The CHEMINF module of PINK Annotation Schema providing a taxonomy for chemical descriptors.
The CHEMINF module of PINK Annotation Schema
This module is a part of the [PINK Annotation Schema](https://pink-project.github.io/PINK-annotation-schema/widoco/index-en.html).A *descriptor* or *indicator* is a property that provides information about the state of a system. It simplifies complex realities into measurable values that can guide decisions. A service for browsing and searching CHEMINF can be found [here](https://ontobee.org/ontology/CHEMINF?iri=http://semanticscience.org/resource/CHEMINF_000123).
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
isAbout
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participatesIn
hasValue
MolecularEntity
Atom
PolyatomicEntity
A chemical entity is any molecular entity or chemical substance.
ChemicalEntity
Molar refractviity is a measure of the total polarizability of a mole of a substance and is dependent on the temperature, the index of refraction, and the pressure.
MolarRefractivity
atomic polarizability sum is the sum of the atomic polarizabilities (including implicit hydrogens).
AtomicPolarizabilitySum
sum of surface area on positive parts of molecule
PartialPositiveSurfaceArea
partial positive surface area * total positive charge on the molecule
PPSAMinus2
RSStereochemicalDescriptor
RStereochemicalDescriptor
A canonical SMILES descriptor is a SMILES descriptor that is produced using a canonicalization algorithm which results in one special generic SMILES among all valid possibilities.
CanonicalSMILESDescriptor
charge weighted partial positive surface area
ChargeWeightedPartialPositiveSurfaceArea
Atomic order is an atomic descriptor that specifies the ordinal position of an atom.
AtomicOrder
sum of surface area on negative parts of molecule
PartialNegativeSurfaceArea
partial negative surface area * total negative charge on the molecule
PNSAMinus2
An energetic descriptor is a chemical descriptor which captures information about some aspect of the energetic behaviour of a chemical entity.
EnergeticDescriptor
A SMILES descriptor is a structure descriptor that denotes a molecular structure as a graph.
SMILESDescriptor
A SMARTS descriptor is a molecular structure descriptor that conforms to the SMARTS specification.
SMARTSDescriptor
A physical descriptor is a chemical descriptor which describes some physical property (quality or disposition) of a chemical entity.
PhysicalDescriptor
A stereochemical descriptor is a chemical descriptor which describes some aspect of the three dimensional structure of a chemical entity.
StereochemicalDescriptor
an isomeric SMILES descriptor is a SMILES descriptor that written with isotopic and chiral specifications.
IsomericSMILESDescriptor
SStereochemicalDescriptor
A positional descriptor is a chemical descriptor which describes some aspect of the position, or location of a chemical entity, or of the relative parts of a chemical entity with respct to one another.
PositionalDescriptor
A molecular formula is a structure descriptor which identifies each constituent element by its chemical symbol and indicates the number of atoms of each element found in each discrete molecule of that compound.
MolecularFormula
An information entity about a molecular entity which serves to name that molecular entity.
MolecularEntityName
A preferred name is a molecular entity name which is preferred, or recommended, for usage in textual annotations referring to that molecular entity.
PreferredName
The sum of the squared atom degrees of all heavy atoms.
ZagrebIndex
PlusMinusStereochemicalDescriptor
PlusStereochemicalDescriptor
MinusStereochemicalDescriptor
DLStereochemicalDescriptor
DStereochemicalDescriptor
LStereochemicalDescriptor
A chemical connectivity table is a structure descriptor which consists of a connection table representing bonds between atoms in a molecular entity.
ChemicalConnectivityTable
An aromaticity descriptor is a chemical descriptor which indicates the aromaticity of a molecular entity.
AromaticityDescriptor
melt mass flow rate
File
MeltMassFlowRate
A MOLfile is a file which contains a MOLfile encoding of a chemical structure representation. It is the concretization of a MOLfile descriptor.
MOLfile
InChIKey
A dimensional extent descriptor is a physical property descriptor which describes some measurable length, area or volume aspect of a chemical entity.
DimensionalExtentDescriptor
An identifying descriptor is a chemical descriptor which provides an identifier for the chemical entity it is about, which in most cases should aim to be unique and easy to use as an unambiguous reference for the chemical entity.
IdentifyingDescriptor
A bond order descriptor is a descriptor associated with a bond in a chemical entity which indicates the order of the bond (single, double or triple).
BondOrderDescriptor
A Quantitative Structure Activity Relationship (QSAR) descriptor is a chemical descriptor which gives a numeric, quantitative value which is believed to be associated with some aspect of the chemical or biological activity of the chemical entity.
NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community.
QSARDescriptor
A functional group descriptor is a structural descriptor which describes specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules.
FunctionalGroupDescriptor
The (integer) number of neutrons in the atoms nucleus.
NeutronCount
The (integer) number of protons in the atoms nucleus.
ProtonCount
Descriptors which show the relationship between two ligands attached to separate atoms that are connected by a double bond or are contained in a ring. The two ligands are said to be located cis to each other if they lie on the same side of a plane. If they are on opposite sides, their relative position is described as trans. The appropriate reference plane of a double bond is perpendicular to that of the relevant s-bonds and passes through the double bond.[source:IUPAC Gold Book - http://goldbook.iupac.org/C01092.html]
CisMinustransStereochemicalDescriptor
CisStereochemicalDescriptor
TransStereochemicalDescriptor
MassDescriptor
AtomicMassDescriptor
A structural descriptor is a chemical descriptor which is about some aspect of the molecular structure (composition) of a chemical entity.
StructuralDescriptor
ElectronicDescriptor
The mass of a molecule calculated according to some assumption about the isotopic identity of the atoms constituting it.
MolecularMassDescriptor
The integer number of non-H substituents of an atom.
AtomicDegree
A topological descriptor is a chemical descriptor which pertains to spatial properties of a geometric object that are preserved under continuous deformations of objects, for example, deformations that involve stretching.
TopologicalDescriptor
A geometric descriptor is a descriptor that concerns information about size, shape, and relative position.
GeometricDescriptor
ChargeDelocalizationDescriptor
A hybridization descriptor is a chemical descriptor that is about the hybridization of atomic orbitals in a molecular entity.
