenter,fisher:nosym,nosymbol:circled,circle:alpha:beta:gamma:label:top:bottom:left:right:core:ligand,coreligand:highlight:diamond:triangle:cross:active:nostereo:protected:interfering:participating:hshowhetero:hshowterminal:hshowall:ballstick:capped:spacefill:wireframe:selected:expanded:spare1:spare2:spare3:node:symbol:insuperatom,insuper:hidden:firsthidden:groupsymbol
starred boolean
inverted boolean
boxed boolean
groupbox1 boolean
groupbox2 boolean
invisible boolean
secondary boolean
bold boolean
greyed boolean
italic boolean
fischercenter boolean
nosymbol boolean
circled boolean
alpha boolean
beta boolean
gamma boolean
label boolean
top boolean
bottom boolean
left boolean
right boolean
core boolean
ligand boolean
highlight boolean
diamon boolean
triangle boolean
cross boolean
active boolean
nostereo boolean
protected boolean
interfering boolean
participating boolean
hshowheterolboolean boolean
hshowterminal boolean
hshowall boolean
ballstick boolean
capped boolean
spacefill boolean
wireframe boolean
selected boolean
expanded boolean
spare1 boolean
spare2 boolean
spare3 boolean
node boolean
symbol boolean
insuperatom boolean
hidden boolean
firsthidden boolean
groupsymbol boolean
(builtin) never
A_FMC0 float Fragment molecular connectivity level #0
Compiled C module atomchange bondchange mod_a_fmc0.so
A_FMC1 float Fragment molecular connectivity level #1
Compiled C module atomchange bondchange mod_a_fmc1.so
A_FMC2 float Fragment molecular connectivity level #2
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc2.so
A_FMC3 float Fragment molecular connectivity level #3
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc3.so
A_FMC4 float Fragment molecular connectivity level #4
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc4.so
A_FMC5 float Fragment molecular connectivity level #5
Compiled C module B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange mod_a_fmc5.so
A_FORMAL_CHARGE byte Nominal atom charge
(builtin) A_FREE_ELECTRONS never
A_FRACTIONAL_XYZ floatvector Fractional/reciprocal atomic 3D-coordinates. This is used in the CIF I/O module.
x float
y float
z float
A_XYZ E_UNIT_CELL atomchange bondchange stereochange merge 3drelative 3dabsolute
A_FRAGMENT_ID string Fragment identifier for original atom source. This is used in D_CHEMDRAW_PAGE.
never
A_FRAMEWORK byte Framework classification 0=ring, 1=sidechain, 2=linker
ring:sidechain,chain:linker,bridge
(builtin) B_TYPE atomchange bondchange hadd ring
A_FREE_ELECTRONS byte Number of free electrons
(builtin) A_FORMAL_CHARGE never
A_FREE_VALENCE byte Number of free valences
(builtin) A_ELEMENT A_FORMAL_CHARGE A_VALENCE atomchange bondchange hadd
A_F_COUNT int Count the number of fluorine substituents around a central atom
Tcl script A_ELEMENT A_TYPE atomchange bondchange a_f_count.xpd
A_GENERIC_FORCEFIELD_TYPE string Generic Force Field atom type- Used in the IFF I/O module. Computation of this property is linked to various program-specific variants, which can be selected by a parameter.
forcefield: { value: none description: If set to none, use the first type alread present on structure, or fallback to Sybyl2 as last resort enumeration: tinker:macromodel:sybyl2:sybyl:alchemy:babel datatype: string}
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_generic_forcefield_type.xpd
A_GEOMETRY byte Enumerated value of the geometry of an atom (terminal, tetrahedral, etc.)
none:terminal,end,s:linear,sp:trigonalplanar,planar,sp2:tetrahedral,tetraeder,sp3:bipyramidal,tbp,trigonalbipyramidal,bipyramid,sp3d,dsp3:sawhorse,seesaw:tshaped,t-shaped:octahedral,octaeder,sp3d2,d2sp3:squarepyramidal:squareplanar,sp2d,dsp2:other
Compiled C module A_VERTEX_DEGREE A_FREE_ELECTRONS A_TYPE B_TYPE A_FORMAL_CHARGE A_ISAROMATIC A_PICENTER A_IUPAC_GROUP atomchange bondchange mod_a_geometry.so
A_GROUP_FRAMEWORK byte Framework classification 0=group, 1=sidechain, 2=linker, using groups as core elements instead of rings as in standard A_FRAMEWORK
group:sidechain:linker
Compiled C module B_TYPE atomchange bondchange groupchange hadd group mod_a_group_framework.so
A_GROUP_NUMBER int Number (1-indexed group list position) of atoms, with 0 for atoms which are not in a group. This property assumes that an atom is only a member in a single group, if any.
Compiled C module atomchange bondchange groupchange atom bond group mod_a_group_number.so
A_HASH uint64 Basic atomic hashcode
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 0 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE atomchange bondchange hadd
A_HASHGROUP index Hash group id index for basic hash code
(builtin) A_MOL_NUMBER A_HASH atomchange bondchange merge hadd
A_HASH_STEREO byte Stereo descriptor for atoms, based on atomic hashcodes
@M:undef:P
useisotope: { value: 0 datatype: string}
(builtin) A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange hadd
A_HCOUNT byte Number of classically bonded hydrogen atoms
useimplicith: { value: 0 datatype: string}
(builtin) B_TYPE A_ELEMENT atomchange bondchange hadd
A_HEAVY_SUBSTITUENT_COUNT byte Number of classically bonded non-hydrogen atoms
(builtin) B_TYPE A_ELEMENT atomchange bondchange
A_HETERO_SUBSTITUENT_COUNT int Count the number of hetero (not C or H) ligands around a central atom
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange mod_a_hetero_substituent_count.so
A_HSPECIAL byte Flag for hydrogen atoms plotted with symbols by common agreement: 0: no, 1:yes, 2:at cis/trans db, 3:at stereocenter, but not wedge
never: { value: 0 datatype: string}
(builtin) B_STEREOINFO A_STEREOINFO A_ELEMENT A_TERMINAL_DISTANCE B_ORDER A_CSPECIAL B_FLAGS A_FLAGS A_ISOTOPE A_RING_COUNT atomchange bondchange merge hadd
A_HUCKEL_PI_ELECTRON_DENSITY double Pi elektron density (sum of electron count in occupied orbitals multiplied with atomic MO coefficient) according to plain Huckel model
P_HUCKEL_MO_OCCUPANCY atomchange bondchange atom bond pi
A_HYBRIDIZATION byte Hybridization of atom
none:s:sp3:sp2:sp:sp3d:sp3d2
Compiled C module never mod_a_hybridization.so
A_HYDROGENS_NEEDED byte Number of hydrogen atoms missing to fill up to standard valency
maxsulphurvalence: { value: 2 datatype: string}
maxchlorinevalence: { value: 1 datatype: string}
maxphosphorvalence: { value: 3 datatype: string}
hypervalentaddition: { value: 0 datatype: string}
(builtin) B_TYPE A_IUPAC_GROUP A_FORMAL_CHARGE A_FREE_ELECTRONS A_VALENCE A_RADICAL atomchange bondchange shuffle
A_HYDROGEN_BONDING byte Classification of H-Bonding Donor/Acceptor Potential
none:acidic:donor:acceptor:basic
Compiled C module A_FORMAL_CHARGE A_ELEMENT B_TYPE B_ORDER A_FREE_ELECTRONS A_SIGMA_CHARGE A_ISAROMATIC R_AROMATIC A_IUPAC_GROUP atomchange bondchange mod_a_hydrogen_bonding.so
A_IMPLICIT boolean Flag for implicitly added atoms. This information is internally maintained by hydrogen addition etc. subroutines. The compute function copies this internal data into a property.
Compiled C module atomchange mod_a_implicit.so
A_IMPLICIT_HCOUNT byte Number of implicit (automatically added) hydrogens around atom. This is computed from the internal hydrogen origin memory of structures. If this information has been deleted, the result is always zero.
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange mod_a_implicit_hcount.so
A_INAMIDE boolean Flags for atoms in amide-type system (set for n,o,c). Or'ed bits 'extended 1' allow C=S, 'extended 2' allow C=N
extended: { value: 1 datatype: string}
(builtin) A_ELEMENT B_TYPE B_ORDER atomchange bondchange
A_INDEX int Index of atom in internal atom list, not ordered into blocked molecules
Compiled C module atomchange bondchange merge shuffle hadd atom mod_a_index.so
A_ISAROMATIC boolean Flag whether atom is member of aromatic ring or not
(builtin) R_AROMATIC R_TYPE atomchange bondchange ring
A_ISMETAL boolean Flag for metal atoms, as determined by the column in the built-in element table, where the criterion could be modified if necessary.
Compiled C module A_ELEMENT atomchange bondchange mod_a_ismetal.so
A_ISOLATED_RING boolean Flag indicating atom is part of an isolated ring
Compiled C module Y_RING_COUNT atomchange bondchange atom bond mod_a_isolated_ring.so
A_ISOTOPE byte Absolute isotopic mass (12C=12.0000)
never
A_ISOTOPE_HASH uint64 Atomic hashcode with isotopes
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 1 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange hadd
A_ISOTOPE_HASHGROUP index Hash group id index for isotope hash code
(builtin) A_MOL_NUMBER A_ISOTOPE_HASH atomchange bondchange merge
A_ISOTOPE_LABELLING_DEGREE float Isotope labelling degree (0.0..1.0)
A_ISOTOPE atomchange
A_ISOTOPE_STEREO_HASH uint64 Stereospecific and isotope-aware atomic hashcode
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 1 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange stereochange hadd
A_ISOTOPE_STEREO_HASHGROUP index Hash group id index for stereospecific isotope hash code
(builtin) A_MOL_NUMBER A_ISOTOPE_STEREO_HASH atomchange bondchange merge
A_IS_CHARGED_METAL_ION boolean Boolean flag indicating an unbonded, charged metal ion
Tcl script A_TYPE A_ELEMENT A_FORMAL_CHARGE atomchange bondchange a_is_charged_metal_ion.xpd
A_IUPAC_GROUP byte New IUPAC group number in range 1-18, 19=lanthanides, 20=actinides
(builtin) A_ELEMENT A_TYPE atomchange
A_JSTDATA intquad Extended fields in JST-type molfile
atomchange bondchange stereochange merge
A_LABEL int Arbitrary atom label
(builtin) never
A_LABELCOLOR color X11 style color name of atom labels
Tcl script never a_labelcolor.xpd
A_LABEL_STEREO byte Stereo descriptor for atoms, based on atomic labels
M,-=-1:undef=0:P,+=1:U,C=2:Z,N=3:X=4
(builtin) never
A_LHASA_PATH_LABEL byte Path atom label (1-based) for matched Lhasa patterns
X_LHASA_SCORE atomchange bondchange atom bond
A_LIGAND_ANGLE_SUM float Allred/Rochow ligand angle sum for phosphor atoms
Tcl script atomchange bondchange 3drelative a_ligand_angle_sum.xpd
A_LIGAND_ENEG_SUM float
Tcl script atomchange bondchange a_ligand_eneg_sum.xpd
A_LIGAND_RANK intvector Priority-sorted list of ligands around stereocenters according to CIP rules. The vector fields are label values of the stereo-defining root substituents (which may be distand in case of atom-stereogenic allenes). The ligand with highest priority is listed first. Stereogenic electron pairs are not listed, and for such compounds there are only three listed ligands on the stereo atom. Atoms without stereo potential have an empty vector.
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER A_CIP_STEREO B_CIP_STEREO A_LABEL A_ALLENE atomchange bondchange stereochange hadd mod_a_ligand_rank.so
A_LILLY_SPINACH boolean Boolean flag whether the atom is part of what in Eli Lilly lingo is defined "molecular spinach". Atoms which are a ring atom, a ring bridge atom, or connected via a multiple bond to a ring or ring bridge are part of the scaffold and not spinach. J. Med. Chem. 2012, 55, 9763-9772
Compiled C module A_FRAMEWORK B_TYPE B_ORDER atomchange bondchange atom bond ring mod_a_lilly_spinach.so
A_LINEAR_CHAIN_LENGTH int The size of the linear-chain-heavy-atoms-only fragment the atom is a member of. Ring atoms or branch atoms have value 0. Hydrogen atoms inherit the value of their bond partner.
Compiled C module A_TYPE A_RING_COUNT B_TYPE A_SUBSTITUENT_COUNT atomchange bondchange atom bond mod_a_linear_chain_length.so
A_MACROMODEL_TYPE short MacroModel atom type. Used for example in the MMD and MAESTRO I/O modules.
none:C1:C2:C3:CA:CB:CC:CD:CE:CF:CM:CP:CR:unused:C0:O2:O3:OA:OM:OW:OP:OQ:unused:O0:N1:N2:N3:NA:NB:NC:ND:N4:N5:NE:NF:NG:NH:NI:NM:NP:N0:H1:H2:H3:H4:H5:unused:unused:unused:H0:S1:SA:SM:S0:P0:B2:B3:F0:Cl:Br:I0:Si:Z0:Lp:00:Li:Na:K0:Rb:Cs:Ca:Ba:Mg:M2:M3:M4:M5:M6:M7:f2:f3:o2:o3:n2:n3:c1:c2:Zn:m3:m4:m5:m6:unused:unused:unused:unused:unused:unused:unused:unused:SP:S2:Cm:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:PI
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange a_macromodel_type.xpd
A_MAPPING int Atom mapping (for example for reactions), linking to atom labels of complementary structure (reagent <-> product), 0 for unmapped atoms
ignoreexpandedcarbon: { value: 0 datatype: string}
ignoreexpandedhetero: { value: 0 datatype: string}
ignoreexpandedhydrogen: { value: 0 datatype: string}
(builtin) atomchange bondchange merge
A_MAP_STEREO byte Atom stereo descriptor based on reaction mapping
@M,-:undef:P,+
(builtin) A_MAPPING never
A_MDL_VALUE string Custom atom value in MDL files ('V' data lines in Molfiles)
never
A_MOL_LABEL int Label of molecule atom belongs to
(builtin) A_MOL_NUMBER M_LABEL atomchange bondchange merge shuffle hadd mol
A_MOL_NUMBER short Number (index+1) of molecule atom belongs to
(builtin) B_TYPE atomchange bondchange merge shuffle hadd
A_MORGAN uint64 Morgan numbering value (not the atom rank in the Morgan number, this is the full raw value)
includeh: { value: 1 datatype: boolean}
useelement: { value: 0 datatype: boolean}
Compiled C module A_TYPE B_TYPE A_ELEMENT A_VERTEX_DEGREE atomchange bondchange hadd bond mod_a_morgan.so
A_MORGAN_RANK int Ranking of atoms according to Morgan code value (rank 1 has highest rating)
Tcl script A_MORGAN atomchange bondchange merge hadd atom bond a_morgan_rank.xpd
A_NCBI_MMDB compound MMDB source information
mmdb-id int
molecule-id int
molecule-name stringvector
residue-id int
residue-name string
atom-id int
atom-name string
never
A_NCICADD_NORM_CHARGE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
A_NCICADD_RESONANCE_STEREO_DELETED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
A_NCICADD_TAUTO_STEREO_DELETED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
A_NEIGHBOR_COUNT byte Number of ALL bonded neighbor atoms
(builtin) bondchange hadd
A_NH2_COUNT int Count the number of -NH2 substituents around an atom
Tcl script A_ELEMENT A_HCOUNT atomchange bondchange a_nh2_count.xpd
A_NMR_SHIFT float True shift values, computed from shielding parameters and method string
Tcl script A_SHIELDING atomchange bondchange stereochange 3drelative a_nmr_shift.xpd
A_NORMAL_VIBRATIONS xyzvector Raman and IR normal vibrations of the structure
A_XYZ atomchange bondchange stereochange merge 3drelative mol atom bond
A_PATTY_TYPE string Programmable atom typer
patternfile: { value: patty.sma datatype: diskfile constraints: readable}
trace: { value: 0 datatype: boolean}
Tcl script A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange hadd atom bond a_patty_type.xpd
A_PHENYL_COUNT int Count for the number or ESSSR phenyl rings the atom is part of
Compiled C module R_TYPE R_AROMATIC R_HETEROATOM_COUNT atomchange bondchange atom bond ring mod_a_phenyl_count.so
A_PHOSPHOR_SHIFT float True NMR shift values, computed from shielding parameters and method string
Tcl script A_SHIELDING atomchange bondchange stereochange 3drelative a_phosphor_shift.xpd
A_PICENTER byte Flag for atoms with pi system (1:free electrons, 2:multibond or epair)
(builtin) A_PSE_ROW A_FREE_ELECTRONS B_TYPE A_FORMAL_CHARGE B_ORDER atomchange bondchange hadd
A_PISYSTEM_ELECTRON_COUNT short Number of pi electrons in largest pi system the atom is a member of
Compiled C module P_ELECTRON_COUNT atomchange bondchange atom bond pi mod_a_pisystem_electron_count.so
A_PISYSTEM_SIZE short Size (atom count) of the largest pi system the atom is a member of
Compiled C module atomchange bondchange atom bond pi mod_a_pisystem_size.so
A_PI_CHARGE float Gasteiger Pi charges
A_TYPE A_SIGMA_CHARGE atomchange bondchange hadd
A_PI_ELECTRONEGATIVITY float Gasteiger Pi Eneg value
A_TYPE A_PI_CHARGE atomchange bondchange hadd
A_POLARIZABILITY float Atom polarizablities by the Kang & Jhon (sic) algorithm Y. K. Kang, M. S. Jhon, Theor. Chim. Acta 61, 41 (1982)
Compiled C module A_VB_NEIGHBOR_COUNT A_ELEMENT A_FREE_ELECTRONS A_FORMAL_CHARGE A_ISAROMATIC A_AROCONDENSED atomchange bondchange mod_a_polarizability.so
A_PSE_ROW byte Row number in PSE (1 for H,He, 2 for Li ..)
(builtin) A_ELEMENT A_TYPE atomchange
A_QNA_DESCRIPTORS floatpair Filimonov/Zakharov/Lagunin/Poroikov QNA atomic descriptors. The p value correlates with partial atomic hardness, and q with electronegativity. The use of the matrix exponent of the adjaceny matrix ensures a decreasing neighbor influence with increasing topological distance. Further literature references: Chemical Research in Toxicology, 2012, 25, 2378-2385, DOI 10.1021/tx300247r SAR and QSAR in Environmental Research, 2009, 20, 679-709, DOI 10.1080/10629360903438370 Molecular Informatics 30, 2011, 241-250
p double
q double
Compiled C module A_TYPE A_ELEMENT E_EXP_CONNECTIVITY_MATRIX atomchange bondchange atom bond mod_a_qna_descriptors.so
A_QUERY compound Atom query attributes
element,std,normal,standard:any,*,?:list:excllist,neglist:hetero,q:halogen,x:noth,noh:heteroh,qh,notc,noc:metal,m:pull1,y:pull2,z:hdonor,hd:hacceptor,ha:insulator,r:terminator,t,ref,reference:anyh,ah:metalh,mh:halogenh,xh:g,group:gh,grouph:g*,groupx:gh*,grouphx:acy:ach:abc:abh:ayl:ayh:alk:alh:ael:aeh:ahc:ahh:aox:aoh:aam:aah:amox:amoxh:cyc:cyh:cbc:cbh:ary:arh:cal:cah:cel:ceh:chc:chh:har:hah:cxx:cxh:1a:2a:3a:4a:5a:6a:7a:8a:1b:2b:3b:4b:5b:6b:7b:8b:8x:8y:8z:1m:2m:3m:tr:ln:ac,an:4m:nm:alk*,*alk,allalk:alh*,*alh,allalh ^none:stereo:charge:unsaturated,unsat,insaturated,insat:dontmatch,exclude:aromatic:aliphatic,inaromatic:mustmap:picenter:aroneighbor,aroneighbour:noaroneighbor,noaroneighbour:substituted:unsubstituted:fgneighbor,fgneighbor:nofgneighbor,nofgneighbour:aroneighbor_unmatched,aroneighbour_unmatched:noaroneighbor_unmatched,noaroneighbour_unmatched:substituted_unmatched:unsubstituted_unmatched:fgneighbor_unmatched,fgneighbor_unmatched:nofgneighbor_unmatched,nofgneighbour_unmatched:nostereook:nomappingok:nooverlap:exactchange:noextrah:noextrac:noextrax:stereoinversion,inversion:stereoretention,retention:saturated:branched:linear,chain:nochargeok:explicitzerocharge:noextrarings:filledvalence:unfilledvalence:stereochangeofpresence,changeofpresence:noisotopeok:offpath:rgroup:groupsaturated,gsaturated:groupunsaturated,groupinsaturated,gunsaturated,ginsaturated:groupacyclic,gacyclic:groupmonocyclic,gmonocyclic:grouppolycyclic,gpolycyclic:groupcyclic,gcyclic:groupsimple,groupnotpolycyclic,gsimple,gnotpolycyclic:wbond,withdrawingbond:nowbond,nowithdrawingbond,no_withdrawing_bond,no_wbond:branched:unbranched:tertbranched,tbranched:heterocyclic:carbocylic none:H:He:Li:Be:B:C:N:O:F:Ne:Na:Mg:Al:Si:P:S:Cl:Ar:K:Ca:Sc:Ti:V:Cr:Mn:Fe:Co:Ni:Cu:Zn:Ga:Ge:As:Se:Br:Kr:Rb:Sr:Y:Zr:Nb:Mo:Tc:Ru:Rh:Pd:Ag:Cd:In:Sn:Sb:Te:I:Xe:Cs:Ba:La:Ce:Pr:Nd:Pm:Sm:Eu:Gd:Tb:Dy:Ho:Er:Tm:Yb:Lu:Hf:Ta:W:Re:Os:Ir:Pt:Au:Hg:Tl:Pb:Bi:Po:At:Rn:Fr:Ra:Ac:Th:Pa:U:Np:Pu:Am:Cm:Bk:Cf:Es:Fm:Md:No:Lr
type byte
flags bitset
list intvector
substituentcount bitset
valencecount bitset
neighborcount bitset
hydrogencount bitset
ringsize bitset
ringcount bitset
rganchor int
rgmember int
rginstance int
rgattach int
tclproc string
fuzz int
query querytree
component int
heterosubstituentcount bitset
rbcount bitset
repeat bitset
charge bitset
pyfunction string
ringid int
ringsystemid int
fgs bitvector
fgnot bitvector
aliheterosubstituentcount bitset
freeelectroncount bitset
pielectroncount bitset
rgroupid int
pathid int
altpathid int
formula formulamatch
piformula formulamatch
never
A_RACEMATE byte Racemate distribution of stereocenter
undefined,undef:rac,racemat:pure
atomchange bondchange
A_RADICAL byte Flag for radical center
no,none:singlet,yes:doublet:triplet:quartet:quintet
(builtin) A_FREE_ELECTRONS never
A_RADIOACTIVE boolean Marker for radioactive isotope labels.
Tcl script A_ISOTOPE A_ELEMENT atomchange bondchange atom bond a_radioactive.xpd
A_RECAP_LINKER_TYPE byte Connection type on this placeholder atom in the RECAP algorithm. The original paper abuses isotope labels for this. J. Chem. Inf. Comput. Sci. 1998, 38, 511-522
none:urea:amide:ester:amines:cyclicamines:ether:olefin:aronitroalicarbon:lactam:arocarbonarocarbon:sulphonamide:aronitroarocarbon
never
A_RENDER_XY floatpair Render coordinate of atoms on images, etc. Only set by render functions is specifically requested.
A_XY E_STDBLE A_FLAGS atomchange bondchange groupchange mol atom bond ring group
A_RESIDUE compound Residue information, esp. for proteins from PDB
atomtag string
grouptag string
groupindex int
segmentid string
resid string
chain string
weight double
hetatm boolean
atomchange bondchange
A_RINGHASH uint64 Atom hash code for atoms which are part of ring systems
usebondorder: { value: none datatype: string}
(builtin) A_TYPE A_FRAMEWORK A_ELEMENT B_TYPE atomchange bondchange 3drelative 3dabsolute ring
A_RINGHASH_GROUP index Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping.
