molecular entity
type: Class
has alternative id: CHEBI:23367
subclass of: chemical entity
preferred label: MolecularEntity

atom
type: Class
has alternative id: CHEBI:33250
subclass of: chemical entity
preferred label: Atom

polyatomic entity
type: Class
has alternative id: CHEBI:36357
subclass of: molecular entity
preferred label: PolyatomicEntity

is about
type: ObjectProperty
IAO_0000112: This document is about information artifacts and their representations
IAO_0000114: IAO_0000125
IAO_0000115: A (currently) primitive relation that relates an information artifact to an entity.
IAO_0000116: 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.
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
preferred label: isAbout

participates in
type: ObjectProperty
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
IAO_0000115: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in
has alternative id: OBO_REL:0000020
has OBO namespace: relationship
label: participates_in
preferred label: participatesIn

chemical entity
type: Class
description: A chemical entity is any molecular entity or chemical substance.
has alternative id: CHEBI:24431
has alternative id: obo:24431
preferred label: ChemicalEntity

molar refractivity
type: Class
description: 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.
subclass of: charge delocalization descriptor
preferred label: MolarRefractivity

atomic polarizability sum
type: Class
description: atomic polarizability sum is the sum of the atomic polarizabilities (including implicit hydrogens).
subclass of: charge delocalization descriptor
preferred label: AtomicPolarizabilitySum

partial positive surface area
type: Class
description: sum of surface area on positive parts of molecule
short name: PPSA-1
subclass of: surface area descriptor
preferred label: PartialPositiveSurfaceArea

PPSA-2
type: Class
description: partial positive surface area * total positive charge on the molecule
short name: PPSA-2
subclass of: surface area descriptor
preferred label: PPSAMinus2

RS stereochemical descriptor
type: Class
subclass of: absolute configuration stereochemical descriptor
preferred label: RSStereochemicalDescriptor

R stereochemical descriptor
type: Class
subclass of: RS stereochemical descriptor
disjoint with: S stereochemical descriptor
preferred label: RStereochemicalDescriptor

canonical SMILES descriptor
type: Class
description: 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.
subclass of: SMILES descriptor
preferred label: CanonicalSMILESDescriptor

charge weighted partial positive surface area
type: Class
description: charge weighted partial positive surface area
short name: PPSA-3
subclass of: surface area descriptor
preferred label: ChargeWeightedPartialPositiveSurfaceArea

atomic order
type: Class
description: Atomic order is an atomic descriptor that specifies the ordinal position of an atom.
subclass of: positional descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: AtomicOrder

partial negative surface area
type: Class
description: sum of surface area on negative parts of molecule
short name: PNSA-1
subclass of: surface area descriptor
preferred label: PartialNegativeSurfaceArea

has value
type: DatatypeProperty
preferred label: hasValue

PNSA-2
type: Class
description: partial negative surface area * total negative charge on the molecule
short name: PNSA-2
subclass of: surface area descriptor
preferred label: PNSAMinus2

energetic descriptor
type: Class
description: An energetic descriptor is a chemical descriptor which captures information about some aspect of the energetic behaviour of a chemical entity.
subclass of: chemical descriptor
preferred label: EnergeticDescriptor

SMILES descriptor
type: Class
description: A SMILES descriptor is a structure descriptor that denotes a molecular structure as a graph.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: SMILESDescriptor

SMARTS descriptor
type: Class
description: A SMARTS descriptor is a molecular structure descriptor that conforms to the SMARTS specification.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: SMARTSDescriptor

physical descriptor
type: Class
description: A physical descriptor is a chemical descriptor which describes some physical property (quality or disposition) of a chemical entity.
subclass of: chemical descriptor
preferred label: PhysicalDescriptor

stereochemical descriptor
type: Class
description: A stereochemical descriptor is a chemical descriptor which describes some aspect of the three dimensional structure of a chemical entity.
subclass of: chemical descriptor
preferred label: StereochemicalDescriptor

isomeric SMILES descriptor
type: Class
description: an isomeric SMILES descriptor is a SMILES descriptor that written with isotopic and chiral specifications.
subclass of: SMILES descriptor
preferred label: IsomericSMILESDescriptor

S stereochemical descriptor
type: Class
subclass of: RS stereochemical descriptor
preferred label: SStereochemicalDescriptor

positional descriptor
type: Class
description: 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.
subclass of: chemical descriptor
preferred label: PositionalDescriptor

molecular formula
type: Class
description: 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.
subclass of: constitutional descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: MolecularFormula

molecular entity name
type: Class
description: An information entity about a molecular entity which serves to name that molecular entity.
subclass of: identifying descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: MolecularEntityName

preferred name
type: Class
description: A preferred name is a molecular entity name which is preferred, or recommended, for usage in textual annotations referring to that molecular entity.
subclass of: molecular entity name
preferred label: PreferredName

zagreb index
type: Class
description: The sum of the squared atom degrees of all heavy atoms.
subclass of: count descriptor
preferred label: ZagrebIndex

+/- stereochemical descriptor
type: Class
subclass of: relative configuration stereochemical descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: PlusMinusStereochemicalDescriptor

+ stereochemical descriptor
type: Class
subclass of: +/- stereochemical descriptor
disjoint with: - stereochemical descriptor
preferred label: PlusStereochemicalDescriptor

- stereochemical descriptor
type: Class
subclass of: +/- stereochemical descriptor
preferred label: MinusStereochemicalDescriptor

DL stereochemical descriptor
type: Class
subclass of: relative configuration stereochemical descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: DLStereochemicalDescriptor