HybridizationDescriptor
Atomic valence is an atomic descriptor that specifies the maximum number of univalent atoms (originally hydrogen or chlorine atoms) which may combine with an atom of the element under consideration, or with a fragment, or for which an atom of this element can be substituted [source: IUPAC Gold Book - http://goldbook.iupac.org/V06588.html]
AtomicValence
An atomic hardness descriptor is an atomic descriptor that estimates the difference between the ionization potential and the electron affinity of a given atom.
AtomicHardnessDescriptor
An atomic softness descriptor is an atomic descriptor which is about the charge delocalizing ability of a given atom.
AtomicSoftnessDescriptor
A molecular QSAR descriptor is a OSAR descriptor which gives a quantitative value to some aspect of a molecular entity.
MolecularQSARDescriptor
The cycle basis of a molecular structure is the smallest set of cycles (closed paths) formed in the graph representation of the structure, from which all other cycles can be computed.
CycleBasis
A systematic name is a molecular entity name which is formulated systematically from the structure of the molecular entity.
SystematicName
An IUPAC name is a systematic name which is formulated according to the rules and recommendations for chemical nomenclature set out by the International Union of Pure and Applied Chemistry (IUPAC).
IUPACName
A trivial name is a molecular entity name that is in common public use and may not be related to the structure of the molecular entity.
TrivialName
The fused cycles in a molecular structure are those cycles from the cycle basis which share at least one bond.
FusedCycles
An atomic QSAR descriptor is a QSAR descriptor which gives a quantitative value to some aspect of an atom which is part of a molecular entity.
AtomicQSARDescriptor
An InChI descriptor is a structure descriptor which conforms to the InChI format specification.
InChIDescriptor
A MOLfile descriptor is a structure descriptor which conforms to the MOLfile format specification.
MOLfileDescriptor
An atomic connectivity index is an atomic descriptor that is a measure of atomic connectivity, which can take various forms (e.g. zero-order, or first-order).
AtomicConnectivityIndex
Half the sum of all the distance matrix entries, topological index of atom-atom distances.
WienerPathNumber
The formal charge gives the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity. The formal charge of any atom in a molecule can be calculated by the following equation: FC = number of valence electrons of the atom in isolation (atom in ground state) - number of non-bonding electrons on this atom in the molecule - half the total number of electrons shared in covalent bonds with other atoms in the molecule. [source:wikipedia]
FormalChargeDescriptor
A partial charge descriptor gives the charge with an absolute value of less than one elementary charge unit (that is, smaller than the charge of the electron). [source:wikipedia]
PartialChargeDescriptor
An electronegativity descriptor is a chemical descriptor that is about the electronegativity quality of an atom.
ElectronegativityDescriptor
A chemical descriptor is a data item (quantity or value) about a chemical entity that conforms to a specification for how it is calculated, measured or recorded.
ChemicalDescriptor
A bond multiplicity descriptor is a chemical descriptor that in primitive cases is defined as half of the difference between the number of bonding and antibonding electrons in a particular system, but may also be defined with relation to the strength of a single bond.
BondMultiplicityDescriptor
A charge descriptor is a chemical descriptor which indicates the charge of a chemical entity.
ChargeDescriptor
A bond length descriptor is a dimensional extent descriptor which gives the measured or predicted (idealised) length of an atom to atom bond within a chemical entity.
BondLengthDescriptor
ConstitutionalDescriptor
Half the sum of all the distance matrix entries with a value of 3
WienerPolarityNumberDescriptor
PubChemCompoundIdentifier(CID)
PubChemSubstanceIdentifier(SID)
TopologicalSurfaceAreaDescriptor
a generic SMILES descriptor is a SMILES descriptor that denotes only the labeled molecular graph (i.e. atoms and bonds, but no chiral or isotopic information).
generic SMILES descriptor
GenericSMILESDescriptor
topological polar surface area descriptor
TopologicalPolarSurfaceAreaDescriptor
charge weighted partial negative surface area
ChargeWeightedPartialNegativeSurfaceArea
DPSAMinus1
DPSAMinus2
DPSAMinus3
FPSAMinus1
FPSAMinus2
FPSAMinus3
FNSAMinus1
FNSAMinus2
FNSAMinus3
PPSA-1 * total molecular surface area / 1000
WPSAMinus1
PPSA-2 * total molecular surface area /1000
WPSAMinus2
PPSA-3 * total molecular surface area /1000
WPSAMinus3
PNSA-1 * total molecular surface area /1000
WNSAMinus1
PNSA-2 * total molecular surface area /1000
WNSAMinus2
PNSA-3 * total molecular surface area /1000
WNSAMinus3
most positive charge / total positive charge
RelativePositiveCharge
most negative charge / total negative charge
RelativeNegativeCharge
RelativePositiveChargeSurfaceArea
RelativeNegativeChargeSurfaceArea
sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2
THSA
sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2
TPSA
RHSA
RPSA
CollectionOf3DCoordinates
CollectionOf3DAtomicCoordinates
Sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens)
molecular polarizability
MolecularPolarizability
fragment complexity descriptor
FragmentComplexityDescriptor
vertex adjacency matrix descriptor
VertexAdjacencyMatrixDescriptor
A measure of the anisotropy in a molecule (as per Petitjean et al)
Petitjean Topological Shape Index
PetitjeanTopologicalShapeIndex
A measure of the anisotropy in a molecule (as per Bath et al)
Petitjean Geometric Shape Index
PetitjeanGeometricShapeIndex
the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph. The distance is obtained from the distance matrix as the count of edges between the two vertices. If r i is the largest matrix entry in row i of the distance matrix D, then the radius is defined as the smallest of the r i . The graph diameter D is defined as the largest vertex eccentricity in the graph. Petitjean Number is the value of ( diameter - radius ) diameter .
Petitjean number
PetitjeanNumber
A measure of the anisotropy in a molecule
Petitjean Shape Index
PetitjeanShapeIndex
A LogP descriptor based on the atom-type method described in Wang, R., Fu, Y., and Lai, L.. A New Atom-Additive Method for Calculating Partition Coefficients, Journal of Chemical Information and Computer Sciences. vol. 37. 1997, pp. 615-621.
XLogP descriptor
XLogPDescriptor
A LogP descriptor based on a simple equation using the number of carbons and hetero atoms.