Compiled C module A_RINGSYSTEM_NUMBER A_RINGHASH atomchange bondchange merge hadd ring mod_a_ringhash_group.so
A_RINGLABEL int Renumbered labels of atoms in ring system- Atoms not in ring get label 0, the ring atoms start with one. The order of the labelled atoms follows their standard atom label rank.
Tcl script A_LABEL ring a_ringlabel.xpd
A_RINGS intvector Labels of the rings the atom is member in
(builtin) R_LABEL A_RING_COUNT R_TYPE atomchange bondchange merge ring
A_RINGSYSTEM_NUMBER int Number (1-indexed ringsystem list position) of atoms, with 0 for atoms which are not in a ringsystem.
Compiled C module Y_LABEL atomchange bondchange atom bond ring mod_a_ringsystem_number.so
A_RINGSYSTEM_SIZE short Number of ESSSR rings in the ringsystem the atom is a member of, 0 for chain atoms
Compiled C module atomchange bondchange ring mod_a_ringsystem_size.so
A_RING_BOND_COUNT byte Number of ring bonds atom is participating in
Compiled C module B_RING_COUNT bondchange ring mod_a_ring_bond_count.so
A_RING_COUNT short Number of simple (non-envelope) rings an atom is member of
countenvelopes: { value: 0 datatype: string}
(builtin) R_TYPE atomchange bondchange ring
A_RING_HETEROATOM_COUNT_BITS bitset A bit is set at bit position n for any ESSSR ring the atom is a member of which has n hetero atoms. Chain atoms have value 0. If the atom is a member of a carbocyclic ESSSR ring, bit position 0 is set.
Compiled C module R_HETEROATOM_COUNT R_TYPE atomchange bondchange atom bond mod_a_ring_heteroatom_count_bits.so
A_RING_SIZE_BITS bitset Bit mask for ring sizes the atom participates in
ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
Compiled C module R_SIZE R_TYPE B_TYPE A_RING_COUNT bondchange ring mod_a_ring_size_bits.so
A_RING_SUBSTITUENT_SIZE intpair Number of atoms and maximum bond distance in ring substituent
size int
depth int
(builtin) A_FRAMEWORK ring
A_SCIDEX_DATA dictionary Scidex-specific atom attribute support for MDL SD-files. Handles data encoded in "S SDX" lines.
atomchange bondchange atom bond
A_SEQUENCE_NUMBER int Sequential atom number (trad. atoms only)
(builtin) A_MOL_NUMBER M_ATOM_RANGE A_TYPE atomchange bondchange merge shuffle hadd mol
A_SHELL_ELECTRONS byte Number of shell electrons in unbonded atom
(builtin) A_ELEMENT A_TYPE atomchange bondchange
A_SHIELDING float Isotropic magnetic shielding (NMR spectroscopy). This is a field in the SHARC spectroscopy archive format.
atomchange bondchange stereochange merge 3drelative hadd
A_SHIELD_TENSOR tensor Anisotropic magnetic shielding tensor. Used as data field in the SHARC NMR archive format.
atomchange bondchange stereochange merge 3drelative hadd
A_SIGMA_CHARGE float Gasteiger sigma charges
Compiled C module A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 atomchange bondchange mod_a_sigma_charge.so
A_SIGMA_ELECTRONEGATIVITY float Gasteiger sigma electronegativities
A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_SP A_SP2 atomchange bondchange
A_SIMILARITY_PATTERN float Quantitative evaluation of fragment-bit similarity
cmplist: { value: {} datatype: string}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange a_similarity_pattern.xpd
A_SMALLEST_RING int Size of smallest ESSSR ring the atom is a member of (0 for non-ring atoms)
Compiled C module R_SIZE ring mod_a_smallest_ring.so
A_SMILES_INDEX int Atom index in SMILES string (-1 for implicit atoms not explicitly encoded in the SMILES string). The result data is automatically set when computing E_SMILES, which has many options which influence the atom sequence in the string.
E_SMILES A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL_STEREO B_LABEL_STEREO A_ISOTOPE A_MAPPING A_QUERY B_QUERY atomchange bondchange merge hadd mol
A_SMILES_RANK int Unique SMILES ranking of atoms
Compiled C module A_ELEMENT B_TYPE A_TYPE B_ORDER A_FORMAL_CHARGE atomchange bondchange merge hadd mod_a_smiles_rank.so
A_SP boolean Flags for atoms forced into sp hybridisation by charge equilibration or aromaticity
useimplicith: { value: 1 datatype: boolean}
Compiled C module A_ELEMENT B_TYPE B_ORDER A_HYDROGENS_NEEDED atomchange bondchange mod_a_sp.so
A_SP2 boolean Flags for atoms forced into sp2 hybridisation by charge equilibration or aromaticity
useimplicith: { value: 1 datatype: boolean}
Compiled C module A_FORMAL_CHARGE B_ORDER B_TYPE A_HYDROGENS_NEEDED A_ELEMENT atomchange bondchange mod_a_sp2.so
A_SPAN float Largest distance of this atom to any atom in molecule, divided by molecule span
Compiled C module B_TYPE M_SPAN A_TOPO_DISTANCE atomchange bondchange hadd atom bond mod_a_span.so
A_SPIRO byte Number of spiro ring joins atom is participating in ESSSR ring set
(builtin) A_RING_COUNT R_TYPE atomchange bondchange ring
A_SSMATCH int Ensemble is structure, property data encodes labels of matching substructure atoms, 0 for unmatched parts
sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
Tcl script never a_ssmatch.xpd
A_SSMATCH_COUNT int Atom match count for structure matching. This is set on the *structure* ensemble when specific match flags are set in the substructure match routine.
sshandle: { value: {} datatype: substructure}
Tcl script never a_ssmatch_count.xpd
A_SSMATCH_ENVIRONMENT datatree Classigied unmatched structure environment of the substructure atoms, i.e. data on the characteristics of the unmatched structure atoms sprouting from the structure atom matched by this substructure atom. Set by a substructure hit option, not directly computable.
atomchange bondchange atom bond
A_STANDARD_GROUP_LABEL int Label of group which contains the atoms which form a standard group
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
A_STEREOGENIC byte Can this atom be a stereocenter ?
no:maybe:checkno:yes,checkyes:ringct
(builtin) atomchange bondchange hadd
A_STEREOINFO byte Stereo descriptor availability info: 1:Label,2:R/S,4:D/L:8:hash,16:map
^none,st_none:label,st_label:cip,st_cip:dl,st_dl:hash,st_hash:map,st_map
(builtin) A_HASH_STEREO A_LABEL_STEREO A_CIP_STEREO A_DL_STEREO A_MAP_STEREO atomchange bondchange stereochange
A_STEREO_CHANGE byte Stereo change during course of reaction
unknown:inversion:retention:changeofpresence
atomchange bondchange atom bond
A_STEREO_GROUP short MDL-style stereo group. The enumeration values correspond to the official MDL names of these groups. They are read and set by SDF3000/RXN3000 file format modules, and also used in PubChem I/O via ASN.
abs=99:or15=-15:or14=-14:or13=-31:or12=-12:or11=-11:or10=-10:or9=-9:or8=-8:or7=-7:or6=-6:or5=-5:or4=-4:or3=-3:or2=-2:or1=-1:none=0:&1,and1=1:&2,and2=2:&3,and3=3:&4,and4=4:&5,and5=5:&6,and6=6:&7,and7=7:&8,and8=8:&9,and9=9:&10,and10=10:&11,and11=11:&12,and12=12:&13,and13=13:&14,and14=14:&15,and15=15
A_TYPE B_TYPE atomchange bondchange stereochange
A_STEREO_HASH uint64 Stereospecific basic atomic hashcode
usebondorder: { value: 0 datatype: string}
seedproperty: { value: {} datatype: string}
filter: { value: {} datatype: string}
useisotope: { value: 0 datatype: string}
usesubstitution: { value: 0 datatype: string}
usesuperatom: { value: 0 datatype: string}
uselocalcharge: { value: 0 datatype: string}
usering: { value: 1 datatype: string}
usequery: { value: 0 datatype: string}
ignoreh: { value: 0 datatype: string}
usecharge: { value: 1 datatype: string}
useradical: { value: 0 datatype: string}
useringelectrons: { value: 0 datatype: string}
useenantiomer: { value: 0 datatype: string}
excludebonds: { value: {} datatype: string}
printseed: { value: 0 datatype: string}
seedmodulo: { value: 0 datatype: string}
seedoffset: { value: 0 datatype: string}
(builtin) A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE atomchange bondchange stereochange hadd
A_STEREO_HASHGROUP index Hash group id index for basic stereospecific hash code
(builtin) A_MOL_NUMBER A_STEREO_HASH atomchange bondchange merge hadd
A_STMATCH int Ensemble is substructure, property data encodes labels of matching structure atoms, 0 for unmatched parts
sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
Tcl script never a_stmatch.xpd
A_STMATCH_COUNT int Atom match count for structure matching. This is set on the *substructure* ensemble when specific match flags are set in the substructure match routine.
sthandle: { value: {} datatype: structure}
Tcl script never a_stmatch_count.xpd
A_SUBSTITUENT_COUNT int Count the number of non-H neighbors around a central atom
Compiled C module A_ELEMENT A_TYPE B_TYPE atomchange bondchange mod_a_substituent_count.so
A_SUBSTITUENT_VECTOR float Angle of the mid of the largest gap in the 2D layout of the substituent sphere
excludeatoms: { value: {} datatype: string}
(builtin) A_XY atomchange bondchange hadd
A_SUPERATOMSTRING string Descriptive string for atoms and especially superatoms
never
A_SUPERATOM_SSMATCH string A_SUPERATOMSTRING of matching substructure superatom, empty for unmatched parts. This is set by the substructure match routine if suitable flags are set.
sshandle: { value: {} datatype: structure}
Tcl script never a_superatom_ssmatch.xpd
A_SURFACE_AREA double Estimated surface area from simple intersection of bonded VdW spheres on A_XYZ coordinates P. Labute, Methods in Molecular Biology, 275, 261ff
vdwscale: { value: 0.8 description: scaling parameter for VdW radii datatype: double}
bondsonly: { value: 1 description: if set, only compute sphere intersections of bonded atoms datatype: boolean}
Compiled C module A_XYZ A_TYPE A_ELEMENT A_ISAROMATIC A_VDW_RADIUS atomchange bondchange 3dabsolute hadd atom bond mod_a_surface_area.so
A_SURFACE_SPHERE_RADIUS float Radius of sphere used for surface calculation
A_XYZ atomchange bondchange stereochange 3drelative
A_SYBYL2_TYPE shortstring Atom type as used in the Sybyl mol2 format
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_sybyl2_type.xpd
A_SYBYL_TYPE byte Atom type as used in the Sybyl mol format (version 1, not mol2)
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_sybyl_type.xpd
A_SYMBOL shortstring Atomic symbol
querysymbol: { value: ? datatype: string}
(builtin) A_ISOTOPE A_ELEMENT A_QUERY never
A_SYMVISIBLE boolean Flag for atoms typically plotted with symbol
(builtin) A_HSPECIAL A_CSPECIAL A_TYPE A_ELEMENT A_FLAGS atomchange bondchange
A_TAUTOMER_SYSTEM int Tautomer system ID of the atoms. Atoms outside any tautomer system receive ID 0, the rest of the systems are numbered starting with one.
Compiled C module B_ISTAUTOMERIC atomchange bondchange atom bond mod_a_tautomer_system.so
A_TERMINAL_DISTANCE short Number of bonds from terminal atom (0 if itself terminal)
(builtin) B_TYPE atomchange bondchange
A_TEXTLABEL compound Arbitrary textual atom label plus alignment info for plots
{} @above:left:center:right:below
label string
align byte
level: { value: 0 datatype: string}
(builtin) never
A_TINKER_TYPE short Atom type as used in the Tinker xyz format
forcefield: { value: none datatype: string}
Tcl script A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE atomchange bondchange a_tinker_type.xpd
A_TOPO_DISTANCE shortvector Topological distance matrix (minimum number of bonds between atoms)
bondclasses: { value: VB datatype: string}
Compiled C module B_TYPE bondchange mod_a_topo_distance.so
A_TOTAL_CHARGE float Atomic charge on Sigma and Pi systems
(builtin) A_TYPE A_ELEMENT B_TYPE B_ORDER A_SIGMA_CHARGE A_PI_CHARGE atomchange bondchange
A_TRAJECTORY xyzvector 3D atomic path trajectory, for example from a molecular modelling study. This property is for example used in the I/O modules for the GROMACS, XBSA, XYZ and GHEMICAL formats.
A_TYPE B_TYPE B_ORDER A_ELEMENT atomchange
A_TRANSFORM_STATUS byte Atom status as result of SMIRKS transformation. None: not matched in transform, matched: matched, but unchanged, changed: element or attribute changed, new: fragment introduced by transform
none:matched:changed:new
atomchange bondchange atom bond
A_TYPE int Classification, 0:Undef,1:Normal,2:Search,4:Epair,8:3DPoint,16:Super,32:Deloc,64:Polymer,128:Annotation,256:Open,512:Enzyme,1024:Unspecified
^undef:normal,element:search,query:epair,electron,ep,lp:3dpoint,bq,du:super,superatom:anchor,delocalized,deloc,@:polymer,poly:annotation,annot:open:enzyme,e,protein:unspecified
never
A_UNDEF_FLOAT1 float Some undefined atom property read from file formats with anonymous atom data
atomchange bondchange stereochange merge 3drelative 3dabsolute
A_UNSATURATION byte Sum of bond orders in excess of one of all non-aromatic bonds atom is participating in
aroisunsaturated: { value: 1 description: If set, aromatic bonds count as unsaturated datatype: boolean}
Compiled C module A_TYPE B_TYPE B_ORDER B_ISAROMATIC atomchange bondchange mod_a_unsaturation.so
A_VALD double Molconn-Z atom value parameter
never
A_VALENCE byte Number of classical bond valences
(builtin) B_ORDER B_TYPE bondchange hadd
A_VAMP_CHARGE float Atomic Charge as computed by the Vamp program. This is computed indireclty by requesting computation of heat for formation via Vamp (property E_HEAT_OF_FORMATION).
A_XYZ atomchange bondchange
A_VB_NEIGHBOR_COUNT byte Number of classically bonded neighbor atoms
(builtin) B_TYPE bondchange hadd
A_VDW_INTERACTION floatvector Atom-by-atom nonbonding interaction coefficients, dependent on the elements of an atom pair. The result s a float vector on each atom. The vector length is the number of atoms. The element value at each index is computed by formula hardness(a1)*hardness(a2).pow(VdwBumperRad(element1)+VdWBumperRad(element2),12). The atom hardness value is either the standard atom hardness (default 0.3) or a special hydrogen hardness (default 0.09). The diagonals are set to 0, and interactions to non-standrd atoms to -1. Note that is is only a helper property. it is not dependen on the actual atomic coordinates. It is used by the computation functions of properties E_NONBONDING_ENERGY and E_CONFORMER_ENERGY.
stdhardness: { value: 0.30 datatype: double}
hydrogenhardness: { value: 0.09 datatype: double}
Compiled C module A_TYPE A_ELEMENT atomchange atom mod_a_vdw_interaction.so
A_VDW_RADIUS float Default van-der-Waals radius
(builtin) A_ELEMENT A_TYPE atomchange
A_VECTOR floatvector Directional 3D vector originating from atoms, generic purpose
atomchange bondchange 3drelative 3dabsolute
A_VERTEX_DEGREE byte Number of neighbors which are real atoms and are connected by vb or complex bonds
Compiled C module A_TYPE B_TYPE atomchange bondchange hadd mod_a_vertex_degree.so
A_VIRTUAL_HCOUNT byte Sum of actual hydrogen count (A_HCOUNT) and hydrogens needed for full set (A_HYDROGENS_NEEDED)
Compiled C module A_HCOUNT A_HYDROGENS_NEEDED atomchange bondchange atom bond mod_a_virtual_hcount.so
A_VORONOI_POLYGON xyvector Voronoi polygon around 2D display of atom
polygonsonly: { value: 1 datatype: boolean}
adddummies: { value: 1 datatype: boolean}
extradummies: { value: 1 datatype: boolean}
debug: { value: 0 datatype: boolean}
Compiled C module A_XY never mod_a_voronoi_polygon.so
A_WATERMARK_SENSITIVITY float Guestimated sensitivity of overall compound energy on atom movement for watermarking
datafile: { value: a_watermark_sensitivity.dat datatype: diskfile constraints: readable}
Tcl script A_ELEMENT A_TYPE B_ORDER B_TYPE atomchange bondchange atom bond ring a_watermark_sensitivity.xpd
A_WATERMARK_XYZ floatvector Atomic 3D-coordinates with watermarking
x float
y float
z float
key: { value: LNTSCSWW datatype: string}
message: { value: CACTVS Watermark datatype: string}
scale: { value: 100 datatype: double}
sigma: { value: 1.0 datatype: double}
spread: { value: 1 datatype: boolean}
markhydrogens: { value: 0 datatype: boolean}
alignpmi: { value: 1 datatype: boolean}
usesensitivity: { value: 0 datatype: boolean}
Compiled C module A_XYZ A_TYPE A_ELEMENT A_WATERMARK_SENSITIVITY atomchange bondchange stereochange mod_a_watermark_xyz.so
A_WEIGHT float Atomic weight
allisotopes: { value: 0 datatype: string}
(builtin) A_TYPE A_ISOTOPE A_ELEMENT atomchange
A_WILDMAN_CRIPPEN_TYPE shortstring Atom classification according to the Wildman-Crippen scheme (see litref) J. Chem. Inf. Comput. Sci 1999, 39, 868-873
Compiled C module A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE B_TYPE B_ORDER B_ISAROMATIC A_IUPAC_GROUP atomchange bondchange atom bond mod_a_wildman_crippen_type.so
A_XSYMBOL string Expanded element symbol, lists contain all elements
(builtin) A_ISOTOPE A_SYMBOL A_ELEMENT A_QUERY atomchange
A_XY floatpair Atomic 2D display coordinates
x float
y float
fixbridgeheadstereo: { value: 1 datatype: string}
align: { value: none datatype: string}
optimize: { value: 1 datatype: string}
ringalignment: { value: 1 datatype: string}
heteroringalignment: { value: 1 datatype: string}
bondlength: { value: 1.0 datatype: string}
wedgepairs: { value: none datatype: string}
wedgestyle: { value: default datatype: string}
pseudo3d: { value: 0 datatype: string}
template: { value: {} datatype: string}
aspectratio: { value: 1.2 datatype: string}
ignorewiggleh: { value: 0 datatype: string}
ignoreatoms: { value: {} datatype: string}
templatefile: { value: 2dtpl.cbin datatype: string}
maxops: { value: 210000 datatype: string}
usertemplatefiles: { value: {} datatype: string}
hbondfactor: { value: 0.62 datatype: string}
hwedgefactor: { value: 0.85 datatype: string}
(builtin) never
A_XYDISTANCE floatvector Atomic distance in 2D plot coordinates
Tcl script A_XY atomchange bondchange a_xydistance.xpd
A_XYZ floatvector Atomic 3D-coordinates J. Gasteiger, C. Rudolph, J. Sadowsky, , Tetrahedron Computer Methodol. (1992)
x float
y float
z float
usechembiogrid: { value: 0 datatype: string}
usepubchem: { value: 1 datatype: string}
usecorina: { value: 1 datatype: string}
usepubchemqc: { value: 0 datatype: string}
maxconformers: { value: 1 datatype: string}
corinaoptions: { value: preserve,stergen,r2d,ori,rc,flapn,msc=32,msi=1024,v3000 datatype: string}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS atomchange bondchange stereochange mod_a_xyz.so
B_1ST_ATOM int First atom of a bond
Tcl script A_LABEL atomchange bondchange merge b_1st_atom.xpd
B_2ND_ATOM int Second atom of a bond
Tcl script A_LABEL atomchange bondchange merge b_2nd_atom.xpd
B_3RING boolean Flag indicating bond is part of 3-membered ring
Tcl script atomchange bondchange b_3ring.xpd
B_4RING boolean Flag indicating bond is part of 4-membered ring
Tcl script atomchange bondchange b_4ring.xpd
B_5RING boolean Flag indicating bond is part of 5-membered ring
Tcl script atomchange bondchange b_5ring.xpd
B_6RING boolean Flag indicating bond is part of 6-membered ring
Tcl script atomchange bondchange b_6ring.xpd
B_7RING boolean Flag indicating bond is part of 7-membered ring
Tcl script atomchange bondchange b_7ring.xpd
B_ALLYLIC boolean A allylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to a carbon-carbon double bond, excluding bonds that lead back to the C=C double bond. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
A_ALLYLIC atomchange bondchange atom bond
B_ANGLE float Angle of atom triples, encoded as pseudo-bond
(builtin) A_XYZ atomchange bondchange 3drelative
B_ANNOTATION string Bond annoations (stereo information etc.), primarily for 2D plots
(builtin) B_FLAGS B_CISTRANS_STEREO B_CIP_STEREO B_LABEL_STEREO B_QUERY atomchange bondchange stereochange
B_ARORING_COUNT short Number of aromatic rings the bond is member of
countenvelopes: { value: 0 datatype: string}
(builtin) R_AROMATIC R_TYPE B_TYPE atomchange bondchange ring
B_ATOMS intpair Sequence numbers of atoms of traditional bond, with lower number listed first
(builtin) A_SEQUENCE_NUMBER atomchange bondchange merge hadd
B_BENZYLIC boolean A benzylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to an aromatic carbon, excluding bonds that lead back to an aromatic atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
A_BENZYLIC atomchange bondchange atom bond
B_BRICS_FRAGMENTATION boolean Bond which would be cut in the BRICS fragmentation method ChemMedChem 2008, 3, 1503
atomchange bondchange atom bond
B_BUGGY1 int Test case of buggy property computation to test recovery mechanisms
Compiled C module atomchange bondchange mod_b_buggy1.so
B_BUGGY2 int Test case of buggy property computation to test recovery mechanisms
Compiled C module atomchange bondchange mod_b_buggy2.so
B_BUGGY3 int Test case of buggy property computation to test recovery mechanisms
Compiled C module B_BUGGY1 atomchange bondchange mod_b_buggy3.so
B_CENTRALITY double Centrality rating of the bond (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN)
Compiled C module A_TOPO_DISTANCE M_SPAN B_TYPE atomchange bondchange atom bond mod_b_centrality.so
B_CIP_STEREO byte Bond chirality descriptor based on CIP (E/Z) rules
@E:undef:Z
(builtin) atomchange bondchange
B_CISTRANS_STEREO byte Bond chirality descriptor based on cis/trans rules
@cis:undef:trans
(builtin) atomchange bondchange
B_CLASSIFICATION bitset Simple bond classification bits
^none:ccbond:chbond:cxbond:xhbond:xxbond:single:double:triple:multiple:aromatic:xaromatic:caromatic:ring:smallring:mediumring:bigring:a-ring:a-aromatic:a-multiple:a-cxbond:b-ring:b-aromatic:b-multiple:b-cxbond
Compiled C module B_TYPE B_ORDER A_TYPE A_ELEMENT B_ISAROMATIC B_RINGS R_HETEROATOM_COUNT R_AROMATIC atom bond ring mod_b_classification.so
B_COLOR colorvector Bond rendering color
color: { value: white datatype: string}
(builtin) never
B_CONJUGATED boolean A conjugated bond according to the Lhasa definition. These are bonds which have a spanning atom alpha to a multiply bonded atom. CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47
A_CONJUGATED atomchange bondchange atom bond
B_DAYLIGHT_ARORING_COUNT short Number of aromatic rings the bond is member of, using explicit Daylight aromaticity in R_DAYLIGHT_AROMATIC instead of aromodel-configurable R_AROMATIC
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE B_TYPE atomchange bondchange ring mod_b_daylight_aroring_count.so
B_DELTA_PI_CHARGE float Difference of Gasteiger pi-charges of the bond atoms
Tcl script A_PI_CHARGE B_TYPE atomchange bondchange b_delta_pi_charge.xpd
B_DELTA_PI_ELECTRONEGATIVITY float Difference of Gasteiger pi-electronegativity of the bond atoms. The value is dependent on the order of the atoms in the bond.
Tcl script A_PI_ELECTRONEGATIVITY B_TYPE atomchange bondchange b_delta_pi_electronegativity.xpd
B_DELTA_SIGMA_CHARGE float Difference of Gasteiger sigma charges of the bond atoms
Tcl script A_SIGMA_CHARGE B_TYPE atomchange bondchange b_delta_sigma_charge.xpd
B_DELTA_SIGMA_ELECTRONEGATIVITY float Difference of Gasteiger sigma electronegativity of the bond atoms
Tcl script A_SIGMA_ELECTRONEGATIVITY B_TYPE atomchange bondchange b_delta_sigma_electronegativity.xpd
B_DELTA_TOTAL_CHARGE float Difference of Gasteiger charges (sum of pi and sigma parts) of the bond atoms
Tcl script A_TOTAL_CHARGE B_TYPE atomchange bondchange b_delta_total_charge.xpd
B_DELTA_TOTAL_WALK_COUNT double Difference in total walk count E_TOTAL_WALK_COUNT if bond is cut J. Chem. Inf. Comput. Sci. 2000, 40, 99-106
usexatoms: { value: 1 description: If set, use heteroatom vs. carbon for additional differentiation. By default, non-hydrogen atoms are anonymous datatype: boolean}
usebo: { value: 1 description: If set, use bond order for additional walks datatype: boolean}
Compiled C module M_HEAVY_ATOM_COUNT B_TYPE B_ORDER B_ISAROMATIC B_RING_COUNT A_TYPE A_ELEMENT E_TOTAL_WALK_COUNT atomchange bondchange mol atom bond mod_b_delta_total_walk_count.so
B_FG_SUBSTITUENTS bitvector Functional group substituents on bonds as per the LHASA definition
ketone boolean
aldehyde boolean
acid boolean
ester boolean
amide*1 boolean
amide*2 boolean
amide*3 boolean
carbonium boolean
isocyanate boolean
acid*halide boolean
thioester boolean
amine*3 boolean
aziridine boolean
amine*2 boolean
amine*1 boolean
nitroso boolean
diazo boolean
haloamine boolean
hydrazone boolean
oxime boolean
imine boolean
thiocyanate boolean
isocyanide boolean
nitrile boolean
azo boolean
hydroxylamine boolean
nitro boolean
enamine boolean
amine*oxide boolean
thiol boolean
episulfide boolean
sulfide boolean
sulfoxide boolean
sulfone boolean
c*sulfonate boolean
anhydride boolean
lactam boolean
phosphine boolean
phosphonate boolean
epoxide boolean
ether boolean
peroxide boolean
alcohol boolean
enol*ether boolean
nitrite boolean
o*sulfonate boolean
fluoride boolean
chloride boolean
bromide boolean
iodide boolean
gem*dihalide boolean
trihalide boolean
acetylene boolean
olefin boolean
vic*dihalide boolean
halohydrin boolean
glycol boolean
hydrate boolean
hemiketal boolean
ketal boolean
hemiacetal boolean
acetal boolean
azide boolean
disulfide boolean
allene boolean
vinylsilane boolean
lactone boolean
vinylw boolean
vinyld boolean
esterx boolean
amidz boolean
methylene boolean
carbonyl boolean
carboxyl boolean
halide boolean
amine boolean
amide boolean
selenide boolean
trialkylsilyl boolean
trialkylsiloxy boolean
silylenolether boolean
n*urea*h boolean
n*urea*c boolean
carbamate*h boolean
carbamate*c boolean
o*carbamate boolean
n*carbamate boolean
o*carbonate boolean
dithioacetal boolean
dithioketal boolean
requested boolean
withdrawing boolean
expandable*withdrawing boolean
nonexpandable*withdrawing boolean
donating boolean
leaving boolean
good*leaving boolean
Compiled C module A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE atomchange bondchange atom bond mod_b_fg_substituents.so
B_FLAGS bitset Display attributes for bond
^none:bold,fat:dotted:dashed:lowarrowtip,lowarrow:higharrowtip,higharrow:highwedgetip,highwedge,hightip,lowbase:lowwedgetip,lowwedge,lowtip,lowbase:slash,intersect,intersection:split,wintersect,wslash,wavyslash,wavyintersect,wavyintersection:lowparallelarrow,lowparallel,lowarrow:highparallelarrow,highparallel,higharrow:right:left:crossed:wavy,zigzag:circle,mark1:square,mark2:cross,mark3:anchor,mark4:wedgelocation,wedgehere,wedgeposition:selected:front:back:protected:colorsplit:highlight:doubleslash:hash:resonance:aromatic:invisible:secondary:edge
bold boolean
dotted boolean
dashed boolean
lowarrowtip boolean
higharrowtip boolean
highwedgetip boolean
lowwedgetip boolean
slash boolean
split boolean
lowparallelarrow boolean
highparallelarrow boolean
right boolean
left boolean
crossed boolean
wavy boolean
circle boolean
square boolean
cross boolean
anchor boolean
wedgelocation boolean
selected boolean
front boolean
back boolean
protected boolean
colorsplit boolean
highlight boolean
doubleslash boolean
hash boolean
resonance boolean
aromatic boolean
invisible boolean
secondary boolean
edge boolean
(builtin) never
B_FRAGMENT_CARBON_CHAIN_LENGTH int Maximum length of linked carbon atoms in the fragments containing the respective bond atoms as first path atom if the bond were cut.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_carbon_chain_length.so
B_FRAGMENT_CARBON_COUNT int Number of carbon atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT(carbon). For a bond to hydrogen, one value is zero and the other the molecule carbon count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_carbon_count.so
B_FRAGMENT_COMPLEXITY double The fragment complexity (M_COMPLEXITY equivalent) of the fragment containing the first and second atom after cutting the bond
B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring
B_FRAGMENT_DIRECTION short Indicator whether the bond, as seen from its first atom to its second atom, is the principal substituent connection (i.e. if the bond is cut, the second atom is in the smaller substituent, and the first atom in the core).
magic=-1:none:asstored:symmetrical:reversed:ringbond
criteria: { value: B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH description: Properties used as criteria to determine the core-side and substituent atoms of the bond, in order of decreasing significance datatype: string constraints: propertylist}
Compiled C module B_TYPE B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH B_RING_COUNT atomchange bondchange atom bond mod_b_fragment_direction.so
B_FRAGMENT_ELEMENT_COUNT shortvector Element counts in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_element_count.so
B_FRAGMENT_FORMULA string Hill formula of the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_FORMULA. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
format: { value: ascii enumeration: ascii:html datatype: string}
usequeryatoms: { value: 0 datatype: string}
Compiled C module B_FRAGMENT_ELEMENT_COUNT atomchange bondchange mol atom bond ring mod_b_fragment_formula.so
B_FRAGMENT_HASH uint64 The hashcode (M_HASHY equivalent) of the fragment containing the first and second atom after cutting the bond
Compiled C module B_TYPE B_ORDER B_ISAROMATIC B_HASHGROUP A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_hash.so
B_FRAGMENT_HEAVY_ATOM_COUNT int Number of heavy atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HEAVY_ATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heavy atom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_heavy_atom_count.so
B_FRAGMENT_HETEROATOM_COUNT int Number of heteroatoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HETEROATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heteroatom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom.
Compiled C module B_TYPE A_TYPE A_ELEMENT atomchange bondchange mol atom bond ring mod_b_fragment_heteroatom_count.so
B_FRAGMENT_STEREO_HASH uint64 The hashcode (M_HASHSY equivalent) of the fragment containing the first and second atom after cutting the bond
Compiled C module B_TYPE A_TYPE B_ISAROMATIC B_STEREO_HASHGROUP A_ELEMENT A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange mol atom bond ring mod_b_fragment_stereo_hash.so
B_FRAMEWORK byte Framework classification 0=ring, 1=sidechain, 2=linker
ring:sidechain,chain:linker,bridge
(builtin) A_FRAMEWORK atomchange bondchange
B_HASH uint64 Bond hashcode
pathlength: { value: 30 datatype: string}
(builtin) A_FRAMEWORK A_HASH B_TYPE B_FRAMEWORK atomchange bondchange
B_HASHGROUP index Hash group id index for bond hash code
(builtin) B_MOL_NUMBER B_HASH atomchange bondchange merge
B_HASH_STEREO byte Hashcode-based bond chirality descriptor
@M:undef:P
useisotope: { value: 0 datatype: string}
(builtin) A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange
B_HETERO_AROMAT_COUNT short Count for the number of heteroaromatic rings the bond participates in
Tcl script B_ISAROMATIC R_HETEROATOM_COUNT R_AROMATIC atomchange bondchange ring b_hetero_aromat_count.xpd
B_ISALPHAARO boolean Flag for bonds which are not aromatic themselves but linked to aromatic atom
(builtin) A_ARORING_COUNT B_TYPE B_ARORING_COUNT atomchange bondchange ring
B_ISAROMATIC boolean Flag whether bond is aromatic or not
(builtin) R_AROMATIC R_TYPE B_TYPE atomchange bondchange ring
B_ISAROTAUTOMERIC short Tautosytem-number for bonds which are in a potentially tautomeric system, including those which would destroy an aromatic system
useimplicith: { value: 0 datatype: string}
maxpathlen: { value: 18 datatype: string}
arotautomers: { value: 1 datatype: boolean}
Compiled C module A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT atomchange bondchange hadd mod_b_isarotautomeric.so
B_ISTAUTOMERIC short Tautosystem number for bonds which are in a potentially tautomeric system
useimplicith: { value: 0 datatype: string}
maxpathlen: { value: 18 datatype: string}
arotautomers: { value: 0 datatype: string}
(builtin) A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT atomchange bondchange hadd
B_LABEL int Arbitrary bond label
(builtin) never
B_LABELCOLOR string X11 style color name of bond labels
color: { value: black datatype: color}
Tcl script never b_labelcolor.xpd
B_LABEL_STEREO byte Label-based bond chirality descriptor
@M,MI,-:undef:P,PL,+
(builtin) never
B_LENGTH float Bond length (taken from 3D-coordinates)
(builtin) A_XYZ atomchange bondchange stereochange 3drelative
B_MAP_STEREO byte Bond stereo descriptor based on reaction mapping
@M,MI,-:undef:P,PL,+
(builtin) A_MAPPING never
B_MOL_LABEL int Label of molecule bond belongs to
(builtin) A_MOL_LABEL atomchange bondchange merge shuffle hadd mol
B_MOL_NUMBER short Number of molecule bond belongs to
(builtin) A_MOL_NUMBER atomchange bondchange merge shuffle hadd mol
B_MOVED_SIGMA_CHARGE float Charge moved during PEOE equilibration during Gasteiger sigma charge/eneg iternation
A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 atomchange bondchange
B_NCICADD_RESONANCE_CROSSED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
B_NCICADD_TAUTO_CROSSED boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
B_ORDER byte Bond order
never
B_ORDER_ESTIMATE float Estimation of fractional bond order from 3D coordinates via element pair plus base length/exponent table. Uses external data file b_order_estimate.dat (usually located in ${data_directory}/propdata/b_order_estimate directory) for the atom pair parameters. Bonds perceived from close atom distances are created as type "link" if not yet present, and their frational bond order is larger than the threshold parameter.
threshold: { value: 0.25 description: Minimal found bond order to act upon datatype: double}
patternfile: { value: b_order_estimate.dat datatype: diskfile constraints: readable}
Tcl script A_XYZ A_ELEMENT never b_order_estimate.xpd
B_POLARIZABILITY float Average of atom polarizabilities involved in bond
Compiled C module A_TYPE A_POLARIZABILITY atomchange bondchange mod_b_polarizability.so
B_QUERY compound Bond attributes for structure queries
^none:stereo:aromatic,aro:aliphatic,ali,nonaromatic,inaromatic,unaromatic:ringsystem,ringcount:doublearo,doubleoraro,da,d/a:singlearo,singleoraro,sa,s/a:mustmap:nostereook:symmetric,symmetry:asymmetric,asymmetry:nooverlap:implicitbondorder,implicit,implicitbo:kekulecmp:any:multiaro,multioraro,ma,m/a:multiple,m:offpath:daylightaromatic,daylightaro:singledouble,s/d:singledoublearo,s/d/a
flags bitset
order bitset
ringsize bitset
ringcount bitset
aroringcount bitset
tclproc string
query querytree
varbo double
pyfunction string
never
B_RACEMATE byte Racemate distribution of stereobond
undefined,undef:rac,racemat:pure
atomchange bondchange
B_REACTION_CENTER int Reaction Center information from MDL rxn/rdf file
never
B_RECAP_FRAGMENTATION boolean Bond which would be cut in the RECAP fragmentation method J. Chem. Inf. Comput. Sci. 38, 1998, 511-522
atomchange bondchange atom bond
B_RINGS intvector Labels of the rings the bond is member in
(builtin) R_LABEL R_TYPE B_TYPE atomchange bondchange merge ring
B_RINGSIZE uint64 Bits indicate membership in ring of size N
ringset: { value: esssr datatype: string}
(builtin) R_TYPE B_TYPE atomchange bondchange ring
B_RING_COUNT short Number of simple (non-enevelope) rings a bond is member of
countenvelopes: { value: 0 datatype: string}
(builtin) B_TYPE R_TYPE atomchange bondchange ring
B_RING_HETEROATOM_COUNT_BITS bitset A bit is set at bit position n for any ESSSR ring the bond is a member of which has n hetero atoms. Chain and bridge bonds have value 0. If the bond is a member of a carbocyclic ESSSR ring, bit position 0 is set.
Compiled C module R_HETEROATOM_COUNT R_TYPE B_TYPE atomchange bondchange atom bond mod_b_ring_heteroatom_count_bits.so
B_RING_SIZE_BITS bitset Bit mask for ring sizes the bond participates in
Compiled C module R_SIZE R_TYPE B_TYPE bondchange ring mod_b_ring_size_bits.so
B_RING_SUBSTITUENT_PATTERN compound Compute relative alignment of ring atom substituents in cases where the ring plane is the stereo-defining anchor, This is done both for ring substituents which are on directly connected ring atoms and those which are distant (for example, 1.4 cis/trans relationships in six-membered rings) and where the ring acts as a pseudo-doublebond. In the first case, the property is set on the ring bond between the substituted ring atoms. In the second case, all bonds which are on one of the shortest paths between two same-ring atoms where the A_STEREOGENIC value is "ringct" get the descriptor. For a simple 1.4 cyclohexane, these are all ring atoms. Note that a 1.3-substituted cyclohexane gets no descriptors in this property: Neither share the substituted ring atoms a bond, nor is the ring acting as a pseudo doublebond. Across-ring stereodescriptors are not set if other ring substituents impress normal atom stereogenicity on the substituted ring atoms, which is for example the case in any 1.x.4 substituent pattern. Field descriptor is the label-based stereo decriptor for the bond(s). Value 1/P: low-label off-ring substituents on different sides of ring plane, 1.2-substituents Value -1/M: Low-label off-ring substituents on same side of ring plane, 1.2-substituents Value 2/p: low-label off-ring substituents on different sides of ring plane, distant substituents Value -2/m: Low-label off-ring substituents on same side of ring plane, distant substituents Value 0: no ring substituent stereo Fields ligatom1a/ligatom2a are the low-label off-ring substitituent atoms. Fields ligatom1b/ligatom2b are the secondary off-ring substituent atoms.
@m:M:none:P:p
descriptor byte
ligatom1a int
ligatom1b int
ligatom2a int
ligatom2b int
Compiled C module A_LABEL_STEREO R_TYPE A_LABEL B_TYPE A_STEREOGENIC atomchange bondchange stereochange ring mod_b_ring_substituent_pattern.so
B_ROTATABILITY byte Classification of bond rotatability. Ring bond flag must have precedence over multi-bond flag for E_EFFECTIVE_ROTOR_COUNT
undef:terminal:ring:multiple:spheric,round,roundligand:linear,linearligand:yes:locked:forced
Compiled C module B_TYPE B_ORDER A_TYPE A_ELEMENT A_INAMIDE A_TERMINAL_DISTANCE atomchange bondchange hadd mod_b_rotatability.so
B_SEQUENCE_NUMBER int Sequential bond number for CTX output
(builtin) B_MOL_NUMBER A_SEQUENCE_NUMBER A_TYPE atomchange bondchange merge shuffle hadd mol
B_SSMATCH int Ensemble is structure, property data encodes labels of matching substructure bonds, 0 for unmatched parts
sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
Tcl script never b_ssmatch.xpd
B_SSMATCH_ENVIRONMENT datatree Classigied unmatched structure environment of the substructure bonds, i.e. data on the characteristics of the unmatched structure bonds sprouting from the structure bond matched by this substructure bond. Set by a substructure hit option, not directly computable.
atomchange bondchange atom bond
B_STEREOGENIC byte Can this bond be a stereocenter ?
no:maybe:checkno:checkyes:ringct
simple: { value: 0 datatype: string}
ringsizecheck: { value: 1 datatype: string}
electronegativitycheck: { value: 1 datatype: string}
(builtin) atomchange bondchange hadd
B_STEREOINFO byte Stereo descriptor availability info: 1:Label,2:E/Z,4:cis/trans,8:hash,16:map
^none:label:cip:cistrans:hash:map
(builtin) B_CISTRANS_STEREO B_LABEL_STEREO B_HASH_STEREO B_CIP_STEREO B_MAP_STEREO atomchange bondchange stereochange
B_STEREO_HASH uint64 Stereospecific bond hashcode
(builtin) A_FRAMEWORK A_STEREO_HASH B_FRAMEWORK B_TYPE atomchange bondchange
B_STEREO_HASHGROUP index Hash group id index for stereospecific bond hash code
(builtin) B_MOL_NUMBER B_HASH A_HASH_STEREO B_HASH_STEREO atomchange bondchange merge
B_STMATCH int Ensemble is substructure, property data encodes labels of matching structure bonds, 0 for unmatched parts
sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
Tcl script never b_stmatch.xpd
B_STRAINED boolean Flags for strained bonds according to the Lhasa definition. These are: endocylic 3/4-membered ring bonds endocyclic 5-membered ring bonds which are part of a [2.1.1], [2.2.1] or [3.2.1] bicyclic system trans C=C double bonds in rings smaller than size 10 C=C double bonds exocyclic to 3/4-membered rings
Compiled C module R_TYPE B_TYPE B_ORDER A_TYPE A_LABEL A_ELEMENT B_LABEL_STEREO A_RING_COUNT bondchange ring mod_b_strained.so
B_TEXTLABEL compound Arbitrary textual bond label plus alignment info for plots
@left:center:right
label string
align byte
never
B_TORSION_ANGLE float Torsion angle of atom quartets, encoded as pseudo bond
(builtin) A_XYZ atomchange bondchange 3drelative
B_TRANSFORM_STATUS byte Bond status as result of SMIRKS transformation. Possible values are none: not matched in transform, matched: matched, but unchanged, changed: bond order or attribute changed, new: bond introduced by transform
none:matched:changed:new
atomchange bondchange atom bond
B_TYPE int Bond type
^none:link:normal,valence,vb:hbond,hydrogen:dative:3center:angle,dihedral,3atom:torsion,torsional,4atom:rgroup,rg:nobond,searchnot,not:deloc,delocalized:complex:ionic
never
C_COMMENT string Connection (edge) comment in free format
never
C_DIRECTED boolean Flag indicating whether connection/edge is directed. Global default is given in N_DIRECTED.
Compiled C module atomchange bondchange atom bond mod_c_directed.so
C_GRAPHICS compound Connection (edge) graphics
none:arc:bitmap:image:line:oval,ellipse,ellipsis:polygon:rectangle,rect:text:box:circle:rhombus,diamond:ver_ellipsis:hor_ellipsis:triangle:pentagon:hexagon:octagon:roundedrectangle,roundrectangle,roundrect,roundedrect
type int
attributes dictionary
usehtml: { value: 0 description: Whether to use HTML encoding of the text annotation datatype: boolean}
fontsize: { value: -1 description: Font size (negative value: unset) datatype: int}
font: { value: Verdana description: Font name datatype: string}
fontcolor: { value: black description: Font color (empty is unset) datatype: color constraints: emptycolor}
color: { value: black description: Connection line color (empty is unset) datatype: color constraints: emptycolor}
Tcl script C_NAME never c_graphics.xpd
C_IDENT string Connection (edge) ident string
Compiled C module never mod_c_ident.so
C_LABEL int Connection (edge) label of connections in network objects
Compiled C module never mod_c_label.so
C_LABEL_GRAPHICS compound Connection (edge) label graphics
none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon
type int
attributes dictionary
never
C_NAME string Connection (edge) name in free format
never
C_ONTOLOGY_LINK int Ontology link type
none:is_a:has_part:is_conjugate_base_of:is_conjugate_acid_of:is_tautomer_of:is_enantiomer_of:has_functional_parent:has_parent_hydride:is_substituent_group_from:has_role
never
C_PARTITION int Partition code for connections (edges). If a symbolic name is available, I/O modules modify the enumeration field of the property.
atomchange bondchange atom bond
C_TEXT string Connection (edge) text label
never
C_TYPE string Connection (edge) type in free format
never
C_URL url Connection reference URL
atomchange bondchange atom bond
C_WEIGHT double Graph connection (edge) weight
Compiled C module never mod_c_weight.so
D_AUTHOR string Dataset author as free-form string
never
D_CHEMDRAW_PAGE diskfile
(switchable between blob diskfile)
Tabular display of structure collection in ChemDraw page
ncols: { value: 3 minvalue: 1 maxvalue: 20 datatype: int}
nrows: { value: 4 minvalue: 1 maxvalue: 20 datatype: int}
offset: { value: 0 minvalue: 0 datatype: int}
filename: { value: {} datatype: string constraints: writeable}
format: { value: cdx enumeration: cdx:cdxml datatype: int}
grid: { value: 1 datatype: boolean}
gridcolor: { value: black datatype: color}
gridselectcolor: { value: orange datatype: color}
papersize: { value: a4 enumeration: a3:a4:a5:a6:a7:b3:b4:b5:b6:letter:legal:executive datatype: int}
border: { value: 12.0 minvalue: 0 maxvalue: 99 datatype: double}
boxspacing: { value: 6.0 minvalue: 0 maxvalue: 99 datatype: double}
bonds: { value: 8 minvalue: 1 maxvalue: 25 datatype: int}
boxborder: { value: 3.0 minvalue: 0 maxvalue: 99 datatype: double}
orientation: { value: portrait enumeration: portrait:landscape datatype: int}
cdxversion: { value: 8.0 datatype: double}
journalstyle: { value: acs enumeration: default:acs,jacs datatype: int}
multipage: { value: 0 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: propertylist}
headerformat: { value: {} datatype: string}
headerfont: { value: Arial datatype: string}
headercolor: { value: black datatype: color}
headerhighlightcolor: { value: red datatype: color}
headerhighlightfilter: { value: {} datatype: string constraints: filtername}
headerfontstyle: { value: none datatype: string}
headerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
header2property: { value: {} datatype: string constraints: propertylist}
header2format: { value: {} datatype: string}
header2font: { value: Arial datatype: string}
header2color: { value: black datatype: color}
header2highlightcolor: { value: red datatype: color}
header2highlightfilter: { value: {} datatype: string constraints: filtername}
header2fontstyle: { value: none datatype: string}
header2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
footerproperty: { value: E_NAME datatype: string constraints: propertylist}
footerformat: { value: {} datatype: string}
footerfont: { value: Arial datatype: string}
footerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
footercolor: { value: black datatype: color}
footerhighlightcolor: { value: red datatype: color}
footerhighlightfilter: { value: {} datatype: string constraints: filtername}
footerfontstyle: { value: none datatype: string}
footer2property: { value: {} datatype: string constraints: propertylist}
footer2format: { value: {} datatype: string}
footer2font: { value: Arial datatype: string}
footer2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int}
footer2color: { value: black datatype: color}
footer2highlightcolor: { value: red datatype: color}
footer2highlightfilter: { value: {} datatype: string constraints: filtername}
footer2fontstyle: { value: none datatype: string}
headercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int}
footercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int}
Tcl script atomchange bondchange stereochange groupchange dataset d_chemdraw_page.xpd
D_COPYRIGHT string Copyright information
never
D_CREATION_TIME datetime Date of dataset generation
Tcl script never d_creation_time.xpd
D_DATE date Dataset creation date
atomchange bondchange atom bond
D_DESCRIPTION string Free-form description of dataset
never
D_DIVERSITY_SET dataset Select a diverse subset from the source dataset.