MLogP descriptor
MLogPDescriptor
maximal ratio of length to breadth descriptor
MaximalRatioOfLengthToBreadthDescriptor
A descriptor characterizing the ratio of the length to the breadth of a given entity.
ratio of length to breadth descriptor
RatioOfLengthToBreadthDescriptor
minimal ratio of length to breadth descriptor
MinimalRatioOfLengthToBreadthDescriptor
An ionization energy descriptor is a descriptor that describes the minimum amount of energy required to remove an electron (to an infinite distance) from an atom or molecule in a gaseous state. X + energy → X+ + e- The term 'ionization potential' has historically been used but is now no longer recommended.
ionization energy descriptor
IonizationEnergyDescriptor
eccentric connectivity index descriptor
EccentricConnectivityIndexDescriptor
equilibrium constant
EquilibriumConstant
the acid dissociation constant, Ka, is quantitative measure of the strength of an acid in solution. It is the equilibrium constant for a chemical reaction known as dissociation in the context of acid-base reactions.
acid dissociation constant
AcidDissociationConstant
the logarithmic measure of the acid dissociation constant (Ka)
pKa
PKa
A molecular weight descriptor calculated by a relevant module of the Pipeline Pilot software tool.
molecular weight calculated by pipeline pilot
MolecularWeightCalculatedByPipelinePilot
An absolute SMILES descriptor is an isomeric SMILES descriptor that is produced using a canonicalization algorithm.
absolute SMILES descriptor
AbsoluteSMILESDescriptor
a count descriptor that denotes the number of tautomers.
tautomer count
TautomerCount
stereocenter count
StereocenterCount
atom stereocenter count
AtomStereocenterCount
defined atom stereocenter count
DefinedAtomStereocenterCount
A formation energy descriptor is an energetic descriptor which gives the value for the energy of formation of a chemical entity.
FormationEnergyDescriptor
A solvation energy descriptor is a chemical descriptor which gives the value for the energy of dissolving a particular chemical entity in a solvent.
SolvationEnergyDescriptor
A count descriptor is a chemical descriptor which is calculated by counting the number of features of a certain kind which are present in the chemical entity.
CountDescriptor
A dissociation energy descriptor is an energetic descriptor which gives a value for the dissociation energy for a chemical entity.
DissociationEnergyDescriptor
undefined atom stereocenter count
UndefinedAtomStereocenterCount
bond stereocenter count
BondStereocenterCount
defined bond stereocenter count
DefinedBondStereocenterCount
undefined bond stereocenter count
UndefinedBondStereocenterCount
The mass of a molecule calculated using the average mass of each element weighted for its natural isotopic abundance. E.g., Carbon has two natural isotopes 12 and 13 with relative abundances of 98.9% and 1.1% to yield an average mass of 12.011 g/mol
average molecular weight descriptor
AverageMolecularWeightDescriptor
an exact mass descriptor corresponds to the mass of the most intense molecule/ion peak in an MS spec, and when calculated denotes the mass of an ion or a molecule containing most likely isotopic composition for a single random molecule.
exact mass descriptor
ExactMassDescriptor
The mass of a molecule calculated using the mass of the most abundant isotope of each element. E.g., Carbon has a monoisotopic mass of 12.000 g/mol.
monoisotopic mass descriptor
MonoisotopicMassDescriptor
A complexity descriptor denotes the how complicated a structure is, seen from both the point of view of the elements contained and its structural features .
complexity descriptor
ComplexityDescriptor
The integer number of atoms in a pi-orbital system.
PiMinussystemSize
Bond dissociation Gibbs energy descriptor captures the Gibbs energy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.
bond dissociation Gibbs energy descriptor
BondDissociationGibbsEnergyDescriptor
The molecular entity solvation Gibbs energy descriptor reflects the Gibbs energy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
SolvationGibbsEnergyDescriptor
BondChargeDensityDescriptor
A surface area descriptor is a descriptor which describes a measure or calculation of the surface area of a chemical entity.
SurfaceAreaDescriptor
A charge density descriptor is a chemical entity descriptor which indicates the distribution of the electric charge over the volume of the chemical entity.
ChargeDensityDescriptor
A descriptor that provides the integer count of aromatic atoms in a given molecular entity.
AromaticAtomCount
A descriptor that specifies the integer count of bonds in a given molecular entity.
BondCount
PubChem conformer identifier
PubChemConformerIdentifier
A bond aromaticity descriptor is an aromaticity descriptor associated with a bond within a chemical entity which indicates whether that bond belongs to an aromatic system.
BondAromaticityDescriptor
The formation Gibbs energy descriptor captures the Gibbs energy associated with the formation of a molecular entity, relative to the standard state of constituent atoms. This can be measured, calculated in vacuo, or calculated with respect to a specific solvent, at a particular temperature and pressure. When calculated, the formation Gibbs energy value depends on the molecular conformation.
FormationGibbsEnergyDescriptor
The largest aliphatic chain size descriptor is a count descriptor that gives the integer length (number of atoms) in the largest unbranched chain of atoms that does not contain aromatic atoms, within a given molecular entity.
SizeOfLargestAliphaticChain
Molecular entity formation enthaply descriptor captures the enthalpy associated with the formation of the molecular entity in question, relative to the standard state of constituent atoms. This could be measured or calculated in vacuo or in a specific Solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
FormationEnthalpyDescriptor
A volume descriptor is a descriptor which describes a measure or calculation of the volume of a chemical entity.
VolumeDescriptor
A descriptor that provides the integer count of aromatic bonds in a given molecular entity.
AromaticBondCount
A descriptor that reflects the integer number of hydrogen bond donors in a given molecular entity, as determined by a given method. In highly simplified terms, this is usually the count of all negatively or partially negatively charged heteroatoms (e.g. alcohol oxygen) that have covalently attached to them partially positively charged hydrogen atoms that are capable of participating in a hydrogen bond.
HydrogenBondDonorCount
A descriptor that reflects the integer number of hydrogen bond acceptors in a given molecular entity, as determined by a given method. In highly simplified terms, this is usually the count of all negatively or partially negatively charged heteroatoms (e.g. alcohol oxygen) capable of accepting a hydrogen bond.
HydrogenBondAcceptorCount
The largest chain size descriptor is a count descriptor that gives the integer length (number of atoms) in the largest chain in a molecular entity.