property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property}
query: { value: all description: Structure filter query expression datatype: string}
size: { value: 50 description: Target size minvalue: 1 datatype: int}
startindex: { value: -1 description: First structure source index, -1 is random datatype: int}
minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int}
Tcl script atomchange bondchange atom bond d_diversity_set.xpd
D_EMF_IMAGE diskfile Dataset rendered as WMF/EMF image, from assembled E_EMF_IMAGE structure renderings
ncols: { value: 3 minvalue: 1 datatype: int}
nrows: { value: 4 minvalue: 1 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
framewidth: { value: 1 datatype: int}
boxwidth: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int}
boxheight: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headerheight: { value: 0 minvalue: 0 datatype: int}
footerheight: { value: 0 minvalue: 0 datatype: int}
comment: { value: {} datatype: string}
commenttype: { value: text enumeration: none:text:property,prop datatype: int}
filename: { value: {} datatype: diskfile constraints: writeable}
format: { value: pwmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
font: { value: arialn datatype: string}
annotationfontsize: { value: -1 datatype: double}
offset: { value: 0 datatype: int}
imgproperty: { value: E_EMF_IMAGE datatype: string constraints: property}
padding: { value: 1 datatype: int}
boxbgcolor: { value: transparent datatype: color}
boxhighlightcolor: { value: red datatype: string}
selectlist: { value: {} datatype: intvector}
colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,grayscale,greyscale:color,colour datatype: int}
downloadfilename: { value: {} datatype: string}
Compiled C module E_EMF_IMAGE dataset mod_d_emf_image.so
D_FRAGMENT_NETWORK network Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies.
trace: { value: 0 description: If set, print trace information on the progress of the process datatype: boolean}
mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int}
maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int}
minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int}
bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list}
Tcl script dataset d_fragment_network.xpd
D_FRAGMENT_TABLE table Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies.
mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int}
maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int}
minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double}
columns: { value: E_SMILES E_HASHY count frequency source destination description: Result table columns datatype: string constraints: list}
maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int}
bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list}
Tcl script dataset d_fragment_table.xpd
D_FUZZY_MCSS structure Maximum common substructure of dataset, determined by non-deterministic fuzzy matching
maxfuzz: { value: 5 datatype: string}
Compiled C module atomchange bondchange stereochange dataset mod_d_fuzzy_mcss.so
D_GIF diskfile
(switchable between string blob diskfile url)
GIF image table of the contents of a dataset, assembled by tiles of E_GIF structure images
ncols: { value: 3 datatype: int}
nrows: { value: 4 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
framewidth: { value: 1 datatype: int}
boxwidth: { value: 200 datatype: int}
boxheight: { value: 200 datatype: int}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headerheight: { value: 0 datatype: int}
footerheight: { value: 0 datatype: int}
comment: { value: {} datatype: string}
commenttype: { value: text enumeration: none:text:property datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
format: { value: gif enumeration: gif:png,png24:png8 datatype: string}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
headercolor: { value: black datatype: string}
footercolor: { value: black datatype: string}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: string}
font: { value: arialn datatype: string}
annotationfontsize: { value: -1 datatype: double}
interlace: { value: 0 datatype: boolean}
offset: { value: 0 description: First dataset object to use datatype: int}
imgproperty: { value: E_GIF datatype: string constraints: property}
padding: { value: 1 datatype: int}
boxbgcolor: { value: transparent datatype: color}
boxhighlightcolor: { value: red datatype: color}
selectlist: { value: {} description: Indices of dataset objects to include, if empty, use all datatype: intvector}
downloadfilename: { value: {} description: Save file name if http header is used datatype: string}
fixiepngsize: { value: 1 description: Circumvent Windows bug in older releases datatype: boolean}
Compiled C module E_GIF dataset mod_d_gif.so
D_HASHISY uint64 Stereospecific and isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHISY dataset mod_d_hashisy.so
D_HASHIY uint64 Non-stereospecific but isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHIY dataset mod_d_hashiy.so
D_HASHSY uint64 Stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHSY dataset mod_d_hashsy.so
D_HASHY uint64 Non-stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset
Compiled C module E_HASHY dataset mod_d_hashy.so
D_HTML_PAGE blob
(switchable between blob diskfile)
filename: { value: {} description: Output file name, empty for tmp file datatype: string}
htmlpage: { value: 0 description: If set, write complete HTML page, otherwise write only ExtJS generator statements. datatype: boolean}
title: { value: {} description: Graph title datatype: string}
Tcl script atomchange bondchange atom bond dataset d_html_page.xpd
D_IDENT string Ident string of dataset
atomchange bondchange atom bond
D_MATCHED_PAIRS compoundvector Identify matched pair molecules, or matched series molecules, in a dataset.
id int
datasetindex int
bond int
centrality double
size int
setindex int
structure structure
mode: { value: pairs description: In pairs mode, always find molecule pairs under any ID. In series mode, if there are more than 2 structures linked, group them all under a common ID. Example: F/Cl/Br-benzene, In pairs mode, find 3 structure pairs, in series mode, find one series with 3 members enumeration: pairs:series datatype: string}
copystructures: { value: 0 description: If set, duplicate the matched pair/set structures with highlighted bonds in B_FLAGS into the "structure" field of this property. If it is not set, only the id/dataset index/bond fields are filled and the structure field is set to NULL datatype: boolean}
cutxhbonds: { value: 1 description: If set, allow bonds between hydrogen and heteroatom to be part of a pair or set definition datatype: boolean}
cutchbonds: { value: 1 description: If set, allow bonds between hydrogen and carbon to be part of a pair or set definition datatype: boolean}
cutcxbonds: { value: 1 description: If set, allow bonds between carbon and heteroatom to be part of a pair or set definition datatype: boolean}
cutccbonds: { value: 1 description: If set, allow bonds between carbon to be part of a pair or set definition datatype: boolean}
cutxxbonds: { value: 1 description: If set, allow bonds between heteroatoms to be part of a pair or set definition datatype: boolean}
cutchainchainbonds: { value: 1 description: If set, allow bonds between two chain atoms to be part of a pair or set definition datatype: boolean}
cutringchainbonds: { value: 1 description: If set, allow bonds between a ring and a chain atom to be part of a pair or set definition datatype: boolean}
cutringringbonds: { value: 1 description: If set, allow non-ring bonds between ring atoms to be part of a pair or set definition datatype: boolean}
cutpreference: { value: first description: Define which bonds should be preferred if there a multiple possibilities to define a pair or set. All: report all possibilities, first: report first possibility found, core: report most central cut, peripheral: report most peripheral cut for any given set or series enumeration: all:first:core,central:peripheral datatype: string}
minheavyatoms: { value: 0 description: Minimum number of heavy atoms which must be present in the R-group part datatype: int}
maxheavyatoms: { value: 999 description: Maximum number of heavy atoms which must be present in the R-group part datatype: int}
formulafilter: { value: {} description: A formula match expression which possible R-groups must match datatype: formulamatch}
removesubsets: { value: 0 description: If set, remove (in series mode) sets which are a subset of a larger set datatype: boolean}
Compiled C module B_FRAGMENT_HASH B_FRAGMENT_DIRECTION B_FRAGMENT_ELEMENT_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_CENTRALITY B_STEREO_HASHGROUP A_RING_COUNT A_TYPE A_ELEMENT atomchange bondchange atom bond dataset mod_d_matched_pairs.so
D_MCSS structure Maximum common substructure of dataset
cmpflags: { value: bondorder datatype: string}
hitflags: { value: {} datatype: string}
exclflags: { value: st_h|ss_h datatype: string}
Compiled C module atomchange bondchange stereochange dataset mod_d_mcss.so
D_NAME string Free-form user-defined dataset name
never
D_NEW_FLAG boolean Dataset flag for new compounds. THis is primarily used in the CHAI file format.
never
D_PROGRAM string Program source of dataset
never
D_PS_PAGES diskfile Postscript dataset rendering
filename: { value: {} datatype: diskfile constraints: writeable}
httpheader: { value: 0 datatype: boolean}
ncols: { value: 2 datatype: int}
nrows: { value: 3 datatype: int}
papersize: { value: A4 enumeration: none:a3:a4:a5:a6:a7:b3:b4:b5:b6:letter,usletter:legal,uslegal:executive,exec,usexecutive,usexec datatype: string}
border: { value: 10 datatype: int}
title: { value: {} datatype: string}
comment: { value: {} datatype: string}
space: { value: 5 datatype: int}
frame: { value: line enumeration: none:line:shadow datatype: string}
boxproperty: { value: E_NAME datatype: string constraints: property}
orientation: { value: portrait enumeration: none:landscape,wide,quer,querformat:portrait,tall,hoch,hochformat datatype: string}
colormode: { value: bow enumeration: bow,bw:wob:cow,color:cob datatype: string}
headerfontsize: { value: 12 datatype: double}
footerfontsize: { value: 12 datatype: double}
labelfontsize: { value: 10 datatype: double}
pagelimit: { value: 100 minvalue: 1 maxvalue: 9999 datatype: int}
pageoffset: { value: 0 minvalue: 0 maxvalue: 9999 datatype: int}
psheader: { value: all enumeration: all:none:prolog:trailer datatype: string}
pagecount: { value: 0 minvalue: -1 maxvalue: 9999 datatype: int}
shadow: { value: 3 datatype: int}
eps: { value: 0 datatype: boolean}
binder: { value: none enumeration: none:left:top:right:bottom datatype: string}
binderwidth: { value: 30 datatype: int}
logotext: { value: {} datatype: string}
printpagecount: { value: -1 datatype: int}
headerheight: { value: 14 datatype: int}
footerheight: { value: 14 datatype: int}
labelheight: { value: 12 datatype: int}
nameheight: { value: 12 datatype: int}
namefontsize: { value: 10 datatype: int}
atomcolor: { value: {} description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string constraints: emptycolor}
downloadfilename: { value: {} datatype: string}
Compiled C module E_EPS_IMAGE atomchange bondchange stereochange groupchange dataset mod_d_ps_pages.so
D_SCAFFOLD_TABLE table A list of Ertl-type scaffolds extracted from a file. The table contains the counts and SMILES strings as columns, plus row-attached structures.
maxrecs: { value: -1 description: The maximum number of records to process, -1 is infinite datatype: int}
maxscaffolds: { value: -1 description: The maximum number of scaffolds to record, -1 is infinite datatype: int}
maxsimplification: { value: 1 description: The maximum number of scaffolds simplification steps to perform, -1 is infinite datatype: int}
compoundfilter: { value: all description: A compound filter expression (see 'ens scan' command) scaffolds must match datatype: string}
Tcl script E_SMILES E_SCAFFOLD_TREE_STRUCTURE atomchange bondchange stereochange atom bond d_scaffold_table.xpd
D_SCAFFOLD_TREE datatree The scaffolds of the structures in the dataset in sorted, hierarchical order. The first node a an empty root node, and its children are the irreducible scaffolds. The individual scaffold nodes of the tree contain SMILES strings as value and the (non-stereo/non-isotope) ensemble hashcode as name, followed by all more complex scaffolds which are reduced to the current scaffold by one simplification step. J. Chem. Inf. Model. 2007, 47, 47-58
maxlevel: { value: -1 description: Maximum tree depth to generate, -1 for unlimited datatype: int}
includeoriginals: { value: 0 description: If set, include the base structures. By default, only the scaffolds are included datatype: boolean}
hashcode: { value: E_HASHY description: The hashcode property to be used to check structure identity datatype: string constraints: property}
nodenameproperty: { value: E_HASHY description: Instance values of this property are stored as node names. datatype: string constraints: property}
auxproperties: { value: {} description: Instance data of these properties is appended to the right of the SMILES data in the nodes datatype: string constraints: propertylist}
Tcl script atomchange bondchange atom bond dataset d_scaffold_tree.xpd
D_SIMILARITY_MATRIX intmatrix Similarity matrix between structures in dataset, with dataset element indices as matrix indices
property: { value: E_SCREEN datatype: string constraints: property}
method: { value: tanimoto datatype: string}
Tcl script E_SCREEN atomchange bondchange merge atom bond dataset d_similarity_matrix.xpd
D_SIZE int Dataset size
Tcl script dataset d_size.xpd
D_SMALLWORLD_NETWORK network Sample implementation of R. Sayles SmallWorld network for accelerated MCSS searching
useelements: { value: 1 datatype: boolean}
usebondorders: { value: 1 datatype: boolean}
addsingleatomfragments: { value: 0 datatype: boolean}
Compiled C module E_HASHY B_HASHGROUP A_ELEMENT A_LABEL B_LABEL A_TYPE B_TYPE B_ISAROMATIC B_RING_COUNT A_SUBSTITUENT_COUNT E_NMOLECULES E_HEAVY_ATOM_COUNT atomchange bondchange atom bond dataset mod_d_smallworld_network.so
D_SOURCE string Free-form dataset source description
never
D_SUBSTRUCTURE_HIERARCHY network A tree-style network of substructure hierarchies of the structures in the dataset.
storestructures: { value: 0 description: If set, store the structures in the nodes in property V_STRUCTURE datatype: boolean}
storeimages: { value: 0 description: If set, store an image of the structures in the nodes in property V_GRAPHICS datatype: boolean}
directory: { value: img description: Image directory datatype: string constraints: directory}
imgparameters: { value: width 100 height 100 bgcolor black atomcolor element bondcolor white format png frame 0 bonds 6 description: Image parameters datatype: dictionary}
ssmatchflags: { value: -excludeh all description: Extra flags to pass to the substructure matcher datatype: string}
auxlinks: { value: 0 description: if set, create additional links to alternative matches in the same level datatype: boolean}
Tcl script atomchange bondchange atom bond dataset d_substructure_hierarchy.xpd
D_TREE_DATA_GIF diskfile
(switchable between string blob diskfile url)
Rendering of tree-style property data (must be of property datatype "datatree") as a GIF/PNG image using a modified Reingold-Tilford tree layout algorithm.
property: { value: D_SCAFFOLD_TREE description: Property to read rendered data from datatype: string constraints: property}
treeindex: { value: 0 datatype: string}
maxlevel: { value: -1 datatype: int}
boxwidth: { value: 100 datatype: int}
boxheight: { value: 100 datatype: int}
treedistance: { value: 10 description: Minimum horizontal distance between boxes on a level which do not have the same parent datatype: int}
siblingdistance: { value: 5 description: Minimum horizontal distance between boxes on a level which do have the same parent datatype: int}
leveldistance: { value: 25 description: Distance between lower box Y of parent level and upper box Y of child level datatype: int}
border: { value: 5 description: Unused pixels around tree datatype: int}
decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean}
showname: { value: 0 description: If set, include the node name in rendering datatype: boolean}
showcount: { value: 0 description: If set, include non-negative count node fields in rendering datatype: boolean}
interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean}
alignstructures: { value: 1 description: If structures are rendered, align them hierarchically datatype: boolean}
excluderoot: { value: 0 description: If set, do not render root node datatype: boolean}
framewidth: { value: 0 datatype: int}
bgcolor: { value: white datatype: color}
framecolor: { value: black datatype: color}
linecolor: { value: red datatype: color}
boxframecolor: { value: blue datatype: color}
boxbgcolor: { value: grey90 datatype: color}
format: { value: png enumeration: gif:png,png24:png8 datatype: string}
font: { value: arialn datatype: string}
fontsize: { value: 8.0 datatype: double}
filename: { value: {} description: Output file name, if data type is diskfile. If empty, generate /tmp file datatype: diskfile constraints: writeable}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
Compiled C module atomchange bondchange atom bond dataset mod_d_tree_data_gif.so
D_WATERMARK double Watermark detection in a set of structures with 3D coordinates
key: { value: LNTSCSWW description: Message encoder key datatype: string}
message: { value: CACTVS Watermark description: Encoded message datatype: string}
scale: { value: 100 datatype: double}
sigma: { value: 1.0 datatype: double}
spread: { value: 1 datatype: int}
markhydrogens: { value: 0 description: Include hydrogens in atoms encoding the message datatype: boolean}
alignpmi: { value: 1 description: Align 3D atomic coordinates to PMI datatype: boolean}
usesensitivity: { value: 0 description: If set, use A_WATERMARK_SENSITITIVY data to tune coordiante shifts to minimize energy distortions datatype: boolean}
Compiled C module A_XYZ A_ELEMENT A_TYPE A_SMILES_RANK A_WATERMARK_SENSITIVITY E_HASHY dataset mod_d_watermark.so
D_XYPLOTENERGY double Plot pseudo energy - debug property, not intended for production use
maximprove: { value: 100 datatype: int}
maxcycle: { value: 100 datatype: int}
uselast: { value: 0 datatype: boolean}
Compiled C module A_XY A_ELEMENT A_TYPE B_TYPE dataset mod_d_xyplotenergy.so
E_ACROS_URL url Catalog URL of structure for Acros Organics/Fisher Scientific
Tcl script atomchange bondchange atom bond e_acros_url.xpd
E_ACTIVE_AIDSET intvector Set of PubChem assay IDs testing this compound as active
Tcl script E_CID atomchange bondchange stereochange e_active_aidset.xpd
E_ADJACENCY_MATRIX intmatrix Standard non-canonical adjacency matrix for the representation of compounds, with bond orders in i/j elements and free electrons in i/i elements. If there is no bond, the matrix element value is zero.
Tcl script A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS atomchange bondchange atom bond e_adjacency_matrix.xpd
E_AIDSET intvector Set of PubChem assay IDs where this compoundwas tested
Tcl script E_CID atomchange bondchange stereochange e_aidset.xpd
E_AIDSET_URL url PubChem assay database URL
Tcl script E_AIDSET atomchange bondchange stereochange merge e_aidset_url.xpd
E_ALFA_AESAR_ID string Structure ID in the AlfaAesar catalog(www.alfa.com)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_alfa_aesar_id.xpd
E_ALFA_AESAR_URL url Data page in the AlfaAesar catalog (www.alfa.com)
Tcl script E_ALFA_AESAR_ID atomchange bondchange atom bond e_alfa_aesar_url.xpd
E_ALIRING_COUNT short Number of aliphatic rings the ensemble contains
Compiled C module R_AROMATIC R_TYPE atomchange bondchange ring mod_e_aliring_count.so
E_AMINO_ACID_SEQUENCE string Amino acid sequence in 1- or 3-letter letter code. Can be computed from molecular structure with standard amino acid set.
nomenclature: { value: a description: Whether to use single-letter amino acid codes (a) or 3-letter codes (aaa) enumeration: a,letter1=1:aaa,letter3=3 datatype: int}
Compiled C module M_AMINO_ACID_SEQUENCE atomchange bondchange mol mod_e_amino_acid_sequence.so
E_ANNOTATION choicevector Graphical annotation objects of an ensemble. Thre various graphicsl objects supported by this property are described as separate proerties referred as choice variant fields.
text compound
rectangle compound
ellipse compound
roundedrectangle compound
polyline compound
bracket compound
A_XY never
E_AOPWIKI_URL url Display URL in the AOP Wiki (Adverse Outcome Pathway, https://aopwiki.org)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_aopwiki_url.xpd
E_ARORING_COUNT short Count of aromatic rings in ESSSR
Compiled C module R_AROMATIC R_TYPE atomchange bondchange atom bond ring mod_e_aroring_count.so
E_ASCII_IMAGE string
(switchable between string unicode)
ASCII (or Unicode) rendering of a chemical structure. Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the last line.
width: { value: 40 minvalue: 25 maxvalue: 256 datatype: int}
height: { value: 30 minvalue: 25 maxvalue: 256 datatype: int}
showcharge: { value: 0 datatype: boolean}
useunicode: { value: 1 datatype: boolean}
bonds: { value: 10 minvalue: 3 maxvalue: 25 datatype: double}
usecolor: { value: 0 datatype: boolean}
usefontstyle: { value: 0 datatype: boolean}
showradical: { value: 0 datatype: boolean}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,exten ded,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,y es datatype: int}
csymbol: { value: all enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: white datatype: color}
highlightcolor: { value: red datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
frame: { value: 0 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
crop: { value: left|right|top|bottom enumeration: ^none:left:right:top:bottom datatype: bitset}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
usealtcharset: { value: 0 datatype: boolean}
leadnewline: { value: 0 datatype: boolean}
tailnewline: { value: 0 datatype: boolean}
framecolor: { value: black datatype: color}
hcolor: { value: {} datatype: string}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
unicodeforringbonds: { value: macrocycles enumeration: no,never:macrocycles,largerings:yes,always datatype: int}
badunicodechars: { value: 0x2571 0x2572 0x2573 0x2afd description: Codes of Unicode chars which should not be used, for example because they are missing in the terminal font comment: 0x2afd: double slash, 0x244a: double backslash, 0x2500: horizontal single line, 0x2501: horizontal bold single line, 0x2502: vertical single line, 0x2504: vertical bold single line, 0x2504: horizontal dotted line, 0x2506: vertical dotted line, 0x250c: corner lower right, 0x2510: corner lower left, 0x2514: corner upper right, 0x2518: corner upper left, 0x2550: horizontal double line, 0x2551: vertical double line, 0x2554: double corner lower right, 0x2557: double corner lower left, 0x255A: double corner upper right, 0x255D: double corner upper left, 0x2571: diagonal lower left to upper right, 0x2572: diagonal upper left to lower right, 0x2573: cross, 0x2630: horizontal triple line datatype: string constraints: list}
Compiled C module A_TYPE A_ELEMENT A_FLAGS B_FLAGS A_QUERY B_QUERY A_FORMAL_CHARGE A_RESIDUE A_SYMBOL A_XSYMBOL A_XY A_HSPECIAL A_CSPECIAL A_COLOR A_ANNOTATION B_TYPE B_LABEL B_ORDER B_COLOR R_TYPE atomchange bondchange stereochange merge mol atom bond mod_e_ascii_image.so
E_ASTATECH_ID string Catalog ID from AstaTech (astatechinc.om)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_astatech_id.xpd
E_ASTATECH_URL url Catalog display URL for AstaTech catalog (astatechinc.om)
Tcl script E_ASTATECH_ID atomchange bondchange stereochange atom bond e_astatech_url.xpd
E_ASYNCSERVER string Dummy property to test async client/server communication
never
E_ATOMHASH_COUNT int Number of different basic atom hash codes
(builtin) E_HASHGROUP_COUNT_A atomchange bondchange merge
E_AUTHOR string Information about the original author of a structure or related document
never
E_AUTODOCK4_TORSIONAL_FREEDOM byte Torsional freedom parameter for Audock 4. Used in the I/O modules for the Autodoc4 PDBQT file format.
atomchange bondchange stereochange 3drelative
E_AUXILIARY_SCREEN bitvector Auxiliary custom structure search screens, configurable via pattern parameter or file
patternfile: { value: {} datatype: diskfile constraints: readable}
patterns: { value: N=[N+]=[N-] datatype: string}
aromode: { value: strict enumeration: strict:lenient:default datatype: int}
Tcl script atomchange bondchange stereochange hadd e_auxiliary_screen.xpd
E_BARCODE blob
(switchable between string blob diskfile)
Barcodes in various formats as image data, returned either as a blob or disk file
code: { value: qrcode description: barcode encoding standard enumeration: code39,39:code39x,39x:code128,128:ucc,ean,ucc/ean,ean/ucc:qrcode,qr,qrc datatype: int}
format: { value: png description: image format enumeration: gif:png,png24:png8 datatype: string}
mode: { value: property description: encode either property data or directly specified data value enumeration: property:value datatype: int}
value: { value: E_IDENT datatype: string}
filename: { value: {} datatype: string constraints: writeable}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
width: { value: -1 minvalue: -1 maxvalue: 512 datatype: int}
height: { value: 15 minvalue: 8 maxvalue: 50 datatype: int}
checksum: { value: 1 datatype: boolean}
bgcolor: { value: white datatype: color}
fgcolor: { value: black datatype: color}
showtext: { value: default description: Whether to also print ASCII text on the label enumeration: no:default:yes datatype: int}
font: { value: arialn datatype: string}
fontsize: { value: 8 minvalue: 7 maxvalue: 24 datatype: int}
antialias: { value: 1 datatype: boolean}
widebarfactor: { value: 3 description: Multiplier for 'wide' bars for codes which support that minvalue: 2 maxvalue: 5 datatype: int}
linewidth: { value: 1 description: Minimum line width minvalue: 1 maxvalue: 3 datatype: int}
downloadfilename: { value: {} description: If http header is generated, default download filename at client side datatype: string}
eclevel: { value: Q description: error correction level for qr encoding enumeration: L:M:Q:H datatype: int}
Compiled C module never mod_e_barcode.so
E_BARCODE_ID string Barcode tracking ID
never
E_BEILSTEIN_NUMBER int Beilstein registry number for structure ensemble
Tcl script atomchange bondchange stereochange merge
E_BENZENOID_INDEX double The count of benzene ESSSR rings divided by the total number of aromatic ESSSR rings. Zero in case there are no aromatic rings. Roughley and Jordan, J. Med. Chem. 2011, 54, 3451-3479
Compiled C module R_TYPE R_AROMATIC R_HETEROATOM_COUNT atomchange bondchange atom bond mod_e_benzenoid_index.so
E_BINDINGDB_URL url Structure display URL for BindingDB database (www.bindingdb.org)
Tcl script atomchange bondchange atom bond e_bindingdb_url.xpd
E_BINDING_AFFINITY qualifiedfloat General binding affinity descriptor
atomchange bondchange stereochange atom bond
E_BIOCYC_ID string Database identifier in the BioCyc database (biocyc.org)
Tcl script E_CID atomchange bondchange atom bond e_biocyc_id.xpd
E_BIOCYC_URL url Display URL for a compound in the BioCyc database (biocyc.org)
Tcl script E_BIOCYC_ID atomchange bondchange atom bond e_biocyc_url.xpd
E_BOND_ORDER_COUNT intvector Count of bond orders (index 5==aromatic, other bond orders are index to count vector, bond order 0 for non-standard bonds)
special int
single int
double int
triple int
quadruple int
aromatic int
excludeh: { value: 0 datatype: boolean}
Compiled C module B_TYPE B_ORDER A_TYPE A_ELEMENT atomchange bondchange mod_e_bond_order_count.so
E_BP floatpair Boiling point in Kelvin, with optional temperature range
value float
range float
pressure: { value: 760 datatype: double}
pressureunit: { value: Torr datatype: string}
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE atomchange bondchange
E_BRACKET_ANNOTATION compound Bracket as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION.