SizeOfLargestChain
The molecular entity solvation entropy descriptor reflects the entropy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
SolvationEntropyDescriptor
The molecular entity solvation enthalpy descriptor reflects the enthalpy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
SolvationEnthalpyDescriptor
The logarithm of octanol-water partition coefficient, which is the ratio of the molecules dissolved in octanol to those dissolved in pure un-ionized water upon mixture equilibration. This can be measured or predicted. The value is dimensionless. May depend on molecular conformation when computed.
LogPDescriptor
Bond dissociation enthalpy descriptor captures the enthalpy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.
BondDissociationEnthalpyDescriptor
Chemical substance refractive index descriptor is a unitless descriptor that specifies the ratio of the speed of light in vacuum to that in a given chemical substance. [IUPAC: http://goldbook.iupac.org/R05240.html]
RefractiveIndexDescriptor
a bond count that denotes the integer number of rotors in the molecule, generally single bonds torsion around which produces non-identical geometric molecular configurations.
RotatableBondCount
Melting point descriptor specifies the temperature at which a chemical substance undergoes the transition from solid to liquid state under standard conditions.
MeltingPointDescriptor
The boiling point descriptor indicates the temperature at which a chemical substance undergoes a state transition from liquid to gas, at standard conditions.
BoilingPointDescriptor
Molecular entity formaiton entropy descriptor captures the entropy associated with the formation of the molecular entity in question, relative to the standard state of constituent atoms. This could be measured or calculated in vacuo or in a specific Solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
FormationEntropyDescriptor
The relative permittivity descriptor specifies the ratio of the electric field strength in vacuum to that in a given medium. It was formerly called the dielectric constant. [IUPAC Gold Book: http://goldbook.iupac.org/R05273.html ]
RelativePermittivityDescriptor
A descriptor that specifies the integer count of atoms in a given molecular entity.
AtomCount
AtomicChargeDensityDescriptor
Bond dissociation entropy descriptor captures the entropy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.
BondDissociationEntropyDescriptor
Chemical substance constitutes matter of constant composition, that may contain a collection of molecular entities. [IUPAC: http://goldbook.iupac.org/C01039.html]
ChemicalSubstance
A count descriptor that takes into account flexibility of rings and rotatable bonds.
effective rotor count
EffectiveRotorCount
A charge descriptor that gives the total charge for a molecule
total formal charge descriptor
TotalFormalChargeDescriptor
conformer volume descriptor
ConformerVolumeDescriptor
a count of the number of amino acid residues.
AminoAcidCount
AlanineCount
ArginineCount
AsparagineCount
AspartateCount
CysteineCount
PhenylalanineCount
GlutamateCount
GlutamineCount
GlycineCount
The number of covalent units (molecule / ion) in a chemical structure
covalent unit count
CovalentUnitCount
HistidineCount
IsoleucineCount
ProlineCount
LeucineCount
LysineCount
MethionineCount
SerineCount
ThreonineCount
TyrosineCount
ValineCount
TryptophanCount
A descriptor that the energy of the highest occupied 'molecular' orbital of the chemical entity.
Highest Occupied Molecular Orbital Energy
HighestOccupiedMolecularOrbitalEnergy
A descriptor that the energy of the lowest unoccupied 'molecular' orbital of the chemical entity.
Lowest Unoccupied Molecular Orbital Energy
LowestUnoccupiedMolecularOrbitalEnergy
A descriptor that specifies the integer count of acidic groups in a given molecular entity.
AcidicGroupCount
A descriptor that specifies the integer count of basic groups in a given molecular entity.
BasicGroupCount
The ALogP descriptor described by Ghose and Crippen in 1986 and 1987.
ALogP descriptor
ALogPDescriptor
hybridization descriptor (VSEPR)
HybridizationDescriptor(VSEPR)
inductive atomic hardness
InductiveAtomicHardness
TPSA (fragments)
TPSA(fragments)
VABC volume descriptor
VABCVolumeDescriptor
heavy atom count
HeavyAtomCount
The sum of all atoms enriched with respect to a particular atom isotope
isotope atom count
IsotopeAtomCount
PubChem Identifier
PubChemIdentifier
GenBank Protein Identifier
GenBankProteinIdentifier
GenBank Nucleotide Identifier
GenBankNucleotideIdentifier
ALogPCalculatedByPipelinePilot
PolarSurfaceAreaDescriptor
polar surface area descriptor calculated by Pipeline Pilot
PolarSurfaceAreaDescriptorCalculatedByPipelinePilot
hydrogen bond acceptor count calculated by pipeline pilot
HydrogenBondAcceptorCountCalculatedByPipelinePilot
hydrogen bond donor count calculated by pipeline pilot
HydrogenBondDonorCountCalculatedByPipelinePilot
rotatable bond count calculated by pipeline pilot
RotatableBondCountCalculatedByPipelinePilot
Number of properties defined in Lipinski’s Rule of 5 (RO5) that the compound fails. Conditions which violate the RO5 are: Molecular weight>=500 AlogP>=5 HBD>=5 HBA>=10
RuleOfFiveViolationsDescriptor
rule of five violations calculated by pipeline pilot
RuleOfFiveViolationsCalculatedByPipelinePilot
Rule of 3 passes. It is suggested that compounds that pass all these criteria are more likely to be hits in fragment screening. molecular weight <=300, number of hydrogen bond donors <=3, number of hydrogen bond acceptors <=3 AlogP <=3. RTB <=3 PSA<=60
RuleOfThreePassesDescriptor
rule of three passes calculated by pipeline pilot
RuleOfThreePassesCalculatedByPipelinePilot
MedChem Friendly These are functional groups that may not be desirable from a medicinal chemistry perspective. For example reactive groups will be flagged as “N” (not MedChem Friendly). Molecules which do not contain any of these groups will be flagged as “Y” (MedChem Friendly). The groups are defined by the following list of SMARTS: [N+]([O-])=O [C;!R](-[C;!R]=O)=[C;!R] C(-N)=S P O-N=C OS(=O)=O O1-CC-O-C-1 C(-N)=C [C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2] OC1OCC(O)C1 C=N-C(-O) [N;H]-[C;H]-[N;H] [C;!R]=[C;!R]-N-[C;D1&H3,D2&H2,D3&H1,D4] [S;!R]-[C;!R]-[O;!R] [O;D2]-[C;!H0](([F,Br,I,Cl])([F,Br,I,Cl])([!F,!Br,!I,!Cl])) CC([O;!R])([O;!R]) C1-C-O1 C(=O)-S-C(=S) [S;H] SC#N
MedchemFriendlyDescriptor
medchem friendly descriptor calculated by pipeline pilot
MedchemFriendlyDescriptorCalculatedByPipelinePilot
logP calculated by ACD/Labs PhysChem software
LogPCalculatedByACDLabsPhysChemSoftware
octanol-water distribution coefficient calculated at a given pH.
LogDDescriptor
ACD_LogD(pH7.4) Distribution Coefficient calculated at pH7.4
logD calculated at pH 7.4 by ACD/Labs PhysChem software
most acidic pKa calculated by ACD/Labs PhysChem software library
MostAcidicPKaCalculatedByACDLabsPhysChemSoftwareLibrary
most basic pKa calculated by ACD/Labs PhysChem software library
MostBasicPKaCalculatedByACDLabsPhysChemSoftwareLibrary
Molecular Species is a description of the predominant form of the molecule at pH7.4.
MolecularSpeciesAtPH7.4Descriptor
These are defined according to the definitions: Acid(A) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa<8.5 Bas (B) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa>8.5 Neutral (N) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa<8.5 Zwitterion (ZW) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa>8.5
molecular species at pH 7.4 calculated by ACD/Labs PhysChem software
molecular weight calculated by the pubchem software library
MolecularWeightCalculatedByThePubchemSoftwareLibrary
molecular formula calculated by the pubchem software library
MolecularFormulaCalculatedByThePubchemSoftwareLibrary
total formal charge calculated by the pubchem software library
TotalFormalChargeCalculatedByThePubchemSoftwareLibrary
monoisotopic mass calculated by the pubchem software library
MonoisotopicMassCalculatedByThePubchemSoftwareLibrary
exact mass calculated by pubchem software library
ExactMassCalculatedByPubchemSoftwareLibrary
A molecular entity name that has been supplied by a depositor to the PubChem database. This is just a molecular entity name with additional provenance associated.
pubchem depositor-supplied molecular entity name
PubchemDepositorMinussuppliedMolecularEntityName
Octanol-water distribution coefficient calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01.
logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01
Hydrogen bond acceptor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
hydrogen bond acceptor count calculated by ACD/Labs PhysChem software library version 12.01
Hydrogen bond donor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
hydrogen bond donor count calculated by ACD/Labs PhysChem software library version 12.01
The boiling point of a substance at 760 mmHg pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
Boiling point at 760 mmHg pressure calculated by ACD/Labs PhysChem software library version 12.01
Number of freely rotating bonds that has been calculated by ACD/Labs PhysChem software library version 12.01.
number of freely rotating bonds calculated by ACD/Labs PhysChem software library version 12.01
Polar surface area that has been calculated by ACD/Labs PhysChem software library version 12.01.
polar surface area calculated by ACD/Labs PhysChem software library version 12.01
The molecular weight for the free base chemical structure matching this chemical structure.
molecular weight of the corresponding free base
MolecularWeightOfTheCorrespondingFreeBase
Molar refractivity that has been calculated by ACD/Labs PhysChem software library version 12.01.
molar refractivity calculated by ACD/Labs PhysChem software library version 12.01
Index of refraction that has been calculated by ACD/Labs PhysChem software library version 12.01.
index of refraction calculated by ACD/Labs PhysChem software library version 12.01
Molar volume that has been calculated by ACD/Labs PhysChem software library version 12.01.
molar volume calculated by ACD/Labs PhysChem software library version 12.01
Density that has been calculated by ACD/Labs PhysChem software library version 12.01.
density calculated by ACD/Labs PhysChem software library version 12.01
Flash point that has been calculated by ACD/Labs PhysChem software library version 12.01.
flash point calculated by ACD/Labs PhysChem software library version 12.01
Enthalpy of vaporization that has been calculated by ACD/Labs PhysChem software library version 12.01.
enthalpy of vaporization calculated by ACD/Labs PhysChem software library version 12.01
Vapour pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
vapour pressure calculated by ACD/Labs PhysChem software library version 12.01
Organic carbon adsorption coefficient at pH 5.5 that has been calculated by ACD/Labs PhysChem software library version 12.01.
organic carbon adsorption coefficient at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
Organic carbon adsorption coefficient at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
organic carbon adsorption coefficient at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
bioconcentration factor at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
bioconcentration factor at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
Number of rule of five violations for a chemical structure that has been calculated by ACD/Labs PhysChem software library version 12.01.
number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01
Surface tension, in dyne per centimetre, that has been calculated by ACD/Labs PhysChem software library version 12.01.
surface tension calculated by ACD/Labs PhysChem software library version 12.01
covalent unit count generated by pubchem software library
CovalentUnitCountGeneratedByPubchemSoftwareLibrary
defined atom stereocenter count generated by the pubchem software library
DefinedAtomStereocenterCountGeneratedByThePubchemSoftwareLibrary
defined bond stereocenter count generated by pubchem software library
DefinedBondStereocenterCountGeneratedByPubchemSoftwareLibrary
isotope atom count generated by pubchem software library
IsotopeAtomCountGeneratedByPubchemSoftwareLibrary
heavy atom count generated by pubchem software library
HeavyAtomCountGeneratedByPubchemSoftwareLibrary
undefined atom stereocenter count generated by the pubchem software library
UndefinedAtomStereocenterCountGeneratedByThePubchemSoftwareLibrary
undefined bond stereocenter count generated by the pubchem software library
UndefinedBondStereocenterCountGeneratedByThePubchemSoftwareLibrary
canonical smiles generated by OEChem
CanonicalSmilesGeneratedByOEChem
isomeric SMILES generated by OEChem
IsomericSMILESGeneratedByOEChem
A descriptor that specifies the integer count of cycles in a given molecular entity.
cycle count
CycleCount
A descriptor that specifies the integer count of aromatic cycles in a given molecular entity.
aromatic cycle count
AromaticCycleCount
IUPAC Name generated by LexiChem
IUPACNameGeneratedByLexiChem
hydrogen bond donor count calculated by cactvs
HydrogenBondDonorCountCalculatedByCactvs
hydrogen bond acceptor count calculated by cactvs
HydrogenBondAcceptorCountCalculatedByCactvs
rotatable bond count calculated by cactvs
RotatableBondCountCalculatedByCactvs
structure complexity calculated by cactvs
StructureComplexityCalculatedByCactvs
tautomer count calculated by cactvs
TautomerCountCalculatedByCactvs
TPSA calculated by cactvs
TPSACalculatedByCactvs
xlogp3 calculated by the xlogp3 software
Xlogp3CalculatedByTheXlogp3Software
InChI calculated by library version 1.0.4
InChICalculatedByLibraryVersion1.0.4
InChIKey generated by software version 1.0.4
InChIKeyGeneratedBySoftwareVersion1.0.4
A chemical graph is a structural descriptor in which the connectivity and constitution of the chemical entity are described in terms of a mathematical graph, usually with atoms as vertices and bonds as edges, but other variants exist.