{} {} {} ROUND:SQUARE:BRACES:CHEVRONS SINGLE:DOUBLE
coords floatvector
linecolor color
linewidth float
type int
orientation int
A_XY never
E_BRENDA_ID int Ligand ID in the BRENDA database (www.brenda-enzymes.org)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_brenda_id.xpd
E_BRENDA_URL url Ligand display URL in the BRENDA database (www.brenda-enzymes.org)
Tcl script E_BRENDA_ID atomchange bondchange stereochange atom bond e_brenda_url.xpd
E_BRENK_ALERTS stringvector Structural alerts as per Brenk et al. (see literatrure reference) Brenk, R. et al., ChemMedChem 3, 435 (2008)
Tcl script A_FORMAL_CHARGE A_ELEMENT B_ORDER B_ARORING_COUNT A_ARORING_COUNT atomchange bondchange atom bond e_brenk_alerts.xpd
E_BRICS_FRAGMENTS structure Fragmentation of the structure according to the Raray BRICS rules. ChemMedChem 2008, 3, 1503
shredderpatternfile: { value: brics_shred.smarts datatype: diskfile constraints: readable}
excludepatternfile: { value: brics_exclude.smarts datatype: diskfile constraints: readable}
trace: { value: 0 datatype: boolean}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER B_FRAGMENT_CARBON_COUNT B_FRAGMENT_CARBON_CHAIN_LENGTH atomchange bondchange atom bond e_brics_fragments.xpd
E_BRUNS_WATSON_DEMERIT compound An implementaton of the Bruns/Watson structural MedChem filters as published in J. Med. Chem. 2012, 55, 9763-9772. The return value is a score between 0 (nothing found) up to an integer >= 100. 100 is the threshold where a comoiund should be rejected, values inbetween are scaled demerits. By default the check stops after the threshold has been reached - it can happen that the sum of demerits at that time has reached exactly 100 or a higher value. It is possible to force the use of the complete rule set by a parameter to tally up the complete set of disagreeable features. The rule set is editable and can be user-expanded. The query files are located at $DATADIR/propdata/e_bruns_watson_demerit. J. Med. Chem. 2012, 55, 9763-9772
demerit int
features dictionary
useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold has been reached, the evaluation stops. datatype: boolean}
reportallrules: { value: 0 description: If set, report on the match scores of all applied rules, not just the ones which change the demerit score datatype: boolean}
threshold: { value: 100 description: The threshold after which to stop further computation datatype: int}
Compiled C module E_BRUNS_WATSON_INITIAL_DEMERIT atomchange bondchange atom bond mod_e_bruns_watson_demerit.so
E_BRUNS_WATSON_INITIAL_DEMERIT compound Bruns/Watson non-substructural filters as published in J. Med. Chem. 2012, 55, 9763-9772. The return value is a value between 0 and 100, where 100 is outright rejection, 0 no problems found, and values inbetween for demerit points. J. Med. Chem. 2012, 55, 9763-9772
demerit int
features dictionary
heavy_atom_lower_cutoff: { value: 7 description: Reject compound if fewer heavy atoms found datatype: int}
heavy_atom_upper_cutoff: { value: 40 description: Reject compound if more heavy atoms found datatype: int}
heavy_atom_demerit_threshold: { value: 25 description: Demerit compound if more heavy atoms found datatype: string}
use_formal_charge: { value: 0 description: If set, use A_FORMAL_CHARGE for plus(minus rules. By default, use E_CHARGED_GROUP_COUNTS datatype: boolean}
useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold of 100 has been reached, the evaluation stops. datatype: boolean}
threshold: { value: 100 description: The threshold after which to stop further computation datatype: int}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT A_MOL_NUMBER A_HEAVY_SUBSTITUENT_COUNT A_RING_COUNT A_FORMAL_CHARGE A_ISOTOPE R_TYPE A_UNSATURATION A_CH2_CHAIN_LENGTH E_NSSSR atomchange bondchange atom bond mod_e_bruns_watson_initial_demerit.so
E_CAMEO_ID int Registration ID in Cameo Chemicals safety database (https://cameochemicals.noaa.gov).
Tcl script E_CAS atomchange bondchange stereochange atom bond e_cameo_id.xpd
E_CAMEO_URL url Data display URL in Cameo Chemicals safety database (https://cameochemicals.noaa.gov).
Tcl script E_CAMEO_ID atomchange bondchange stereochange atom bond e_cameo_url.xpd
E_CANONIC_TAUTOMER structure Canonic tautomer form of ensemble, selected from a rated collection of generated tautomers.
maxtautomers: { value: 500 description: Maximum number of tautomers to generate and rate datatype: int}
maxtransforms: { value: -1 description: Maximum number of tautomer transforms to apply datatype: int}
useneutralform: { value: 0 description: If set, compute on E_NEUTRALIZED_STRUCTURE instead of current structure datatype: boolean}
preservegroups: { value: 0 datatype: boolean}
Compiled C module A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange merge mol atom bond mod_e_canonic_tautomer.so
E_CARBON_COUNT int Number of carbon atoms in ensemble - the same as E_ELEMENT_COUNT(6)
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_carbon_count.so
E_CAS string Chemical Abstracts registry number for structure ensemble
useresolver: { value: 1 datatype: string}
usepubchem: { value: 1 datatype: string}
uselookchem: { value: 0 datatype: string}
Tcl script atomchange bondchange stereochange merge
E_CAS_URL url CommonChemistry URL linked via CAS number. By default the validity of the target is not verified - set parameter to perform this check.
verify: { value: 0 datatype: boolean}
Tcl script E_CAS atomchange bondchange stereochange merge e_cas_url.xpd
E_CATALOG compound Catalog data
producer stringvector
catnum stringvector
country stringvector
packsize intvector
purity shortvector
price intvector
atomchange bondchange stereochange merge
E_CATALOG_CAS stringvector CAS numbers of compound in catalog
never
E_CATALOG_NAMES stringvector Names of compound in a catalog
never
E_CCRIS_URL url Display URL in EPA CCRIS (Chemical Carcinogenesis Research Information System, https://toxnet.nlm.nih.gov/newtoxnet/ccris.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_ccris_url.xpd
E_CDXML_IMAGE diskfile
(switchable between blob diskfile xmlstring)
A standard structure rendering in the ChemDraw XML format. This is not a complete file which could be loaded into ChemDraw, but a building block to assemble CDXML files.
width: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int}
height: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int}
bonds: { value: 8 minvalue: 2 maxvalue: 32 datatype: int}
filename: { value: {} datatype: string constraints: writeable}
border: { value: 12 minvalue: 0 maxvalue: 256 datatype: int}
idstart: { value: -1 minvalue: -1 datatype: int}
frame: { value: 0 datatype: boolean}
xoffset: { value: 8 datatype: double}
yoffset: { value: 8 datatype: double}
framecolor: { value: black datatype: color}
markcolor: { value: blue datatype: color}
Compiled C module A_TYPE B_TYPE B_ORDER A_ELEMENT B_FLAGS A_FLAGS atomchange bondchange stereochange merge mol atom bond mod_e_cdxml_image.so
E_CDXML_STRING xmlstring Structure encoded in CDXML (CambridgeSoft)
Tcl script atomchange bondchange stereochange merge hadd atom bond e_cdxml_string.xpd
E_CENTER compound Box, geometric and mass-weighted ensemble center
box floatvector
geo floatvector
mass floatvector
(builtin) E_XYZEXTENT A_WEIGHT A_XYZ atomchange bondchange 3drelative 3dabsolute
E_CHANGEDATE date Change data time stamp for molecule
Tcl script never e_changedate.xpd
E_CHARGE short Sum of charges in ensemble
(builtin) A_FORMAL_CHARGE atomchange
E_CHARGED_ATOM_COUNT int Number of atoms which are formally charged and not direclty adjacent to an atom of opposite formal charge (such as in ionic nitro groups).
Compiled C module A_TYPE A_FORMAL_CHARGE B_TYPE atomchange bondchange atom bond mod_e_charged_atom_count.so
E_CHARGED_GROUP_COUNTS intpair Counts of groups charged positively or negatively under neutral conditions in protic solvents. This is a simple guestimate from A_HYDROGEN_BONDING, using acidic and basic groups as starting points and combining close centers (i.e. a P(=O)(OH)2 group with 2 acidic protons only gets a single positive charge count).
positive int
negative int
Compiled C module M_CHARGED_GROUP_COUNTS atomchange bondchange atom bond mod_e_charged_group_counts.so
E_CHEBI_ID string ChEBI ID (www.ebi.ac.uk/chebi)
Tcl script E_STDINCHI atomchange bondchange stereochange merge e_chebi_id.xpd
E_CHEBI_URL url ChEBI structure data display URL
urlencoding: { value: 1 datatype: boolean}
Tcl script E_CHEBI_ID atomchange bondchange stereochange merge e_chebi_url.xpd
E_CHECKDATE date Check data time stamp for molecule
Tcl script never e_checkdate.xpd
E_CHEMAGORA_URL url Display link for ChemAogra (chemagora.jrc.ec.europa.eu)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_chemagora_url.xpd
E_CHEMBANK_ID int Structure ID in the ChemBank database (http://chembank.broadinstitute.org)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_chembank_id.xpd
E_CHEMBANK_URL url Data display URL in the ChemBank database (http://chembank.broadinstitute.org)
Tcl script E_CHEMBANK_ID atomchange bondchange atom bond e_chembank_url.xpd
E_CHEMBASE_ID int Record ID in Chembase (en.chembase.cn)
matchatomstereo: { value: 1 datatype: boolean}
matchbondstereo: { value: 1 datatype: boolean}
matchisotopes: { value: 1 datatype: boolean}
matchcharges: { value: 1 datatype: boolean}
matchradicals: { value: 1 datatype: boolean}
Tcl script atomchange bondchange atom bond e_chembase_id.xpd
E_CHEMBASE_URL url Display URL in ChemBase database (en.chembase.cn)
Tcl script E_CHEMBASE_ID atomchange bondchange atom bond e_chembase_url.xpd
E_CHEMBL_ASSAY_IDS stringvector ChEMBL assay IDs which test the substance
Tcl script atomchange bondchange atom bond e_chembl_assay_ids.xpd
E_CHEMBL_ID string ChEMBL ID (https://www.ebi.ac.uk/chembl/)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange merge e_chembl_id.xpd
E_CHEMBL_MEDCHEM_FRIENDLY boolean Implementation of the simple CHEMBL MedChemFriendly filter, a simple substructure-based exclusion list.
Tcl script atomchange bondchange atom bond e_chembl_medchem_friendly.xpd
E_CHEMBL_URL url ChEMBL compound data display URL (https://www.ebi.ac.uk/chembl)
Tcl script E_CHEMBL_ID atomchange bondchange stereochange merge e_chembl_url.xpd
E_CHEMBUYERSGUIDE_IDS compoundvector Get company name and their catalog number by querying chembuyersguide.com via full-structure search.
name string
catalogno string
Tcl script atomchange bondchange atom bond e_chembuyersguide_ids.xpd
E_CHEMDB_ID string Structure ID in the NIH NIAID ChemDB database (https://chemdb.niaid.nih.gov)
Tcl script E_CAS atomchange bondchange atom bond e_chemdb_id.xpd
E_CHEMDB_URL url Data display URL for the NIH NIAID ChemDB database
Tcl script E_CHEMDB_ID atomchange bondchange stereochange atom bond e_chemdb_url.xpd
E_CHEMDIV_ID string ID of structure in ChemDiv (chemistryondemand.com) database
Tcl script E_SMILES atomchange bondchange atom bond e_chemdiv_id.xpd
E_CHEMDIV_URL url Data display URL for structure in catalog of chemdiv.com/chemistryondemand.com
atomchange bondchange stereochange atom bond
E_CHEMEO_ID string ID in the Chemeo properties database (www.chemeo.com)
Tcl script atomchange bondchange atom bond e_chemeo_id.xpd
E_CHEMEO_URL url Display URL for the Chemeo properties database (www.chemeo.com)
Tcl script atomchange bondchange atom bond e_chemeo_url.xpd
E_CHEMEXPER_URL url ChemExper data display URL (chemexper.com)
querytype: { value: fs enumeration: fs:ss datatype: int}
Tcl script E_CHEMEXPER_URL mol atom bond e_chemexper_url.xpd
E_CHEMICALBOOK_ID string Database ID for the chemicalbook.com site
Tcl script E_CAS atomchange bondchange stereochange atom bond e_chemicalbook_id.xpd
E_CHEMICALBOOK_URL url Data display URL for the chemicalbook.com site
Tcl script E_CAS atomchange bondchange stereochange atom bond e_chemicalbook_url.xpd
E_CHEMICALIZE_URL url URL to submit compound to chemicalize.org computational service by ChemAxon
Tcl script E_SMILES atomchange bondchange stereochange merge e_chemicalize_url.xpd
E_CHEMICAL_BEAUTY double Chemical beauty score (aka QED, quantitative estimate of drug likeness). Because we are using different logP and HA/HD algorithms, the results are not exactly identical to those from the publication, but close. Bickerton et al., Nature Chemistry, 4, 90 (2012)
weightingscheme: { value: max enumeration: max:mo:u datatype: int}
Tcl script E_BRENK_ALERTS E_WEIGHT E_XLOGP2 E_NHDONORS E_NHACCEPTORS E_NROTBONDS E_TPSA E_ARORING_COUNT atomchange bondchange stereochange atom bond e_chemical_beauty.xpd
E_CHEMIDPLUS_ID string ChemIDPlus structure id (from http://chem.sis.nlm.nih.gov)
Tcl script E_STDINCHIKEY mol atom bond e_chemidplus_id.xpd
E_CHEMIDPLUS_URL url ChemIDPlus URL
Tcl script E_CHEMIDPLUS_ID mol atom bond e_chemidplus_url.xpd
E_CHEMSPIDER_ID string chemspider.com structure record ID
Tcl script E_STDINCHI atomchange bondchange stereochange merge e_chemspider_id.xpd
E_CHEMSPIDER_URL url chemspider.com structure data display URL
Tcl script E_CHEMSPIDER_ID atomchange bondchange stereochange merge e_chemspider_url.xpd
E_CHEMSTABLE_SCORE compound Chemical stability score computed by http://www.rcdd.org.cn/chemstable/index.html J. Comput. Aided Mol. Des. 28, 2014, 941-950
isstable boolean
score double
instable_substructure substructure
Tcl script A_ELEMENT B_TYPE B_ORDER A_FORMAL_CHARGE atomchange bondchange atom bond e_chemstable_score.xpd
E_CHEMSYNTHESIS_ID int ID of structure in ChemSynthesis database (www.chemsynthesis.com)
Tcl script atomchange bondchange merge mol e_chemsynthesis_id.xpd
E_CHEMSYNTHESIS_URL url Data sccess URL of structure in ChemSynthesis database (www.chemsynthesis.com)
Tcl script E_CHEMSYNTHESIS_ID atomchange bondchange merge mol e_chemsynthesis_url.xpd
E_CHIRALITY byte Stereo status and potential of ensemble
none:meso:unspecified:chiral:contradictory
Compiled C module M_CHIRALITY atomchange bondchange stereochange mol atom bond mod_e_chirality.so
E_CHIRAL_POTENTIAL intpair Number of possible chiral atom and bond centers
Tcl script A_STEREOGENIC B_STEREOGENIC A_TYPE atomchange merge atom bond e_chiral_potential.xpd
E_CID int PubChem CID structure identifier
trace: { value: 0 datatype: boolean}
Tcl script E_STDINCHIKEY atomchange bondchange stereochange merge hadd e_cid.xpd
E_CIF_BLOCK table _loop dataset of a CIF file
never
E_CLASSIFIED_BOND_COUNT intvector Counts of used-defined classes of bonds
bondtypes: { value: C-C C=C C*C C-X C=X C*X X-X X=X X*X C-H X-H description: The bond types to look for, in element/bondordersymbol/element notation datatype: string constraints: list}
Compiled C module A_ELEMENT A_TYPE B_TYPE B_ORDER atomchange bondchange merge mod_e_classfied_bond_count.so
E_CLASSIFIED_SURFACE_AREA doublevector Estimated surface area classified by atom type P. Labute, Methods in Molecular Biology, 275, 261ff
total_double double
carbon double
hydrogen double
hetero double
aromatic double
aliphatic double
ring double
chain double
Compiled C module A_SURFACE_AREA A_ISAROMATIC A_ELEMENT A_TYPE A_RING_COUNT atomchange bondchange 3dabsolute hadd atom bond mod_e_classified_surface_area.so
E_CLEANNAME string Name cleaned from purity info and miscellaneous remarks
keeppurity: { value: 1 datatype: boolean}
keepstereo: { value: 1 datatype: boolean}
keepisotope: { value: 1 datatype: boolean}
keepsalt: { value: 1 datatype: boolean}
trace: { value: 0 datatype: boolean}
watch: { value: {} description: String to watch out for, output notification if found datatype: string}
Tcl script E_NAME never e_cleanname.xpd
E_CML_STRING string CML structure record as string
pedantic: { value: 1 datatype: boolean}
Tcl script atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond e_cml_string.xpd
E_CMSSPECTRUM compound Continuous mass spectrum. Filled by reading JCAMP spectrum file of CMS type.
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum floatvector
atomchange bondchange
E_COD_ID int ID of structure in the Crystallography Open Database (www.crystallography.net)
Tcl script atomchange bondchange atom bond e_cod_id.xpd
E_COD_URL url URL to the Crystallography Open Database (www.crystallography.net)
Tcl script E_COD_ID atomchange bondchange atom bond e_cod_url.xpd
E_COLOR color Background color to use in plots
never
E_COMMENT stringvector Free form comment for ensemble
never
E_COMMONCHEMISTRY_URL url Display URL in the ACS CommonChemistry database (commonchemistryy.org)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_commonchemistry_url.xpd
E_COMPLEXITY float Ensemble complexity according to modified Bertz/Hendrickson algorithm W. D. Ihlenfeldt, Ph.D. Thesis, TU Munich 1991
Compiled C module M_COMPLEXITY M_HASH atomchange bondchange merge mol mod_e_complexity.so
E_COMPOSITION string Elemental composition
useimplicith: { value: 1 datatype: boolean}
Tcl script A_WEIGHT A_SYMBOL A_HYDROGENS_NEEDED atomchange e_composition.xpd
E_CONFORMER_ENERGY floatvector Estimation of energy of conformer
Compiled C module A_CONFORMER A_TYPE A_TOPO_DISTANCE A_VDW_INTERACTION atomchange bondchange stereochange merge 3drelative hadd mod_e_conformer_energy.so
E_CONNECTIVITY boolean Pseudo property for connectivity reconstruction
(builtin) never
E_CONNECTIVITY_MATRIX floatmatrix Connectivity matrix, configurable in several variants
usefe: { value: 0 description: If set, the diagonal contains the atom free electron count datatype: boolean}
usebo: { value: 0 description: If set, atom pair matrix elements contain the VB bond order, not just 1 for an existing bond datatype: boolean}
usearo: { value: 0 description: If set, and bond orders are use, the bond order for aromatic bonds is 1.5 (Kekule VB otherwise) datatype: boolean}
Compiled C module B_ORDER B_TYPE B_ISAROMATIC A_FREE_ELECTRONS atomchange bondchange atom bond mod_e_connectivity_matrix.so
E_CONSENSUSPATHDB_URL url Display URL in MPG ConsensusPathDB (http://consensuspathdb.org/)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_consensuspathdb_url.xpd
E_CONVENTION string Free-form description of structure encoding convention
never
E_COSMO_DATA dictionary COSMO runtime information
atomchange bondchange stereochange merge 3drelative
E_CREST_URL url Display URL in the CREST (Chemical attributes, Regulatory approaches and Experimental STudies, http://www.rmeonline.net/CREST/r1/start.php) database
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_crest_url.xpd
E_CTDBASE_ID string CTD database ID (ctdbase.org)
Tcl script E_CAS atomchange bondchange atom bond e_ctdbase_id.xpd
E_CTDBASE_URL url CTD database (ctdbase.org) data display URL
Tcl script E_CTDBASE_ID atomchange bondchange atom bond e_ctdbase_url.xpd
E_DATABASE compound Info about the database the molecule was read from
dbtype string
database string
host string
port int
table string
id int
time date
atomchange bondchange stereochange merge
E_DAYLIGHT_ARORING_COUNT short Count of aromatic rings in ESSSR, always using Daylight aromaticity definition
Compiled C module R_DAYLIGHT_AROMATIC R_TYPE atomchange bondchange atom bond ring mod_e_daylight_aroring_count.so
E_DBREFERENCE stringvector Generic free-form database references associated with ensemble
never
E_DECORATED_STRUCTURES dataset Exhaustive set of structures generated by decorating a core with any combination of user-supplied substituents.
substituents: { value: {} description: Substituent fragments in line notation. The first atom oif these is their attachment point datatype: string constraints: list}
coreatomfilters: { value: hydrogen chbond description: These atoms on the core will be replaced by combinations of fragments datatype: string constraints: filterlist}
duphash: { value: E_HASHY description: Hash code used to remove duplicates datatype: string constraints: property}
Tcl script atomchange bondchange atom bond e_decorated_structures.xpd
E_DENSITY float Density of compound at room temperature in kg/L
Tcl script A_ELEMENT A_ISOTOPE atomchange bondchange e_density.xpd
E_DICTIONARY_OF_NATURAL_PRODUCTS_ID string Entry ID in dictionary of natural products (dnp.chemnetbase.com)
Tcl script E_MRV_STRING atomchange bondchange stereochange atom bond e_dictionary_of_natural_products_id.xpd
E_DICTIONARY_OF_NATURAL_PRODUCTS_URL url Display URL in dictionary of natrual products (dnp.chemnetbase.com)
Tcl script E_DICTIONARY_OF_NATURAL_PRODUCTS_ID atomchange bondchange atom bond e_dictionary_of_natural_products_url.xpd
E_DIPOLEMOMENT compound Dipole Moment. The computation links indirectly vie E_HEAT_OF_FORMATION to a VAMP run.
pointcharge floatvector
hybrid floatvector
sum floatvector
A_XYZ atomchange bondchange stereochange 3drelative
E_DOTSURFACE xyzvector Coordinates of points on dot-surface
distance: { value: 0 description: dot distance to VDW surface (nm) datatype: double}
density: { value: 30 description: average number of dots per atom datatype: int}
A_XYZ A_ELEMENT atomchange bondchange stereochange 3drelative 3dabsolute
E_DRUGBANK_ID string Drugbank ID, looked up over the Internet
Tcl script E_SMILES atomchange bondchange stereochange merge e_drugbank_id.xpd
E_DRUGBANK_URL url Drugbank data display URL
Tcl script E_DRUGBANK_ID atomchange bondchange stereochange merge e_drugbank_url.xpd
E_DRUGINFO_URL url Display URL for the NIH DrugInfo prtal (druginfo.nlm.nih.gov)
Tcl script E_UNII atomchange bondchange atom bond e_druginfo_url.xpd
E_EC50 compound EC50 aids screen data
concentration float
concunit shortstring
flag shortstring
ecconc float
nexperiments short
atomchange bondchange merge
E_ECHA_URL url Display number for a structure in the EU ECHA (European Chemicals Agency) registration system.
E_CAS atomchange bondchange stereochange atom bond
E_ECHEMPORTAL_URL url Link into the OECD echemportal.org site
Tcl script E_CAS atomchange bondchange atom bond e_echemportal_url.xpd
E_EC_FINGERPRINT bitvector
(switchable between bitvector bytevector shortvector intvector)
An ECFP-style fingerprint implementation. This property merges atomic enviroment hash codes from property A_EC_HASH for different numbers of spheres into a fingerprint or count vector. The number of enviroment spheres used is controlled by the settings of A_EC_HASH - this is a vector, and each element is the hashed atom enviroment including an additional sphere. If changed from default data type bitvector to bytevector, shortvector or intvector, the number of found atom environments in A_EC_HASH is counted.
diameter: { value: -1 description: Maximum neighbor distance to consider. Must be <= length of A_EC_HASH vector, use -1 to use vector length minvalue: -1 maxvalue: 15 datatype: int}
length: { value: 1024 description: Folded bitvector length minvalue: 16 maxvalue: 32768 datatype: int}
counts: { value: 0 description: Whether to use counts enumeration: no:linear:exponential datatype: int}
debug: { value: 0 description: If set, print debug info datatype: boolean}
Compiled C module A_EC_HASH atomchange bondchange atom bond mod_e_ec_fingerprint.so
E_EC_NUMBER string The European Community registration number for a compound with the European Chemicals Agency (ECHA, echa.europa.eu). This replaces the EINECS system (property E_EINECS_ID). Note that this identifier is very different from the enzyme commission EC number for proteins.
usepubchem: { value: 0 datatype: boolean}
useecha: { value: 1 datatype: boolean}
Tcl script E_CID E_CAS atomchange bondchange stereochange atom bond e_ec_number.xpd
E_EEROS_URL url Data display URL for compound in Wiley Electronic Encyclopedia of Reagents for Organic Synthesis (https://onlinelibrary.wiley.com/doi/book/10.1002/047084289X)
Tcl script E_STDINCHIKEY atomchange bondchange atom bond e_eeros_url.xpd
E_EFFECTIVE_ROTOR_COUNT double Effective rotor count, computed from rotatable bonds (B_ROTATABILITY) and fractional values for ring flexibility.
usecanonictautomer: { value: 0 description: If set, compute on standard tautomer instead of current structure datatype: boolean}
Tcl script B_ROTATABILITY atomchange bondchange e_effective_rotor_count.xpd
E_EGAN_BIOAVAILABILITY_FLAG boolean Veber bioavailability flag (E_XLOGP2<=5.88 && E_TPSA<=131.6) Journal of Medicinal Chemistry, Vol. 43, pp. 3867-3877, 2000
Compiled C module E_XLOGP2 E_TPSA atomchange bondchange atom bond mod_e_egan_bioavailability_flag.so
E_EIGENVALUES floatvector MO Eigenvalues
A_XYZ atomchange bondchange
E_EINECS_ID string EINECS ID. Note that this is now an outdated identifier with the launch of the EU REACH system. It should be replaced by the ECHA (https://echa.europa.eu) European Commission EC number (property E_EC_NUMBER, this is not the same as the Enzyme Commission protein EC number).
Tcl script E_SDF_STRING atomchange bondchange stereochange merge e_einecs_id.xpd
E_ELECTRONIC_ENERGY float Measured or computed electronic energy, as returned by, for example, a QM program. This property currently is used for reading VAMP data.
atomchange bondchange
E_ELEMENT_COUNT shortvector Count of element types of atoms of ensemble
? short
h short
he short
li short
be short
b short
c short
n short
o short
f short
ne short
na short
mg short
al short
si short
p short
s short
cl short
ar short
k short
ca short
sc short
ti short
v short
cr short
mn short
fe short
co short
ni short
cu short
zn short
ga short
ge short
as short
se short
br short
kr short
rb short
sr short
y short
zr short
nb short
mo short
tc short
ru short
rh short
pd short
ag short
cd short
in short
sn short
sb short
te short
i short
xe short
cs short
ba short
la short
ce short
pr short
nd short
pm short
sm short
eu short
gd short
tb short
dy short
ho short
er short
tm short
yb short
lu short
hf short
ta short
w short
re short
os short
ir short
pt short
au short
hg short
tl short
pb short
bi short
po short
at short
rn short
fr short
ra short
ac short
th short
pa short
u short
np short
pu short
am short
cm short
bk short
cf short
es short
fm short
md short
no short
lr short
rf short
db short
sg short
bh short
hs short
mt short
ds short
(builtin) A_ELEMENT A_TYPE atomchange merge hadd
E_ELLIPSE_ANNOTATION compound Ellipse as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION.
{} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold
coords floatvector
linecolor color
linewidth float
bgcolor color
style bitset
A_XY never
E_EMBL_SIDER_URL url Data display link in the EMBL Sider database (http://sideeffects.embl.de)
Tcl script E_CID atomchange bondchange stereochange atom bond e_embl_sider_url.xpd
E_EMBL_STITCH_URL url Data display URL in the STITCH database (http://stitch.embl.de)
Tcl script E_CID atomchange bondchange stereochange atom bond e_embl_stitch_url.xpd
E_EMF_IMAGE diskfile
(switchable between blob diskfile url)
Metafile WIN32 structure drawing
width: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int}
height: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue" datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: string}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: smiles datatype: string}
metadata: { value: 1 datatype: boolean constraints: writeable}
filename: { value: {} datatype: diskfile}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.4 datatype: double}
colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
symbolfontsize: { value: -1 datatype: double}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
usehatch: { value: 0 datatype: boolean}
format: { value: wmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int}
frame: { value: 1 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 2.0 datatype: double}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
circlecolor: { value: {} description: A property name or a color name datatype: string}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 6 datatype: int}
wiggleamplitude: { value: 1.5 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
crop: { value: -1 datatype: int}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Arial datatype: string}
usesubscripts: { value: 1 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR A_ANNOTATION B_FLAGS A_FLAGS atomchange bondchange stereochange merge hadd mol mod_e_emf_image.so
E_EMOLECULES_ID string EMolecules Web database ID (www.emolecules.com)
baseurl: { value: https://ordersc.emolecules.com datatype: url}
catalog: { value: all enumeration: SC:BB:all datatype: string}
Tcl script E_SMILES atomchange bondchange stereochange merge e_emolecules_id.xpd
E_EMOLECULES_URL url EMolecules (www.emolecules.com) Web database display URL
Tcl script E_EMOLECULES_ID atomchange bondchange stereochange merge e_emolecules_url.xpd
E_ENANTIOMER structure Enantiomer of ensemble (i.e. all tetrahedral stereochemistry is reversed)
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange merge e_enantiomer.xpd
E_ENERGY float Ensemble energy
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange stereochange merge 3drelative
E_ENS_COUNT int Pseudo-property: Number of ens in ensemble - always 1, needed for generality in processing bind sets in "scan" queries
Compiled C module atomchange bondchange atom bond mod_e_ens_count.so
E_EPA_ACTOR_URL url EPA Actor data access
Tcl script E_CAS atomchange bondchange stereochange e_epa_actor_url.xpd
E_EPA_COMPTOX_URL url Data display URL for the new EPA CompTox portal
Tcl script E_STDINCHIKEY atomchange bondchange atom bond e_epa_comptox_url.xpd
E_EPA_HPVIS_URL url Data display URL in US EPA High Production Volume Information System (HPVIS), https://www.epa.gov/hpvis
Tcl script E_CAS atomchange bondchange atom bond e_epa_hpvis_url.xpd
E_EPRSPECTRUM compound EPR spectrum, usually read from JCAMP file
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum floatvector
atomchange bondchange stereochange
E_EPS_IMAGE diskfile
(switchable between blob diskfile)
A 2D-plot of the structure as EPS image file
width: { value: 180 datatype: int}
height: { value: 180 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: string}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: string}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: string}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: string}
comment: { value: E_NAME datatype: string}
structure: { value: none enumeration: none:smiles:stdinchi:cactvs:molfile datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3,tetrahedral:sp2,planar:all datatype: string}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.3 datatype: double}
colormode: { value: mono datatype: string}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
symbolfontsize: { value: -1 datatype: double}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: string}
frame: { value: 0 datatype: boolean}
linespacing: { value: 2.5 datatype: double}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filterlist}
circlecolor: { value: {} description: A property name or a color name datatype: string}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filterlist}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 3.0 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Helvetica datatype: string}
contractgroups: { value: 0 datatype: boolean}
framecolor: { value: black datatype: color}
downloadfilename: { value: {} datatype: string constraints: writeable}
labelproperty: { value: {} datatype: string constraints: property}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
usegrouplabels: { value: 0 datatype: boolean}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION atomchange bondchange stereochange merge hadd mod_e_eps_image.so
E_EXACT_MASS floatpair Exact mass of most abundant compound isotope combination, assuming natural abundance
weight double
abundance double
useimplicith: { value: 1 description: Whether to include implicit hydrogens datatype: boolean}
Compiled C module atomchange merge atom mod_e_exact_mass.so
E_EXPERIMENT string Experimental setup used to obtain structure data
never
E_EXP_CONNECTIVITY_MATRIX floatmatrix Exponent of the connectivity matrix, as per the work of Alexey Lagunin Molecular Informatics 30, 2011, 241-250
multiplier: { value: -0.5 description: multiplier for all matrix elements applied before exponent computation datatype: double}
Compiled C module E_CONNECTIVITY_MATRIX atomchange bondchange atom bond mod_e_exp_connectivity_matrix.so
E_FDA_OBJECT_CODE compound FDA data code triple from SPL file, identiying for example the type of structure extracted
code string
codesystem string
displayname string
atomchange bondchange atom bond
E_FDA_SPL_URL url
Tcl script E_UNII atomchange bondchange atom bond e_fda_spl_url.xpd
E_FDA_SRS_URL url Link into FDA SRS (structure registration system) database
Tcl script E_UNII atomchange bondchange atom bond e_fda_srs_url.xpd
E_FEATURES bytevector Count of structural features defined as parameters by SMARTS expressions
carboxylic_acid byte
acid_halogenide byte
aldehyde byte
ketone byte
amine byte
primary_amine byte
secondary_amine byte
tertiary_amine byte
quarternary_amine byte
hydrazine byte
urea byte
12diamine byte
pyridine byte
thp byte
piperidine byte
piperazine byte
morpholine byte
thiomorpholine byte
amide byte
ester byte
alpha_aminoacid byte
betaaminoacid byte
alpha_ketoacid byte
betaketoacid byte
alcohol byte
phenol byte
thiol byte
thiophenol byte
ether byte
thioether byte
epoxide byte
acetal byte
enol byte
lactone byte
oxime byte
nitro byte
isocyanate byte
thioisocyanate byte
anhydride byte
cyanide byte
sulfonic_acid byte
sulfonic_acid_halogenide byte
sulfonamide byte
phosphoric_acid byte
boronic_ester byte
silyl_hydride byte
siloxyl byte
aliphatic_halogen byte
aromatic_halogen byte
trifluoromethyl byte
11_diphenyl_methyl byte
alpha_haloketone byte
chalcone byte
aromatic_nitrogen byte
aromatic_oxygen byte
aromatic_sulphur byte
cc_doublebond byte
cc_triplebond byte
phenyl byte
patterns: { value: {{carboxylic acid} C(=O)O[#1]} {{acid halogenide} C(=O)[Cl,Br,I,F]} {aldehyde CC(=O)[#1]} {ketone CC(=O)C} {amine N([Cx1,cx1,#1])([Cx1,cx1,#1])[Cx1,cx1,#1]} {{primary amine} [Cx1,cx1][NH2;v3]} {{secondary amine} [NH;v3]([Cx1,cx1])([Cx1,cx1])} {{tertiary amine} [N;v3]([Cx1,cx1])([Cx1,cx1])[Cx1,cx1]} {{quarternary amine} [N;v4](C)(C)(C)C} {hydrazine [N;R0][N;R0]} {urea [N;x0]C(=O)[N;x0]} {{1.2-diamine} [NH2]CC[NH2]} {pyridine n1ccccc1} {tetrahydropyrrole N1CCCC1} {piperidine [N;A]1CCCCC1} {piperazine N1CCNCC1} {morpholine N1CCOCC1} {thiomorpholine S1CCOCC1} {amide CC(=O)N([C,c,#1])[C,c,#1]} {ester CC(=O)[O;R0]C} {{alpha-aminoacid} NCC(=O)O} {{beta-aminoacid} NCCC(=O)O} {{alpha-ketoacid} O=CC(=O)O} {{beta-ketoacid} O=CCC(=O)O} {alcohol [C;X4;A]O[#1]} {phenol [c]O[#1]} {thiol [C;X4;A]S[#1]} {thiophenol [c]S[#1]} {ether [Cx1,cx1][O;!r3][Cx1,cx1]} {thioether [Cx1,cx1][S;!r3][Cx1,cx1]} {epoxide C1OC1} {acetal [Cx1,cx1]O[Cx2]O[Cx1,cx1]} {enol C=CO} {lactone [C;R](=O)[O;R]} {oxime C=NO} {nitro N(=O)O} {isocyanate N=C=O} {thioisocyanate N=C=S} {anhydride {C(=O)OC(=O)C}} {cyanide C#N} {{sulfonic acid} S(=O)(=O)O[#1]} {{sulfonic acid halogenide} S(=O)(=O)[F,Cl,Br,I]} {sulfonamide S(=O)(=O)N} {{phosphoric acid derivative} P(=[O,S,N])[N,O,S,F,Cl,Br,I]} {{boronic ester} C[B](O[C,#1])O[C,#1]} {{silyl hydride} [SiH]} {{siloxyl} [Si]O} {{aliphatic halogen} [C;A][F,Cl,Br,I]} {{aromatic halogen} [c][F,Cl,Br,I]} {trifluoromethyl C(F)(F)F} {{1.1-diphenyl-methyl} c1ccccc1C(c1ccccc1)[!C;!c;!#1]} {{alpha-haloketone} CC(=O)C[F,Cl,Br,I]} {chalcone CC(=O)[C;A]=[C;A]} {{aromatic nitrogen} [n]} {{aromatic oxygen} [o]} {{aromatic sulphur} [s]} {{C-C double bond} [C;A]=[C;A]} {{C-C triple bond} C#C} {{phenyl ring} c1ccccc1} datatype: string}
Tcl script A_ELEMENT B_ORDER B_TYPE atomchange bondchange merge hadd atom bond ring e_features.xpd
E_FELDMAN_FINGERPRINT bitvector Feldman and Hodes, JCICS 1975 15(3) 147-152
Python script atomchange bondchange atom bond e_feldman_fingerprint.xpd
E_FG_COUNT shortvector Count of functional groups in ensemble, summed up from molecular FG counts in M_FG_COUNT
Compiled C module M_FG_COUNT atomchange bondchange mod_e_fg_count.so
E_FICTS_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICTS datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICTS_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHISY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficts_id.xpd
E_FICTS_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICTU_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICTu datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICTU_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHIY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_fictu_id.xpd
E_FICTU_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICUS_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICuS datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICUS_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHISY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficus_id.xpd
E_FICUS_STRUCTURE structure Standardized structure for FICUS computations. Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICUU_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICuu datatype: string}
scope: { value: public datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICUU_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHIY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficuu_id.xpd
E_FICUU_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FICXX_ID string Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
primarytag: { value: FICxx datatype: string}
scope: { value: private datatype: string}
addsecondarytag: { value: 1 datatype: string}
addtag: { value: 1 datatype: string}
tagseparator: { value: - datatype: string}
debug: { value: 0 datatype: string}
forcemagic: { value: 0 datatype: string}
test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string}
addprimarytag: { value: 1 datatype: string}
structurepropname: { value: E_FICXX_STRUCTURE datatype: string}
norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string}
secondarytag: { value: 01-xx datatype: string}
csbasehash: { value: E_HASHIY datatype: string}
post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string}
Tcl script A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond e_ficxx_id.xpd
E_FICXX_STRUCTURE structure Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO atomchange bondchange stereochange atom bond
E_FILE compound Info about the file the molecule was read from
filename string
startrecord int
endrecord int
line int
format string
offset int64
length int
atomchange bondchange merge
E_FLEXNOVO_FILTER boolean Test whether structure passes the FlexNovo smarts pattern filter (which removes reactive or non-druglike componds)
patternfile: { value: flexnovo_exclude.sma datatype: diskfile constraints: readable}
trace: { value: 0 datatype: boolean}
Tcl script atomchange bondchange atom bond e_flexnovo_filter.xpd
E_FLG_FICTS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_FICTU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_FICUS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_FICUU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUTS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUTU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUUS_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FLG_UUUUU_UNRELIABLE boolean Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_FORMAT string Original format in data file (I/O module name)
never
E_FORMULA string Molecular formula of ensemble
usecharges: { value: 0 datatype: string}
format: { value: ascii datatype: string}
useimplicith: { value: 1 datatype: string}
usequeryatoms: { value: 0 datatype: string}
(builtin) A_ISOTOPE atomchange merge
E_FRAGMENT_COMPOSITION intvector Get composition of structure using a user-defined hierarchical fragment database with SMILES/SMARTS fragment definition. Larger fragments, and fragments with more specialized attributes have precedence. Multiple solutions may be found and are attached as E_FRAGMENT_COMPOSITION/n. The result is an int vector with the counts for each fragment in their definition file order. The default fragment set is for the UNIFAC method. Various other fragment files for Joback, Lyderson, Sedlbaur methods are also supplied in the data directory.
fragfile: { value: unifac.sma datatype: diskfile constraints: readable}
explicith: { value: 0 datatype: boolean}
debug: { value: 0 datatype: boolean}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange merge hadd e_fragment_composition.xpd
E_FRAGMENT_COUNT dictionary Counts of all (filtered) fragments the structure, The result is a dictionary with SMARTS keys, and occurence count values.
minsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int}
maxsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int}
hydrogen: { value: 0 datatype: boolean}
mode: { value: absolute description: In relative mode, scale to total count 1 enumeration: absolute:relative datatype: int}
keeparo: { value: 0 description: If set, lock A_ISAROMATIC datatype: boolean}
aroquery: { value: 0 description: If set, rewrite SMARTS to match only aromatic fragments where applicable datatype: boolean}
Tcl script A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange merge atom bond e_fragment_count.xpd
E_FRAGMENT_TREE_CUTS datatree Topological fragment hierarchy tree - cut bond classification
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
E_FRAGMENT_TREE_HASH datatree Topological fragment hierarchy tree - hashcodes
maxcuts: { value: 3 datatype: int}
minsize: { value: 2 datatype: int}
cutphenyl: { value: 0 datatype: boolean}
queryhash: { value: 0 datatype: boolean}
dupcheck: { value: hierarchical enumeration: hierarchical:global datatype: string}
Compiled C module A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange mod_e_fragment_tree_hash.so
E_FRAGMENT_TREE_LABELS datatree Topological fragment hierarchy tree - atom labels of fragments
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
E_FRAGMENT_TREE_SMARTS datatree Topological fragment hierarchy tree - SMARTS of fragments
A_TYPE A_ELEMENT B_TYPE B_ORDER atomchange bondchange
E_FRAGMENT_TREE_TABLE table Summary of fragmentation routes
Tcl script E_FRAGMENT_TREE_HASH E_FRAGMENT_TREE_CUTS E_FRAGMENT_TREE_LABELS atomchange bondchange e_fragment_tree_table.xpd
E_FREQUENCY string Generic computed frequencies. Used in Gaussian Archive I/O module
atomchange bondchange merge 3drelative hadd
E_FSP3 double Carbon flatness score - the ratio of SP3 hybridized carbon atoms to total carbon atom count Lovering, F. et al., J.Med.Chem. 2009, 52, 6752-6756
Compiled C module A_TYPE A_ELEMENT A_HYBRIDIZATION atomchange bondchange atom bond mod_e_fsp3.so
E_GC compound Measured gas-chromatograph spectrum. Used for example in JCAMP I/O module
experimental boolean
origin string
author string
date int
spectrometer string
parameters string
reference string
purity float
source string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
spectrum floatvector
atomchange bondchange
E_GDL_ID int Substance ID in German hazardous chemicals database (http://www.gefahrstoff-info.de)
Tcl script E_CAS atomchange bondchange atom bond e_gdl_id.xpd
E_GDL_URL url Data display URL in German hazardous chemicals database (http://www.gefahrstoff-info.de)
Tcl script E_GDL_ID atomchange bondchange atom bond e_gdl_url.xpd
E_GENETOX_URL url Display URL in EPA GENE-TOX (Genetic Toxicology Data Bank, https://toxnet.nlm.nih.gov/newtoxnet/genetox.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_genetox_url.xpd
E_GENOTOXIC_ALERTS shortvector Check for problematic potentially genotoxic groups CE&N Sep 27, 2010 p16ff
patternfile: { value: genotoxic.sma datatype: diskfile constraints: readable}
Tcl script atomchange bondchange merge hadd mol atom bond ring e_genotoxic_alerts.xpd
E_GEOOPT_METHOD string Geometry optimization method description string. Used for example in the Gaussian Input, Gaussian Archive and Sharc file forms.