ChemicalGraph
ChemSpiderIdentifier
DrugBankIdentifier
ChEBIIdentifier
Database identifier used by Human Metabolome Database.
HMDBIdentifier
KEGGIdentifier
ReactomeIdentifier
Identifier used by the ChEMBL database for compounds, assays, target, etc.
ChEMBLIdentifier
A descriptor of the ratio of the amount of a given chemical substance adsorbed per unit weight of organic carbon in soil or sediment to the concentration of the chemical substance in solution at equilibrium.
OrganicCarbonAdsorptionDescriptor
A descriptor of the ratio of the concentration of a chemical substance in an organism immersed in water to that in the surrounding water at equilibrium.
BioconcentrationFactorDescriptor
A descriptor of the volume occupied by one mole of the given substance at a given temperature and pressure.
MolarVolumeDescriptor
A descriptor of the density of a given substance at a given temperature and pressure.
DensityDescriptor
A descriptor of the flash point of a substance at a given pressure. The flash point is the minimum temperature at which a mixture of the substance with air can be ignited, within its explosive range.
FlashPointDescriptor
A descriptor of the energy taken in by a chemical substance on vaporization at a given temperature and pressure.
EnthalpyOfVaporizationDescriptor
A descriptor of the pressure exerted by the vapour phase of a chemical substance on its condensed phase at a given temperature and pressure.
VapourPressureDescriptor
A descriptor of the disposition of a portion of liquid to resist a force.
SurfaceTensionDescriptor
The number of structural alerts, that is, unwanted features as defined according to the procedure followed in Brenk et al., 2008. Brenk R, et al. Lessons learnt from assembling screening libraries for drug discovery for neglected diseases. Chem Med Chem. 2008;3:435–444.
structural alert count
StructuralAlertCount
A descriptor which gives a quantitative estimate of drug likeness according to the procedure outlined in Bickerton et al., 2012. http://www.ncbi.nlm.nih.gov/pubmed/22270643 Nat Chem. 2012 Jan 24;4(2):90-8. doi: 10.1038/nchem.1243. Quantifying the chemical beauty of drugs. Bickerton GR, Paolini GV, Besnard J, Muresan S, Hopkins AL.
weighted quantitative estimate of drug-likeness
WeightedQuantitativeEstimateOfDrugMinuslikeness
A descriptor that indicates the temperature at which a chemical substance undergoes a state transition from gas or liquid to solid, under standard conditions.
freezing point descriptor
FreezingPointDescriptor
Henry's law, formulated by William Henry in 1803, states "At a constant temperature, the amount of a given gas that dissolves in a given type and volume of liquid is directly proportional to the partial pressure of that gas in equilibrium with that liquid." Henry's law can be put into mathematical terms (at constant temperature) as p = kHc where p is the partial pressure of the solute in the gas above the solution, c is the concentration of the solute and kH is a constant with the dimensions of pressure divided by concentration. The constant, known as the Henry's law constant, depends on the solute, the solvent and the temperature.
Henry's Law constant
Henry'sLawConstant
A physical descriptor for the rate constant of a reaction of a chemical entity with OH. This is used to describe the atmospheric behaviour (i.e. stability) of the entity.
atmospheric OH rate constant
AtmosphericOHRateConstant
A physical descriptor for the upper explosive limit of the entity in air as a percentage by volume at room temperature.
upper explosive limit descriptor
UpperExplosiveLimitDescriptor
A physical descriptor for the lower explosive limit in air as a percentage by volume at room temperature
lower explosive limit descriptor
LowerExplosiveLimitDescriptor
A physical descriptor for the minimum explosive concentration.
minimum explosive concentration descriptor
MinimumExplosiveConcentrationDescriptor
A physical descriptor of the ratio of the density of chemical substance to the density of a reference substance. The reference substance is usually water for liquids or air for gases.
specific gravity descriptor
SpecificGravityDescriptor
A descriptor of the relative density of gases referenced to air as 1, which indicates how many times a gas is heavier than air at the same temperature.
relative density descriptor
RelativeDensityDescriptor
A descriptor of the density of a vapour in relation in that of hydrogen, defined as the mass of a certain volume of the given substance divided by the mass of the same volume of hydrogen.
vapor density descriptor
VaporDensityDescriptor
A physical descriptor for the lowest concentration of an odorant chemical entity that is perceivable by the human sense of smell.
odor detection threshold descriptor
OdorDetectionThresholdDescriptor
A physical descriptor which gives a measure of the acidity or basicity of an aqueous solution, defined as the decimal logarithm of the reciprocal of the hydrogen ion activity in a solution.
pH descriptor
PHDescriptor
A physical descriptor of the rate of evaporation of a liquid under standard conditions.
evaporation rate descriptor
EvaporationRateDescriptor
A physical descriptor of the lowest temperature at a substance will spontaneously ignite in a normal atmosphere without an external source of ignition.
autoignition temperature descriptor
AutoignitionTemperatureDescriptor
A physical descriptor for the time it takes for half of a portion of substance of a given type to decompose in soil under standard conditions.
soil half-life descriptor
SoilHalfMinuslifeDescriptor
Identifier used by the Chemical Abstracts Service database.
CASRegistryNumber
A seven-digit identifier for chemical substances for regulatory purposes within the European Union.
ECNumber
EINECSNo
EuropeanCommunityNumber
A descriptor that specifies the integer count of metal atoms in a given chemical entity.
metal atom count
MetalAtomCount
A descriptor that specifies the integer count of oxygen atoms in a given chemical entity.
oxygen atom count
OxygenAtomCount
An identifying descriptor which is used within a particular database system to identify a chemical system.
ChemicalDatabaseIdentifier
A preferred name in ChemSpider by virtue of having been validated by a curator.
ChemSpiderValidatedSynonym
A molecular entity name in the ChemSpider database which has not been validated by a curator.
ChemSpiderUnvalidatedSynonym
A chemical database identifier which has been validated by a curator.
ValidatedChemicalDatabaseIdentifier
A ChemSpider validated synonym that has been identified as a title by the ChemSpider software.
ChemSpiderTitle
average molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01
monoisotopic molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01
A descriptor that describes the energy range in a solid where no electron states can exist. In graphs of the electron band structure of solids, the band gap generally refers to the energy difference (in electron volts) between the top of the valence band and the bottom of the conduction band in insulators and semiconductors. [http://en.wikipedia.org/wiki/Band_gap]
energy band gap
EnergyBandGap
A descriptor describing the mass of the metal element component of a composite substance.
metal element mass descriptor
MetalElementMassDescriptor
Molecular formula for a chemical structure as calculated by ACD/Labs PhysChem software library version 12.01.
molecular formula calculated by ACD/Labs PhysChem software library version 12.01
The ratio of a dissolved substance in a two-phase system, giving a measure of the difference in solubility of the substance in the two phases.
partition coefficient
PartitionCoefficient
NumericChemicalDescriptor
TextualChemicalDescriptor
ChemicalSubstanceDescriptor
Descriptor that returns the group in the periodic table of a given atom.
group of an atom
GroupOfAnAtom
An InChI-like descriptor for nanomaterials.
NInChIDescriptor
TUCAN is an identifier based on a canonicalization and serialization algorithm that is independent of domain-specific concepts of structure and bonding.
TUCANDescriptor
The spatial arrangement of the atoms of a chiral molecular entity (or group) and its stereochemical description e.g. R or S.
absolute configuration stereochemical descriptor
AbsoluteConfigurationStereochemicalDescriptor
The configuration of any stereogenic (asymmetric) centre with respect to any other stereogenic centre contained within the same molecular entity. Unlike absolute configuration, relative configuration is reflection-invariant. Relative configuration, distinguishing diastereoisomers, may be denoted by the configurational descriptors R*, R* (or l) and R*, S* (or u) meaning, respectively, that the two centres have identical or opposite configurations. For molecules with more than two asymmetric centres the prefix rel- may be used in front of the name of one enantiomer where R and S have been used. If any centres have known absolute configuration then only R* and S* can be used for the relative configuration.
relative configuration stereochemical descriptor
RelativeConfigurationStereochemicalDescriptor
A molecular entity name that represents the name of a molecular structure determined by the naming algorithms developed by ACD/Labs.
ACD/Labs index name
ACDLabsIndexName
An InChI descriptor that is not the standard and that is created with the fixedH layer option. The fixedH layer is appended to the standard InChI and lists the exact position of the tautomeric hydrogen atoms. It is useful when one wants to represent a specific tautomer of a given structure, because if the InChIs for the tautomers were created without the fixedH layer option, the normalization performed by the InChI generation program would result in these InChIs being identical.
InChI with fixedH layer
InChIWithFixedHLayer
A ChEBI name is a preferred name annotated by the ChEBI database. The ChEBI name has the additional feature that it is unique within the ChEBI dataset.
ChEBIName
DrugTradeName
International Non-proprietary Name, defined by the WHO.
InternationalNonMinusproprietaryName
Identifier used by the USA Food and Drug Administration.
UniqueIngredientIdentifier
Identifier used by the LipidMaps database, http://www.lipidmaps.org/.
LipidMapsIdentifier
Identifier used by the Cancer Chemotherapy National Service Center.
NationalServiceCenterNumber
Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).
RTECSIdentifier
Identifier used by the European Registry of Materials (https://nanocommons.github.io/identifiers/).
European Registry of Materials identifier
EuropeanRegistryOfMaterialsIdentifier
SwissLipids identifier
SwissLipidsIdentifier
MolMeDB identifier
MolMeDBIdentifier
PDB ligand identifier
PDBLigandIdentifier
PDB structure identifier
PDBStructureIdentifier
number of rule of five violations calculated by RDKit software library version 2015_09_2
hydrogen bond acceptor count calculated by RDKit software library version 2015_09_2
hydrogen bond donor count calculated by RDKit software library version 2015_09_2
logP descriptor calculated by RDKit software library version 2015_09_2
molecular formula calculated by RDKit software library version 2015_09_2
average molecular weight calculated by RDKit software library version 2015_09_2
total polar surface area calculated by RDKit software library version 2015_09_2
Descriptor that calculates the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens).
BondPolarizabilities
Oxidation state is an atomic descriptor that gives the degree of oxidation of an atom in terms of counting electrons. The higher the oxidation state (OS) of a given atom, the greater is its degree of oxidation. [source: IUPAC Gold Book - https://doi.org/10.1351/goldbook.O04365]
OxidationState
A connectivity SMILES descriptor is a SMILES descriptor that does not include any stereochemical or isotopic information.
ConnectivitySMILESDescriptor
Eigenvalue based descriptor noted for its utility in chemical diversity.
BCUT
Descriptor that calculates bond-pi Partial charge of a bond by determining the difference the Partial Pi Charge on atoms A and B of a bond (based in Gasteiger Charge).
bond partial pi charge
BondPartialPiCharge
Descriptor that calculates bond-sigma Partial charge of a bond.
bond partial sigma charge
BondPartialSigmaCharge
Descriptor that calculates bond-total Partial charge of a bond.
bond partial total charge
BondPartialTotalCharge
Descriptor that calculates of bond-Polarizability of a bond by determining the difference the Sigma electronegativity on atoms A and B of a bond.
bond sigma electronegativity
BondSigmaElectronegativity
Descriptor based on the number of bonds on the shortest path between two atoms (topological distance).
This is the shortest distance between a pair of atoms in a graph, defined as the number of edges in the shortest path between the atom pair in the molecular graph.
bonds to Atom
BondsToAtom
Evluates the simple and valence chi chain descriptors (Kier and Hall) of orders 3, 4, 5, 6 and 7.