atomchange bondchange 3drelative 3dabsolute
E_GI50 compound GI50 tumor screen data
concunit shortstring
lcconc float
panel shortstring
cell string
panelnumber short
cellnumber short
nlog_gi50 float
ntest_this short
ntest_max short
atomchange bondchange merge
E_GIF diskfile
(switchable between string blob diskfile url)
A 2D-plot of the structure as a GIF or PNG file
width: { value: 180 datatype: int}
height: { value: 180 datatype: int}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
interlace: { value: 1 datatype: boolean}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
secondarycolor: { value: #00D000 datatype: color}
highlightbonds: { value: {} datatype: intvector}
highlightatoms: { value: {} datatype: intvector}
httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int}
crop: { value: -1 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
format: { value: gif enumeration: gif:png:png8:bmp datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string}
footerproperty: { value: {} datatype: string}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: boolean}
font: { value: arialn datatype: string}
symbolfontsize: { value: -1 datatype: int}
annotationfontsize: { value: -1 datatype: int}
antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
showisotope: { value: 1 datatype: boolean}
isotopemapping: { value: none datatype: string}
showstereoh: { value: 1 datatype: boolean}
suppressedmols: { value: {} datatype: intvector}
linewidth: { value: 1.4 datatype: double}
showempty: { value: 0 datatype: boolean}
voronoicolorproperty: { value: {} datatype: string constraints: property}
voronoifilter: { value: {} datatype: string constraints: filtername}
showmapping: { value: 0 datatype: boolean}
showstereogroups: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
frame: { value: 0 datatype: boolean}
framecolor: { value: black datatype: diskfile}
linespacing: { value: 2.0 datatype: double}
headerfontsize: { value: -1 datatype: int}
footerfontsize: { value: -1 datatype: int}
circlecolor: { value: {} datatype: color}
circlefilter: { value: {} datatype: string}
circleatoms: { value: {} datatype: intvector}
atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int}
wigglecount: { value: 6 datatype: int}
wiggleamplitude: { value: 2.0 datatype: double}
fixiepngsize: { value: 1 datatype: string}
rawcoordinates: { value: 0 datatype: boolean}
checkintersection: { value: 0 datatype: boolean}
usegrouplabels: { value: 0 datatype: boolean}
usesubscripts: { value: 1 datatype: boolean}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
colormode: { value: color datatype: string}
leftfooter: { value: {} datatype: string}
rightfooter: { value: {} datatype: string}
leftheader: { value: {} datatype: string}
rightheader: { value: {} datatype: string}
saverendercoordinates: { value: 0 datatype: boolean}
labelproperty: { value: {} datatype: string}
labelfilterset: { value: !hydrogen datatype: string constraints: filterlist}
labelcolor: { value: darkgreen datatype: color}
labelformat: { value: <%s> datatype: string}
Compiled C module A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION atomchange bondchange stereochange groupchange merge hadd mod_e_gif.so
E_GOLM_URL url Data display link into the GOLM metabolome database (http://gmd.mpimp-golm.mpg.de)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_golm_url.xpd
E_GOOGLE_SCHOLAR_URL url URL for data in the Google Scholar search engine
Tcl script E_STDINCHI E_STDINCHIKEY E_CAS atomchange bondchange stereochange atom bond e_google_scholar_url.xpd
E_GPCR_LIGAND_LIKENESS compound GPCR ligand structural likeness, computed as maximum similarity score with standard similarity property E_SCREEN on a diverse 1K cpds subset of the GLL database. Gatica, Cavasotto, J. Chem. Inf. Model. 2011, 52, 1
similarity byte
structure structure
Tcl script E_SCREEN atomchange bondchange atom bond e_gpcr_ligand_likeness.xpd
E_GRAPHICS_TEXT stringvector Head- and footline for graphics plots
never
E_GRID_VOLUME floatvolume Generic floating-point volume grid data. Used for exmapl ein the STF and Gausscube file I/O modules.
atomchange bondchange stereochange merge 3drelative hadd atom bond ring
E_GROUP_COUNT int Number of groups defined for the ensemble
Compiled C module atomchange bondchange groupchange atom bond mod_e_group_count.so
E_GUIDETOPHARMACOLOGY_ID int Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org)
Tcl script E_SMILES atomchange bondchange stereochange merge e_guidetopharmacology_id.xpd
E_GUIDETOPHARMACOLOGY_URL url Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org)
Tcl script E_GUIDETOPHARMACOLOGY_ID atomchange bondchange stereochange merge e_guidetopharmacology_url.xpd
E_HALIDE_FRACTION double Fraction of molecular weight contributed by halogen atoms
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_halide_fraction.so
E_HASH uint64 Basic ensemble hashcode
(builtin) M_HASHGROUP M_HASH atomchange bondchange merge
E_HASH128 uint128 Perturbed ensemble hashcode, extended to 128 bits
Compiled C module M_HASHGROUP128 M_HASH128 atomchange bondchange merge hadd mod_e_hash128.so
E_HASHGROUP_COUNT_A intvector Population of basic atom hash groups
(builtin) A_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_AI intvector Population of isotope atom hash groups
(builtin) A_ISOTOPE_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_AIS intvector Population of isotopic stereospecific basic atom hash groups
(builtin) A_ISOTOPE_STEREO_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_AS intvector Population of stereospecific basic atom hash groups
(builtin) A_STEREO_HASH atomchange bondchange merge hadd
E_HASHGROUP_COUNT_B intvector Population of bond hash groups
(builtin) B_HASH atomchange bondchange merge
E_HASHGROUP_COUNT_BS intvector Population of stereospecific bond hash groups
(builtin) B_STEREO_HASH atomchange bondchange merge
E_HASHGROUP_COUNT_M intvector Population of perturbed molecule hash groups
(builtin) M_HASHY atomchange bondchange merge hadd
E_HASHGROUP_COUNT_MI intvector Population of isotopic perturbed molecule hash groups
(builtin) M_HASHIY atomchange bondchange merge hadd
E_HASHGROUP_COUNT_MIS intvector Population of isotopic stereospecific perturbed molecule hash groups
(builtin) M_HASHISY atomchange bondchange merge hadd
E_HASHGROUP_COUNT_MS intvector Population of stereospecifc perturbed molecule hash groups
(builtin) M_HASHSY atomchange bondchange merge hadd
E_HASHISY uint64 Perturbed isotope stereo ensemble hashcode
(builtin) M_ISOTOPE_STEREO_HASHGROUP_Y M_HASHISY atomchange bondchange merge hadd
E_HASHIY uint64 Perturbed isotope ensemble hashcode
(builtin) M_ISOTOPE_HASHGROUP_Y M_HASHIY atomchange bondchange merge hadd
E_HASHS uint64 Stereospecific basic ensemble hashcode
(builtin) M_STEREO_HASHGROUP M_HASHS atomchange bondchange merge
E_HASHSY uint64 Perturbed stereospecific ensemble hashcode
useisotope: { value: 0 datatype: string}
(builtin) M_STEREO_HASHGROUP_Y M_HASHSY atomchange bondchange merge hadd
E_HASHY uint64 Perturbed ensemble hashcode
useisotope: { value: 0 datatype: string}
(builtin) M_HASHGROUP_Y M_HASHY atomchange bondchange merge hadd
E_HEAT_OF_FORMATION float Measured or computed Heat of Formation. The computation procedure tries to run a simple VAMP job. This proeprties acts as the cornerstone for a standard set of QM-related properties via windfall/indirect property definition relationships.
filename: { value: {} datatype: string}
prgpath: { value: /usr/local/bin/vamp datatype: string}
method: { value: AM1 datatype: string}
Tcl script A_XYZ atomchange bondchange e_heat_of_formation.xpd
E_HEAVY_ATOM_COUNT int Number of non-hydrogen atoms in the ensemble
Compiled C module A_ELEMENT A_TYPE atomchange bondchange mol atom bond mod_e_heavy_atom_count.so
E_HEAVY_BOND_COUNT int Count of VB bonds which do not contain hydrogen
Compiled C module A_TYPE A_ELEMENT B_TYPE atomchange mod_e_heavy_bond_count.so
E_HETEROATOM_CARBON_RATIO double Number of hetero atoms devided by number of carbon atoms
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_heteroatom_carbon_ratio.so
E_HETEROATOM_COUNT int Number of hetero (not C or H) atoms in the ensemble
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_heteroatom_count.so
E_HISTORY compoundvector Record history
program string
version string
patchlevel string
pgmdate date
user string
date date
machine string
never
E_HIT2LEAD_ID int Catalog number from www.hit2lead.com (aka ChemBridge)
database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
Tcl script E_SDF_STRING atomchange bondchange atom bond e_hit2lead_id.xpd
E_HIT2LEAD_URL url Display URL for a hit2lead (www.hit2lead.com, aka ChemBridge) database entry
database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
Tcl script E_HIT2LEAD_ID atomchange bondchange atom bond e_hit2lead_url.xpd
E_HMDB_ID string ID of structure in the HMDB database (www.hmdb.ca)
Tcl script E_SMILES atomchange bondchange atom bond e_hmdb_id.xpd
E_HMDB_URL url Display URL of structure in the HMDB database (www.hmdb.ca)
Tcl script E_HMDB_ID atomchange bondchange atom bond e_hmdb_url.xpd
E_HSDB_URL url Display URL for the HSDB (http://toxnet.nlm.nih.gov/newtoxnet/hsdb.htm) database
Tcl script E_CAS atomchange bondchange atom bond e_hsdb_url.xpd
E_HYDROGEN_BOND_CENTER_COUNT int Number of heavy atoms that can act as hydrogen donor or acceptor
Tcl script A_HYDROGEN_BONDING never e_hydrogen_bond_center_count.xpd
E_IC50 compound IC50 aids screen data
concentration float
concunit shortstring
flag shortstring
icconc float
nexperiments short
atomchange bondchange merge
E_ICSC_CARD_ID shortstring International Chemical Safety Cards ID (from www.ilo.org)
Tcl script E_CAS atomchange bondchange atom bond e_icsc_card_id.xpd
E_ICSC_CARD_URL url International Chemical Safety Cards display URL (from www.ilo.org)
Tcl script E_ICSC_CARD_ID atomchange bondchange atom bond e_icsc_card_url.xpd
E_IDENT string Short ensemble identification string
never
E_IDENTIFIER_NORM_DATASET dataset Debug property for FICUS suite
atomchange bondchange atom bond
E_IDENTIFIER_NORM_EXEMPTION_LIST stringvector Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540)
atomchange bondchange stereochange atom bond
E_IDTF_MODEL blob
(switchable between blob diskfile mapfile)
3D structure model in Intel IDTF format
style: { value: spacefill enumeration: ballstick:capped:spacefill:wireframe:all datatype: string}
filename: { value: {} datatype: diskfile constraints: writeable}
bondradius: { value: 15 datatype: double}
ignoreh: { value: 0 datatype: boolean}
vdwscaling: { value: 25 datatype: double}
atomhighlightcolor: { value: red datatype: color}
highlightatoms: { value: {} datatype: intvector}
bondhighlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
showbondorder: { value: 0 datatype: boolean}
bondcolor: { value: atomsplit datatype: string}
structure: { value: 0 datatype: boolean}
showlabel: { value: 0 datatype: boolean}
labelcolor: { value: purple datatype: color}
addlights: { value: 0 datatype: boolean}
addview: { value: 0 datatype: boolean}
glossfactor: { value: 75 datatype: double}
labelsize: { value: 15 datatype: int}
tesselation: { value: octahedron 4 20 20 datatype: string}
dynamictesselation: { value: 1 datatype: boolean}
downloadfilename: { value: {} datatype: string}
suppressedatoms: { value: {} datatype: intvector}
suppressedbonds: { value: {} datatype: intvector}
Compiled C module A_XYZ A_ELEMENT B_TYPE B_ORDER B_FLAGS A_FLAGS A_COLOR B_COLOR atomchange bondchange stereochange merge 3drelative 3dabsolute hadd mod_e_idtf_model.so
E_IMAGEMAP string HTML imagemap associated with a GIF/PNG image (property E_GIF)
name: { value: {} datatype: string}
mode: { value: mol enumeration: atom:bond:mol datatype: int}
target: { value: {} datatype: string}
url: { value: {} datatype: string}
title: { value: {} datatype: string}
Tcl script E_GIF never e_imagemap.xpd
E_IMAGE_SCALING doublevector 2D coordinate scaling information (A_XY) for rendering in an image of specified size. The fields are the coordinate scale factor, the x and y offsets (these three values place the drawing into the 0..w/h-1 pixel area), the relative scale factor for the structure needed to fit into the "bonds" size box (1.0 if it fits into the box), and suggested symbol and annotation font sizes in points.
factor double
xoffset double
yoffset double
scale double
symbolfontsize double
annotationfontsize double
width: { value: 25 description: Image width (pixel) datatype: int}
height: { value: 250 description: Image height (pixel) datatype: int}
border: { value: 10 description: Image border (pixel) minvalue: 0 maxvalue: 100 datatype: int}
bonds: { value: 8 description: Number of standard bonds across image minvalue: 1 maxvalue: 20 datatype: int}
hidefragment: { value: {} description: Structure fragment to hide and exclude from computation datatype: structure}
Compiled C module A_XY atomchange bondchange atom bond mod_e_image_scaling.so
E_INACTIVE_AIDSET intvector Set of PubChem assay IDs testing this compound as inactive
Tcl script E_CID atomchange bondchange stereochange e_inactive_aidset.xpd
E_INCHI string First release InChI identifier (E_STDINCHI following the current standard is preferred)
options: { value: DONOTADDH W0 FIXEDH RECMET NEWPS SPXYZ SAsXYZ Fb Fnud description: Set of option words as used in the original NIST software datatype: string}
fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simpel signle bonds, regardless of their real bond type datatype: boolean}
stereoperception: { value: 1 description: If set, perceive stereochemistry, if no, use what is presently set on the structure datatype: boolean}
stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int}
prefix: { value: 1 description: If set, include InChi= prefix in output datatype: boolean}
stripstereolayer: { value: 0 datatype: boolean}
stripisotopelayer: { value: 0 datatype: boolean}
stripfixedhlayer: { value: 0 datatype: boolean}
stripreconnectlayer: { value: 0 datatype: boolean}
stripchargelayer: { value: 0 datatype: boolean}
Compiled C module B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE B_STEREOGENIC B_ISAROMATIC A_ALLENE atomchange bondchange stereochange hadd atom bond mod_e_inchi.so
E_INCHIKEY string Hash of InChI string
prefix: { value: 1 datatype: boolean}
Compiled C module E_INCHI atomchange bondchange stereochange hadd atom bond mod_e_inchikey.so
E_INCHIKEY_OLD string Hash of InChI string, old hashing scheme
prefix: { value: 1 datatype: boolean}
Compiled C module E_INCHI never mod_e_inchikey_old.so
E_INCHI_AUXINFO string InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting E_INCHI
B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE atomchange bondchange stereochange hadd atom bond
E_INCONCLUSIVE_AIDSET intvector Set of PubChem assay IDs testing this compound as inconclusive (neither definitely active or inactive)
Tcl script E_CID atomchange bondchange stereochange e_inconclusive_aidset.xpd
E_INPUTDATE date Time stamp for molecule
Tcl script never e_inputdate.xpd
E_IONIZATION_POTENTIAL float Measured or computed Ionization potential. This can be computed indirectly via E_HEAT_OF_FORMATION by a VAMP run.
A_XYZ atomchange bondchange
E_IRIS_URL url Display URL in EPA IRIS (Integrated Risk Information System, https://toxnet.nlm.nih.gov/newtoxnet/iris.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_iris_url.xpd
E_IRSPECTRUM compound Measured or computed IR spectrum. The compuation function attempts to get an IR spectrum from the NIST WebBook, or run a simple VAMP job depending on the "source" parameter, which should be set to "NIST" or "VAMP".
experimental boolean
origin string
author string
date datetime
spectrometer string
parameters string
specificparams dictionary
page string
reference string
purity float
source string
description string
solvent string
procedure string
resolution double
firstx double
lastx double
xfactor double
yfactor double
xunit string
yunit string
{#points} int
coding string
spectrum xyvector
peaks floatvector
peakshape stringvector
peakintensity floatvector
peakname stringvector
filename: { value: {} description: temporary job file datatype: diskfile constraints: writeable}
prgpath: { value: /usr/local/bin/vamp datatype: diskfile constraints: existing}
method: { value: AM1 datatype: string}
freqfactor: { value: 0.98 datatype: string}
cofreqfactor: { value: 0.90 datatype: string}
source: { value: NIST enumeration: NIST:VAMP datatype: int}
Tcl script A_XYZ atomchange bondchange 3drelative e_irspectrum.xpd
E_IRSPECTRUM_IMAGE diskfile
(switchable between string blob diskfile url)
IR spectrum rendering
height: { value: 250 datatype: int}
width: { value: 500 datatype: int}
bgcolor: { value: white datatype: color}
title: { value: {} datatype: string}
filename: { value: {} datatype: string constraints: writeable}
format: { value: gif enumeration: png,png24:gif:png8 datatype: string}
titlecolor: { value: black datatype: color}
framecolor: { value: black datatype: color}
signalcolor: { value: #DD0000 datatype: color}
ystyle: { value: transmittance enumeration: transmittance:absorbance datatype: int}
xdirection: { value: reverse enumeration: normal:reverse datatype: int}
xstyle: { value: 1/cm enumeration: 1/cm:um datatype: int}
Tcl script E_IRSPECTRUM atomchange bondchange merge mol e_irspectrum_image.xpd
E_ISOTOPE_ATOMHASH_COUNT int Number of different isotopic basic atom hash codes
(builtin) E_HASHGROUP_COUNT_AI atomchange bondchange merge
E_ISOTOPE_COUNT int Number of isotopically labelled atoms
Compiled C module A_TYPE A_ISOTOPE atomchange merge atom bond mod_e_isotope_count.so
E_ISOTOPE_HASH128 uint128 Perturbed isotope-sensitive ensemble hashcode, extended to 128 bits
Compiled C module M_ISOTOPE_HASHGROUP128 M_ISOTOPE_HASH128 atomchange bondchange merge hadd mod_e_isotope_hash128.so
E_ISOTOPE_MOLHASH_COUNT int Number of different isotopic perturbed molecule hash codes
(builtin) E_HASHGROUP_COUNT_MI atomchange bondchange merge hadd
E_ISOTOPE_STEREO_ATOMHASH_COUNT int Number of different isotopic stereospecific basic atom hash codes
(builtin) E_HASHGROUP_COUNT_AIS atomchange bondchange merge
E_ISOTOPE_STEREO_HASH128 uint128 Perturbed isotope-sensitive and stereo-sensitive ensemble hashcode, extended to 128 bits
Compiled C module M_ISOTOPE_STEREO_HASHGROUP128 M_ISOTOPE_STEREO_HASH128 atomchange bondchange merge hadd mod_e_isotope_stereo_hash128.so
E_ISOTOPE_STEREO_MOLHASH_COUNT int Number of different isotopic stereospecific perturbed molecule hash codes
(builtin) E_HASHGROUP_COUNT_MIS atomchange bondchange merge hadd
E_ISOTOPE_STEREO_TAUTO_HASH uint64 Perturbed tautomer-tolerant ensemble isotope stereo hashcode
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_HASHISY atomchange bondchange stereochange merge mod_e_isotope_stereo_tauto_hash.so
E_ISOTOPE_STEREO_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant ensemble isotope stereo hashcode, 128 bit version
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_ISOTOPE_STEREO_HASH128 atomchange bondchange stereochange merge mod_e_isotope_stereo_tauto_hash128.so
E_ISOTOPE_TAUTO_HASH uint64 Perturbed tautomer-tolerant ensemble stereo hashcode, with isotope labels but without stereochemistry
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
setcount: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
stereobondmalus: { value: 0 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_HASHIY atomchange bondchange merge mod_e_isotope_tauto_hash.so
E_ISOTOPE_TAUTO_HASH128 uint128 Perturbed tautomer-tolerant ensemble isotope hashcode, 128 bit version
maxtautomers: { value: 250 datatype: int}
loghandle: { value: {} datatype: string}
scramble: { value: 0 datatype: int}
setcanonictautomer: { value: 0 datatype: boolean}
usekekuleset: { value: 1 datatype: boolean}
stereobondmalus: { value: 1 datatype: boolean}
restrictedtransforms: { value: 0 datatype: boolean}
setcount: { value: 1 datatype: boolean}
useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean}
lockringpielectroncount: { value: 0 datatype: boolean}
usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean}
Compiled C module E_ISOTOPE_HASH128 atomchange bondchange stereochange merge mod_e_isotope_tauto_hash128.so
E_ITER_URL url Display URL in EPA ITER (International Toxicity Estimates for Risk, https://toxnet.nlm.nih.gov/newtoxnet/iter.htm)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_iter_url.xpd
E_IUPAC_ALLOWED_NAME string Allowed IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_allowed_name.xpd
E_IUPAC_OECAS_NAME string IUPAC name (OEChem CAS-like Style). This is a field in PubChem and used by the ASN I/O module.
atomchange bondchange stereochange
E_IUPAC_PREFERRED_NAME string Preferred IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_preferred_name.xpd
E_IUPAC_SYSTEMATIC_NAME string Systematic IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_systematic_name.xpd
E_IUPAC_TRADITIONAL_NAME string Traditional IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software.
Tcl script never e_iupac_traditional_name.xpd
E_IUPHAR_ID int Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org)
Tcl script E_SMILES atomchange bondchange stereochange merge e_iuphar_id.xpd
E_IUPHAR_URL url Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org)
Tcl script E_GUIDETOPHARMACOLOGY_ID atomchange bondchange stereochange merge e_iuphar_url.xpd
E_JCAMP_SPECTRA_BLOCK compound Embedded JCAMP spectral data block. Currently only used in E_NMRSPECTRUM to support the newer NTUPLES data table JCAMP style, with real/imaginary spectrum and real/imaginary FID possibly stored all in one file.
name string
symbol string
{#points} int
firstx double
lastx double
firsty double
lasty double
xfactor double
yfactor double
xunit string
yunit string
data floatvector
atomchange bondchange atom bond
E_JCHECK_URL url Data display URL in Japanese JCHECK databases (www.safe.nite.go.jp)
Tcl script E_CAS E_MITI_ID atomchange bondchange atom bond e_jcheck_url.xpd
E_JGLOBAL_ID string Database ID for the J-GLOBAL registry (https://jglobal.jst.go.jp)
Tcl script atomchange bondchange atom bond e_jglobal_id.xpd
E_JGLOBAL_URL url Display URL for the J-GLOBAL registry (https://jglobal.jst.go.jp)
Tcl script atomchange bondchange atom bond e_jglobal_url.xpd
E_JHOTI_FRAGMENTLIKENESS_VIOLATIONS byte Congreve, Carr, Murray, Jhoti, Drug. Discov. Today 2003, 8, 876
Tcl script E_WEIGHT E_NHDONORS E_NHACCEPTORS E_XLOGP2 atomchange bondchange atom bond e_jhoti_fragmentlikeness_violations.xpd
E_JME_STRING string JME editor structure encoding
Compiled C module A_ELEMENT B_ORDER B_TYPE A_TYPE A_FORMAL_CHARGE A_ISOTOPE atomchange bondchange stereochange hadd mol atom bond ring mod_e_jme_string.so
E_JSTDATA stringvector JST extended molfile data in skip section
atomchange bondchange stereochange merge
E_KEGG_BRITE_CLASSIFICATION stringvector Compound classification codes as per the KEGG BRITE database (http://www.genome.jp/kegg/brite.html). Compounds must be present in KEGG database, i.e. have a KEGG ID.
Tcl script E_KEGG_ID atomchange bondchange atom bond e_kegg_brite_classification.xpd
E_KEGG_ID string KEGG ID (www.genome.jp)
Tcl script atomchange bondchange stereochange merge e_kegg_id.xpd
E_KEGG_URL url KEGG compound display URL (www.genome.jp)
Tcl script E_KEGG_ID atomchange bondchange stereochange merge e_kegg_url.xpd
E_KEKULESET dataset Generated set of alternative Kekule forms of the structure- The generated forms are duplicate-filtered by symmetry hashcodes - that means there is only a single Kekule form for benzene, pyridine, pyrimidine (1.3-diazine) or pyrazine (1.4-diazine) - but two for pyridazine (1.2-diazine, with a double or single bond between the adjacent nitrogens).
maxkekuleforms: { value: 512 datatype: int}
Compiled C module A_TYPE B_TYPE A_ELEMENT B_ORDER atomchange bondchange merge atom bond mod_e_kekuleset.so
E_KEYWORDS stringvector Keywords associated with ensemble
never
E_KLIFS_ID int Database ID for the KLIFS database (http://klifs.vu-compmedchem.nl)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_klifs_id.xpd
E_KLIFS_URL url Data display URL for the KLIFS database (http://klifs.vu-compmedchem.nl)
Tcl script E_KLIFS_ID atomchange bondchange stereochange atom bond e_klifs_url.xpd
E_LC50 compound LC50 tumor screen data
concunit shortstring
lcconc float
panel shortstring
cell string
panelnumber short
cellnumber short
nlog_lc50 float
ntest_this short
ntest_max short
atomchange bondchange merge
E_LEVEL int Ensemble level
never
E_LINCS_ID string Dabase ID of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu)
Tcl script E_SMILES atomchange bondchange stereochange atom bond e_lincs_id.xpd
E_LINCS_URL url Display URL of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu)
Tcl script E_LINCS_ID atomchange bondchange stereochange atom bond e_lincs_url.xpd
E_LINKTEXTS stringvector Toplevel link texts of HTML URLs leading to this molecule
never
E_LIPIDMAPS_ID string Structure ID for the Lipidmaps database
Tcl script atomchange bondchange stereochange atom bond e_lipidmaps_id.xpd
E_LIPIDMAPS_URL url
Tcl script atomchange bondchange atom bond e_lipidmaps_url.xpd
E_LIPINSKI_ACCEPTOR_COUNT int Number of hydrogens on N and O atoms - H-bond acceptors according to simple Lipinski definition. For a more refined definition, use property E_NHACCEPTORS.
Compiled C module A_TYPE A_ELEMENT A_FREE_ELECTRONS atomchange bondchange atom bond mod_e_lipinski_acceptor_count.so
E_LIPINSKI_DONOR_COUNT int Number of oxygen and nitrogen atoms according to really simple Lipinski definition. For a more refined definition, use E_NHDONORS.
Compiled C module A_TYPE A_ELEMENT atomchange bondchange atom bond mod_e_lipinski_donor_count.so
E_LITERATURE_REFERENCE stringvector Auxiliary literature references
never
E_LOOKCHEM_URL url PubChem compound database URL
Tcl script atomchange bondchange stereochange merge e_lookchem_url.xpd
E_MACCS_KEYS bitvector MDL MACCS fingerprint (166 bits)
Tcl script atom bond e_maccs_keys.xpd
E_MANUFACTURERS compoundvector Data about manufactorers of a chemical
catno string
manufacturer string
catalog string
price float
currency string
amount float
unit string
info string
purity string
atomchange bondchange stereochange merge
E_MAP_ANNOTATION compoundvector Map markers to be used in conjuction with D_ANNOTATED_MAP
{} {none:circle:triangle:invtriangle:square:diamond:pentagon:hexagon}
tag string
object string
size int
outlinecolor color
fillcolor color
textcolor color
header string
footer string
atomchange bondchange stereochange 3drelative atom bond
E_MARKED boolean Flag for marked structures
never
E_MASS_PATTERN xyvector Mass distribution pattern
cutoff: { value: 0.01 description: Minimum abundancy to include in output vector minvalue: 0.00 maxvalue: 1.00 datatype: double}
useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean}
Compiled C module A_ELEMENT A_TYPE A_ISOTOPE atomchange mod_e_mass_pattern.so
E_MATRIX_SCIENTIFIC_IDS stringvector ID of the compound Matrix Scientific catalog
Tcl script atomchange bondchange stereochange atom bond e_matrix_scientific_ids.xpd
E_MATRIX_SCIENTIFIC_URLS urlvector URL Matrix Scientific catalog entry
Tcl script E_MATRIX_SCIENTIFIC_IDS atomchange bondchange atom bond e_matrix_scientific_urls.xpd
E_MAX_CHAIN_FRAGMENT_SIZE int The maximum value of A_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-hydrogen atoms.
Compiled C module A_CHAIN_LENGTH atomchange bondchange atom bond mod_e_max_chain_fragment_size.so
E_MAX_CONJUGATED_SYSTEM_SIZE int The maximum size of a conjugated system in the ensemble according to the Shoichet definition (see literature reference). J. Med. Chem. 2003, 46, 4477-4486
Compiled C module A_CONJUGATED_SYSTEM_SIZE atomchange bondchange atom bond mod_e_max_conjugated_system_size.so
E_MAX_LINEAR_CHAIN_FRAGMENT_SIZE int The maximum value of A_LINEAR_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-branching non-hydrogen atoms.
Compiled C module A_LINEAR_CHAIN_LENGTH atomchange bondchange atom bond mod_e_max_linear_chain_fragment_size.so
E_MCULE_ID string Get database ID of structure in MCULE (mcule.com) database
Tcl script E_SMILES atomchange bondchange atom bond e_mcule_id.xpd
E_MCULE_URL url Display URL for MCULE (mcule.com) database
Tcl script E_MCULE_ID atomchange bondchange atom bond e_mcule_url.xpd
E_MDL_NAME string Name as extracted from MDL Molfile header
never
E_MDL_NUMBER string MDL substance number
Tcl script atomchange bondchange atom bond e_mdl_number.xpd
E_MEREG string MDL external registry number
never
E_MESH_ID string MESH ID, extracted from E_MESH_TERMS at the toplevel
Tcl script E_MESH_TERMS atomchange bondchange atom bond e_mesh_id.xpd
E_MESH_TERMS compoundvector Mesh terms associated with structure retrieved from PubChem
id int
terms stringvector
url url
ontotree datatree
Tcl script E_CID atomchange bondchange stereochange merge atom bond e_mesh_terms.xpd
E_MESH_URL url MESH display URL, extracted from E_MESH_TERMS at the toplevel
Tcl script E_MESH_TERMS atomchange bondchange atom bond e_mesh_url.xpd
E_MESO boolean Check whether at least one molecule is a meso compound, and all other molecules are either also meso, or not stereogenic
Tcl script M_MESO M_STEREO_STATUS atomchange bondchange stereochange merge mol atom bond e_meso.xpd
E_METABOLIGHTS_ID string Structure access key for MetaboLights database (https://www.ebi.ac.uk/metabolights)
Tcl script E_INCHI atomchange bondchange stereochange atom bond e_metabolights_id.xpd
E_METABOLIGHTS_URL url Structure data display URL for MetaboLights database (https://www.ebi.ac.uk/metabolights)
Tcl script E_METABOLIGHTS_ID atomchange bondchange atom bond e_metabolights_url.xpd
E_METABOLOMICSWORKBENCH_CLASSIFICATION dictionary Compund description in the Metabolomics Workbench (www.metabolomicsworkbench.org)
Tcl script E_METABOLOMICSWORKBENCH_ID atomchange bondchange stereochange atom bond e_metabolomicsworkbench_classification.xpd
E_METABOLOMICSWORKBENCH_ID int Compund registration ID in the Metabolomics Workbench (www.metabolomicsworkbench.org)
Tcl script E_STDINCHIKEY atomchange bondchange stereochange atom bond e_metabolomicsworkbench_id.xpd
E_METACYC_URL url Link into the MetaCyc database (metacyc.org)
Tcl script atomchange bondchange atom bond e_metacyc_url.xpd
E_METADATA dictionary Dublin Core metadata for structure
never
E_METHOD string QM method description string
atomchange bondchange
E_MIF_IMAGE diskfile
(switchable between string blob diskfile xmlstring)
Ensemble image in MIF FrameMaker format
width: { value: 180 datatype: int}
height: { value: 180 datatype: boolean}
asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue datatype: int}
bonds: { value: 8 datatype: int}
hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int}
csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int}
bgcolor: { value: transparent datatype: color}
border: { value: 12 datatype: int}
bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string}
atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string}
hcolor: { value: {} datatype: color constraints: emptycolor}
header: { value: {} datatype: string}
footer: { value: {} datatype: string}
headercolor: { value: black datatype: color}
footercolor: { value: black datatype: color}
commenttype: { value: property enumeration: none:text:property,prop datatype: int}
comment: { value: E_NAME datatype: string}
structure: { value: none datatype: string}
metadata: { value: 1 datatype: boolean}
filename: { value: {} datatype: diskfile constraints: writeable}
highlightcolor: { value: red datatype: color}
highlightbonds: { value: {} datatype: intvector}
httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int}
wedges: { value: 1 datatype: boolean}
wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int}
markcolor: { value: blue datatype: color}
logofile: { value: {} datatype: diskfile constraints: existing readable}
logoscale: { value: 1 datatype: double}
dashes: { value: 1 datatype: boolean}
headerproperty: { value: {} datatype: string constraints: property}
footerproperty: { value: {} datatype: string constraints: property}
bead: { value: 1 datatype: boolean}
beadcolor1: { value: black datatype: color}
beadcolor2: { value: gray60 datatype: color}
linewidth: { value: 1.2 datatype: double}
showcharge: { value: 1 datatype: boolean}
showradical: { value: 1 datatype: boolean}
showstereo: { value: 1 datatype: string}
highlightgroups: { value: {} datatype: intvector}
boxgroups: { value: {} datatype: intvector}
groupcolor: { value: purple datatype: color}
annotationfontsize: { value: -1 datatype: double}
isotopemapping: { value: none datatype: string}
showisotope: { value: 1 datatype: boolean}
showstereoh: { value: 1 datatype: boolean}
showmapping: { value: 0 datatype: boolean}
frame: { value: 1 datatype: boolean}
showchirality: { value: none enumeration: none:simple:extended datatype: int}
linespacing: { value: 1.5 datatype: double}
unit: { value: {} datatype: string}
headerfontsize: { value: -1 datatype: double}
footerfontsize: { value: -1 datatype: double}
voronoicolorproperty: { value: {} datatype: color constraints: emptycolor}
voronoifilter: { value: {} datatype: string constraints: filtername}
circlecolor: { value: {} description: A property name or a color name datatype: string}
circleatoms: { value: {} datatype: intvector}
circlefilter: { value: {} datatype: string constraints: filtername}
wigglecount: { value: 10 datatype: int}
wiggleamplitude: { value: 3.0 datatype: double}
checkintersection: { value: 0 datatype: boolean}
annotationcolor: { value: {} datatype: color constraints: emptycolor}
showstereogroups: { value: 0 datatype: boolean}
font: { value: Arial datatype: string}
contractgroups: { value: 0 datatype: boolean}
downloadfilename: { value: {} datatype: string}
Compiled C module atomchange bondchange stereochange merge atom bond mod_e_mif_image.so
E_MINIMOL blob Ultracompact structure representation for structure database applications, with precomputed data for most common substructure attributes. Queries with extended attributes are still possible by converting the Minimol into a standard ensemble. The format is designed to be expanded into a simple memory blob for matching, minimizing malloc/free oberhead. In scripting interpreters, "ens create" auto-detects and decodes binary and hex-encoded Minimols.
version: { value: 3 datatype: int}
Compiled C module A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO B_ORDER B_TYPE A_TYPE A_STEREO_GROUP atomchange bondchange stereochange hadd mol atom bond mod_e_minimol.so
E_MIREG string MDL internal registry number. This is a standard field in RD files.
never
E_MITI_ID string Japanese hazardous substance registration number (www.safe.nite.go.jp)
Tcl script E_CAS atomchange bondchange stereochange atom bond e_miti_id.xpd
E_MNA dictionary MNA (multilevel neighborhood of atoms) fragment set, as defined by Poroikov et al. J. Chem. Inf. Comput. Sci. 1999, 39, 666-670
levels: { value: 1 2 description: Neighbor sphere radii to include in the result set datatype: intvector}
Tcl script A_SYMBOL atomchange bondchange atom bond e_mna.xpd
E_MOL2_STRING string Sybyl MOL2 structure encoding as string
Tcl script atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond e_mol2_string.xpd
E_MOLAR_REFRACTIVITY double Molar refractivity computed by the Wildman-Crippen method (see litref) J. Chem. Inf. Comput. Sci. 1999, 39, 868-873
Compiled C module A_WILDMAN_CRIPPEN_TYPE atomchange bondchange atom bond mod_e_molar_refractivity.so
E_MOLBASE_URL url Supplier data display page from molbase.com
Tcl script atomchange bondchange atom bond e_molbase_url.xpd
E_MOLD2_DESCRIPTORS floatvector MOLD2 descriptor collection, computed with original source encapsulated as a Cactvs module. The MOLD2 code unfortunately uses statically allocated data structures, and thus has a limit on 150 atoms, 400 paths and 9 ligands per atom. Larger structures fail. J. Chem. Inf. Model., 2008, 48 (7), pp 1337-1344
d001 float
d002 float
d003 float
d004 float
d005 float
d006 float
d007 float
d008 float
d009 float
d010 float
d011 float
d012 float
d013 float
d014 float
d015 float
d016 float
d017 float
d018 float
d019 float
d020 float
d021 float
d022 float
d023 float
d024 float
d025 float
d026 float
d027 float
d028 float
d029 float
d030 float
d031 float
d032 float
d033 float
d034 float
d035 float
d036 float
d037 float
d038 float
d039 float
d040 float
d041 float
d042 float
d043 float
d044 float
d045 float
d046 float
d047 float
d048 float
d049 float
d050 float
d051 float
d052 float
d053 float
d054 float
d055 float
d056 float
d057 float
d058 float
d059 float
d060 float
d061 float
d062 float
d063 float
d064 float
d065 float
d066 float
d067 float
d068 float
d069 float
d070 float
d071 float
d072 float
d073 float
d074 float
d075 float
d076 float
d077 float
d078 float
d079 float
d080 float
d081 float
d082 float
d083 float
d084 float
d085 float
d086 float
d087 float
d088 float
d089 float
d090 float
d091 float
d092 float
d093 float
d094 float
d095 float
d096 float
d097 float
d098 float
d099 float
d100 float
d101 float
d102 float
d103 float
d104 float
d105 float
d106 float
d107 float
d108 float
d109 float
d110 float
d111 float
d112 float
d113 float
d114 float
d115 float
d116 float
d117 float
d118 float
d119 float
d120 float
d121 float
d122 float
d123 float
d124 float
d125 float
d126 float
d127 float
d128 float
d129 float
d130 float
d131 float
d132 float
d133 float
d134 float
d135 float
d136 float
d137 float
d138 float
d139 float
d140 float
d141 float
d142 float
d143 float
d144 float
d145 float
d146 float
d147 float
d148 float
d149 float
d150 float
d151 float
d152 float
d153 float
d154 float
d155 float
d156 float
d157 float
d158 float
d159 float
d160 float
d161 float
d162 float
d163 float
d164 float
d165 float
d166 float
d167 float
d168 float
d169 float
d170 float
d171 float
d172 float
d173 float
d174 float
d175 float
d176 float
d177 float
d178 float
d179 float
d180 float
d181 float
d182 float
d183 float
d184 float
d185 float
d186 float
d187 float
d188 float
d189 float
d190 float
d191 float
d192 float
d193 float
d194 float
d195 float
d196 float
d197 float
d198 float
d199 float
d200 float
d201 float
d202 float
d203 float
d204 float
d205 float
d206 float
d207 float
d208 float
d209 float
d210 float
d211 float
d212 float
d213 float
d214 float
d215 float
d216 float
d217 float
d218 float
d219 float
d220 float
d221 float
d222 float
d223 float
d224 float
d225 float
d226 float
d227 float
d228 float
d229 float
d230 float
d231 float
d232 float
d233 float
d234 float
d235 float
d236 float
d237 float
d238 float
d239 float
d240 float
d241 float
d242 float
d243 float
d244 float
d245 float
d246 float
d247 float
d248 float
d249 float
d250 float
d251 float
d252 float
d253 float
d254 float
d255 float
d256 float
d257 float
d258 float
d259 float
d260 float
d261 float
d262 float
d263 float
d264 float
d265 float
d266 float
d267 float
d268 float
d269 float
d270 float
d271 float
d272 float
d273 float
d274 float
d275 float
d276 float
d277 float
d278 float
d279 float
d280 float
d281 float
d282 float
d283 float
d284 float
d285 float
d286 float
d287 float
d288 float
d289 float
d290 float
d291 float
d292 float
d293 float
d294 float
d295 float
d296 float
d297 float
d298 float
d299 float
d300 float
d301 float
d302 float
d303 float
d304 float
d305 float
d306 float
d307 float
d308 float
d309 float
d310 float
d311 float
d312 float
d313 float
d314 float
d315 float
d316 float
d317 float
d318 float
d319 float
d320 float
d321 float
d322 float
d323 float
d324 float
d325 float
d326 float
d327 float
d328 float
d329 float
d330 float
d331 float
d332 float
d333 float
d334 float
d335 float
d336 float
d337 float
d338 float
d339 float
d340 float
d341 float
d342 float
d343 float
d344 float
d345 float
d346 float
d347 float
d348 float
d349 float
d350 float
d351 float
d352 float
d353 float
d354 float
d355 float
d356 float
d357 float
d358 float
d359 float
d360 float
d361 float
d362 float
d363 float
d364 float
d365 float
d366 float
d367 float
d368 float
d369 float
d370 float
d371 float
d372 float
d373 float
d374 float
d375 float
d376 float
d377 float
d378 float
d379 float
d380 float
d381 float
d382 float
d383 float
d384 float
d385 float
d386 float
d387 float
d388 float
d389 float
d390 float
d391 float
d392 float
d393 float
d394 float
d395 float
d396 float
d397 float
d398 float
d399 float
d400 float
d401 float
d402 float
d403 float
d404 float
d405 float
d406 float
d407 float
d408 float
d409 float
d410 float
d411 float
d412 float
d413 float
d414 float
d415 float
d416 float
d417 float
d418 float
d419 float
d420 float
d421 float
d422 float
d423 float
d424 float
d425 float
d426 float
d427 float
d428 float
d429 float
d430 float
d431 float
d432 float
d433 float
d434 float
d435 float
d436 float
d437 float
d438 float
d439 float
d440 float
d441 float
d442 float
d443 float
d444 float
d445 float
d446 float
d447 float
d448 float
d449 float
d450 float
d451 float
d452 float
d453 float
d454 float
d455 float
d456 float
d457 float
d458 float
d459 float
d460 float
d461 float
d462 float
d463 float
d464 float
d465 float
d466 float
d467 float
d468 float
d469 float
d470 float
d471 float
d472 float
d473 float
d474 float
d475 float
d476 float
d477 float
d478 float
d479 float
d480 float
d481 float
d482 float
d483 float
d484 float
d485 float
d486 float
d487 float
d488 float
d489 float
d490 float
d491 float
d492 float
d493 float
d494 float
d495 float
d496 float
d497 float
d498 float
d499 float
d500 float
d501 float
d502 float
d503 float
d504 float
d505 float
d506 float
d507 float
d508 float
d509 float
d510 float
d511 float
d512 float
d513 float
d514 float
d515 float
d516 float
d517 float
d518 float
d519 float
d520 float
d521 float
d522 float
d523 float
d524 float
d525 float
d526 float
d527 float
d528 float
d529 float
d530 float
d531 float
d532 float
d533 float
d534 float
d535 float
d536 float
d537 float
d538 float
d539 float
d540 float
d541 float
d542 float
d543 float
d544 float
d545 float
d546 float
d547 float
d548 float
d549 float
d550 float
d551 float
d552 float
d553 float
d554 float
d555 float
d556 float
d557 float
d558 float
d559 float
d560 float
d561 float
d562 float
d563 float
d564 float
d565 float
d566 float
d567 float
d568 float
d569 float
d570 float
d571 float
d572 float
d573 float
d574 float
d575 float
d576 float
d577 float
d578 float
d579 float
d580 float
d581 float
d582 float
d583 float
d584 float
d585 float
d586 float
d587 float
d588 float
d589 float
d590 float
d591 float
d592 float
d593 float
d594 float
d595 float
d596 float
d597 float
d598 float
d599 float
d600 float
d601 float
d602 float
d603 float
d604 float
d605 float
d606 float
d607 float
d608 float
d609 float
d610 float
d611 float
d612 float
d613 float
d614 float
d615 float
d616 float
d617 float
d618 float
d619 float
d620 float
d621 float
d622 float
d623 float
d624 float
d625 float
d626 float
d627 float
d628 float
d629 float
d630 float
d631 float
d632 float
d633 float
d634 float
d635 float
d636 float
d637 float
d638 float
d639 float
d640 float
d641 float
d642 float
d643 float
d644 float
d645 float
d646 float
d647 float
d648 float
d649 float
d650 float
d651 float
d652 float
d653 float
d654 float
d655 float
d656 float
d657 float
d658 float
d659 float
d660 float
d661 float
d662 float
d663 float
d664 float
d665 float
d666 float
d667 float
d668 float
d669 float
d670 float
d671 float
d672 float
d673 float
d674 float
d675 float
d676 float
d677 float
d678 float
d679 float
d680 float
d681 float
d682 float
d683 float
d684 float
d685 float
d686 float
d687 float
d688 float
d689 float
d690 float
d691 float
d692 float
d693 float
d694 float
d695 float
d696 float
d697 float
d698 float
d699 float
d700 float
d701 float
d702 float
d703 float
d704 float
d705 float
d706 float
d707 float
d708 float
d709 float
d710 float
d711 float
d712 float
d713 float
d714 float
d715 float
d716 float
d717 float
d718 float
d719 float
d720 float
d721 float
d722 float
d723 float
d724 float
d725 float
d726 float
d727 float
d728 float
d729 float
d730 float
d731 float
d732 float
d733 float
d734 float
d735 float
d736 float
d737 float
d738 float
d739 float
d740 float
d741 float
d742 float
d743 float
d744 float
d745 float
d746 float
d747 float
d748 float
d749 float
d750 float
d751 float
d752 float
d753 float
d754 float
d755 float
d756 float
d757 float
d758 float
d759 float
d760 float
d761 float
d762 float
d763 float
d764 float
d765 float
d766 float
d767 float
d768 float
d769 float
d770 float
d771 float
d772 float
d773 float
d774 float
d775 float
d776 float
d777 float
Compiled C module atomchange bondchange merge mod_e_mold2_descriptors.so
E_MOLHASH_COUNT int Number of different pertured molecule hash codes
(builtin) E_HASHGROUP_COUNT_M atomchange bondchange merge hadd
E_MOLINSTINCTS_ANALYSIS_URL url Access URL for structure analysis in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_analysis_url.xpd
E_MOLINSTINCTS_CONSTANT_PROPERTY_URL url Display URL for constant properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_constant_property_url.xpd
E_MOLINSTINCTS_DESCRIPTOR_PROPERTY_URL url Display URL for molecular descriptor properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_descriptor_property_url.xpd
E_MOLINSTINCTS_DRUG_PROPERTY_URL url Display URL for molecular drug properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_drug_property_url.xpd
E_MOLINSTINCTS_ID string ID in MolInstincts database (www.molinstincts.com)
Tcl script atomchange bondchange atom bond e_molinstincts_id.xpd
E_MOLINSTINCTS_QUANTUM_PROPERTY_URL url Display URL for molecular quantum properties in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_quantum_property_url.xpd
E_MOLINSTINCTS_SPECTRA_URL url Display URL for structure spectra in the Molinstincts database (molinstincts.com)
Tcl script E_MOLINSTINCTS_ID atomchange bondchange atom bond e_molinstincts_spectra_url.xpd
E_MOLNAME string Ensemble name as free format string, no associated with any specific naming convention
atomchange bondchange merge
E_MOLPORT_ID string ID of structure in the MOLPORT database (www.molport.com)
Tcl script E_SMILES atomchange bondchange stereochange merge e_molport_id.xpd
E_MOLPORT_URL url Display URL in the Molport portal (www.molport.com)
E_MOLPORT_ID atomchange bondchange stereochange merge
E_MONOISOTOPIC_MASS float Mass computed with most abundant isotope only, not natural abundance
useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean}
Compiled C module A_ELEMENT A_TYPE A_ISOTOPE atomchange mod_e_monoisotopic_mass.so
E_MP floatpair Melting Point in Kelvin, with optional range
value float
range float
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE atomchange bondchange
E_MQN shortvector Reymond molecular quantum numbers L. Ruddigkeit, L. C. Blum, J.-L. Reymond, J. Chem. Inf. Model. 2013, 53, 56-65
c int
f int
cl int
br int
i int
s int
p int
an int
cn int
ao int
co int
hac int
asb int
adb int
atb int
csb int
cdb int
ctb int
rbc int
hbam int
hba int
hdbm int
hdb int
neg int
pos int
asv int
adv int
atv int
aqv int
cdv int
dtv int
cqv int
r3 int
r4 int
r5 int
r6 int
r7 int
r8 int
r9 int
rg10 int
afr int
bfr int
Compiled C module