It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
chi chain indices
ChiChainIndices
Evluates the simple and valence chi cluster descriptors (Kier and Hall) of orders 3, 4,5 and 6.
chi cluster indices
ChiClusterIndices
Evaluates the Kier and Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7.
chi path indices
ChiPathIndices
Evaluates the Kier and Hall Chi path cluster indices of orders 4,5 and 6.
chi path-cluster indices
ChiPathMinusclusterIndices
Descriptor characterizing the mass distribution of the molecule.
gravitational index
GravitationalIndex
Descriptor characterizing the mass distribution of the molecule as the square or cube root of the gravitational index.
gravitational index (square and cube roots)
GravitationalIndex(squareAndCubeRoots)
Counts the number of acceptor field atoms for a carbonyl oxygen probe using force field based definition.
acceptor field atoms (Boehm,Klebe)
AcceptorFieldAtoms(Boehm,Klebe)
Descriptor that calculates the number of hydrogen bond acceptors (by Daylight).
SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
hydrogen bond acceptors (Daylight)
HydrogenBondAcceptors(Daylight)
Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe.
acceptors or donors field atoms (Boehm,Klebe)
AcceptorsOrDonorsFieldAtoms(Boehm,Klebe)
Counts the number of donor field atoms for an amino hydrogen probe.
donor field atoms (Boehm,Klebe)
DonorFieldAtoms(Boehm,Klebe)
Descriptor that calculates the number of hydrogen bond donors (by Daylight).
hydrogen bond donors (Daylight)
HydrogenBondDonors(Daylight)
Descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions.
proton belonging to an aromatic system
ProtonBelongingToAnAromaticSystem
Descriptor returns true if the protons is directly bonded to a pi system.
proton belonging to a pi-system
ProtonBelongingToAPiMinussystem
Counts the number of occurrences of the E-state fragments.
Kier Hall SMARTS
KierHallSMARTS
Evaluate molecular distance edge descriptors for C, N and O.
molecular distance edge
MolecularDistanceEdge
Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration.
moments of inertia
MomentsOfInertia
Descriptor that calculates total partial charges of an heavy atom.
partial total charge (MMFF94)
PartialTotalCharge(MMFF94)
Descriptor that returns the period in the periodic table of an atom belonging to an atom container.
period of an atom
PeriodOfAnAtom
Descriptor that check if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighboors of the atoms).
pi-contact of two atoms
PiMinuscontactOfTwoAtoms
Descriptor that calculates partial charges of an heavy atom and its protons based on Gasteiger Marsili (PEOE).
proton total partial charge
ProtonTotalPartialCharge
This is a mixed descriptor: topological, geometrical and electronic descriptor.
RDF proton descriptor
RDFProtonDescriptor
Descriptors are derived from pre-calculated quantum mechanical parameters by using the paramaters for amino acids and evaluating a set of 147 descriptors for peptide sequences.
{@cdk.cite BREN1995} {@cdk.cite BREN1997} {@cdk.cite WHITE2003}
TAE RECON descriptors for amino acid sequences
TAERECONDescriptorsForAminoAcidSequences
The weighted path (molecular ID) descriptors were described by Randic and they characterize molecular branching.
weighted path
WeightedPath
Holistic descriptors described by Todeschini et al.
Todeschini, R. and Gramatica, P.. New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design. 1998, pp. 355-380. Mixed descriptors: molecular size, shape, symmetry, and atom distribution and density. Uses 3D coordinates, PCA and it calculates 10 descriptors.
WHIM
The Moreau-Broto autocorrelation descriptors using partial charges.
Moreau-Broto Autocorrelation (charge) descriptors
The Moreau-Broto autocorrelation descriptors using atomic weight.
Moreau-Broto autocorrelation (mass) descriptors
The Moreau-Broto autocorrelation descriptors using polarizability.
Moreau-Broto autocorrelation (polarizability) descriptors
Characterizes the carbon connectivity in terms of hybridization
C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3, C4SP3
carbon types
CarbonTypes
Descriptor that calculates the carbon connectivity index (order 0).
carbon connectivity index (order 0)
CarbonConnectivityIndex(order0)
Descriptor that calculates atomic valence connectivity index (order 0).
valence connectivity index (order 0)
ValenceConnectivityIndex(order0)
Descriptor that calculates carbon valence connectivity index (order 0).
valence carbon connectivity index (order 0)
ValenceCarbonConnectivityIndex(order0)
Descriptor that calculates carbon connectivity index (order 1).
carbon connectivity index (order 1)
CarbonConnectivityIndex(order1)
Descriptor that calculates atomic valence connectivity index (order 1).
valence connectivity index (order 1)
ValenceConnectivityIndex(order1)
Descriptor that calculates carbon valence connectivity index (order 1).
valence carbon connectivity index (order 1)
ValenceCarbonConnectivityIndex(order1)
Descriptor that calculates the 3D distance between two atoms.
distance to atom
DistanceToAtom
Descriptor that calculates the effective polarizability of a given heavy atom.
EffectiveAtomPolarizabilityDescriptor, effAtomPol
effective polarizability
EffectivePolarizability
Characterizes molecular complexity in terms of carbon hybridization states.
It reports the fraction of sp3 carbons to sp2 carbons as Nsp3/ (Nsp3 + Nsp2). The original form of the descriptor (i.e., simple ratio) has been used to characterize molecular complexity, especially in the are of natural products , which usually have a high value of the sp3 to sp2 ratio. Other short names: HybridizationRatio, HybRatio.
hybridization ratio
HybridizationRatio
Descriptor that calculates Kier and Hall kappa molecular shape indices.
Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs. First kappa shape index is given by n ( n - 1 ) 2 m 2 , second kappa shape index is given by ( n - 1 ) ( n - 2 ) 2 p 2 2 and third kappa shape index is given by ( n - 1 ) ( n - 3 ) 2 p 3 2 for odd n and ( n - 3 ) ( n - 2 ) 2 p 3 2 for enev n, where n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3. Other short names: KappaShapeIndices, Kier1, Kier2, Kier3.
Kier and Hall kappa molecular shape indices
KierAndHallKappaMolecularShapeIndices
Descriptor that calculates pi partial charges in pi-bonded systems of an heavy atom based on based on Gasteiger H.Saller (PEPE).
partial pi charge
PartialPiCharge
Descriptor that calculates sigma partial charges in sigma-bonded systems (PEOE) of an heavy atom based on Gasteiger Marsili.
partial sigma charge
PartialSigmaCharge
Descriptor that returns the pi electronegativity for a given atom.
Pi electronegativity is given by X = a + b q + c ( q 2 ) , where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge. Other short_name: elecPiA.
pi electronegativity
PiElectronegativity