D stereochemical descriptor
type: Class
subclass of: DL stereochemical descriptor
disjoint with: L stereochemical descriptor
preferred label: DStereochemicalDescriptor

L stereochemical descriptor
type: Class
subclass of: DL stereochemical descriptor
preferred label: LStereochemicalDescriptor

chemical connectivity table
type: Class
description: A chemical connectivity table is a structure descriptor which consists of a connection table representing bonds between atoms in a molecular entity.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: ChemicalConnectivityTable

aromaticity descriptor
type: Class
description: An aromaticity descriptor is a chemical descriptor which indicates the aromaticity of a molecular entity.
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: AromaticityDescriptor

file
type: Class
creator: http://orcid.org/0000-0003-3465-8786
date: 2017-02-09T14:29:12+00:00
label: melt mass flow rate
subclass of: physical descriptor
preferred label: File
preferred label: MeltMassFlowRate

MOLfile
type: Class
description: A MOLfile is a file which contains a MOLfile encoding of a chemical structure representation. It is the concretization of a MOLfile descriptor.
subclass of: file

InChIKey
type: Class
subclass of: identifying descriptor
subclass of: Restriction
  on property: is about
  some values from: polyatomic entity

dimensional extent descriptor
type: Class
description: A dimensional extent descriptor is a physical property descriptor which describes some measurable length, area or volume aspect of a chemical entity.
subclass of: geometric descriptor
preferred label: DimensionalExtentDescriptor

identifying descriptor
type: Class
description: 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.
subclass of: chemical descriptor
preferred label: IdentifyingDescriptor

bond order descriptor
type: Class
description: 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).
subclass of: geometric descriptor
preferred label: BondOrderDescriptor

QSAR descriptor
type: Class
description: 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.
has alternative id: BODO:Descriptor
comment: NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community.
subclass of: chemical descriptor
preferred label: QSARDescriptor

functional group descriptor
type: Class
description: 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.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: FunctionalGroupDescriptor

neutron count
type: Class
description: The (integer) number of neutrons in the atoms nucleus.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: NeutronCount

proton count
type: Class
description: The (integer) number of protons in the atoms nucleus.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: ProtonCount

cis-trans stereochemical descriptor
type: Class
comment: 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]
subclass of: relative configuration stereochemical descriptor
preferred label: CisMinustransStereochemicalDescriptor

cis stereochemical descriptor
type: Class
subclass of: cis-trans stereochemical descriptor
preferred label: CisStereochemicalDescriptor

trans stereochemical descriptor
type: Class
subclass of: cis-trans stereochemical descriptor
preferred label: TransStereochemicalDescriptor

mass descriptor
type: Class
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: MassDescriptor

atomic mass descriptor
type: Class
subclass of: mass descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: AtomicMassDescriptor

structural descriptor
type: Class
description: A structural descriptor is a chemical descriptor which is about some aspect of the molecular structure (composition) of a chemical entity.
subclass of: chemical descriptor
preferred label: StructuralDescriptor

electronic descriptor
type: Class
subclass of: chemical descriptor
preferred label: ElectronicDescriptor

molecular mass descriptor
type: Class
IAO_0000115: The mass of a molecule calculated according to some assumption about the isotopic identity of the atoms constituting it.
IAO_0000117: Person: Colin Batchelor
subclass of: mass descriptor
subclass of: Restriction
  on property: is about
  some values from: polyatomic entity
preferred label: MolecularMassDescriptor

atomic degree
type: Class
description: The integer number of non-H substituents of an atom.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: AtomicDegree

topological descriptor
type: Class
description: 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.
subclass of: chemical descriptor
preferred label: TopologicalDescriptor

geometric descriptor
type: Class
description: A geometric descriptor is a descriptor that concerns information about size, shape, and relative position.
subclass of: chemical descriptor
preferred label: GeometricDescriptor

charge delocalization descriptor
type: Class
subclass of: electronic descriptor
preferred label: ChargeDelocalizationDescriptor

hybridization descriptor
type: Class
description: A hybridization descriptor is a chemical descriptor that is about the hybridization of atomic orbitals in a molecular entity.
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: HybridizationDescriptor

atomic valence
type: Class
description: 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]
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: AtomicValence

atomic hardness descriptor
type: Class
description: An atomic hardness descriptor is an atomic descriptor that estimates the difference between the ionization potential and the electron affinity of a given atom.
subclass of: charge delocalization descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: AtomicHardnessDescriptor

atomic softness descriptor
type: Class
description: An atomic softness descriptor is an atomic descriptor which is about the charge delocalizing ability of a given atom.
subclass of: charge delocalization descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: AtomicSoftnessDescriptor

molecular QSAR descriptor
type: Class
description: A molecular QSAR descriptor is a OSAR descriptor which gives a quantitative value to some aspect of a molecular entity.
subclass of: QSAR descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: MolecularQSARDescriptor

cycle basis
type: Class
description: 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.
subclass of: structural descriptor
preferred label: CycleBasis

systematic name
type: Class
description: A systematic name is a molecular entity name which is formulated systematically from the structure of the molecular entity.
subclass of: molecular entity name
preferred label: SystematicName

IUPAC name
type: Class
description: 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).
subclass of: systematic name
preferred label: IUPACName

trivial name
type: Class
description: 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.
subclass of: molecular entity name
preferred label: TrivialName

fused cycles
type: Class
description: The fused cycles in a molecular structure are those cycles from the cycle basis which share at least one bond.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: FusedCycles

atomic QSAR descriptor
type: Class
description: 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.
subclass of: QSAR descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: AtomicQSARDescriptor

InChI descriptor
type: Class
description: An InChI descriptor is a structure descriptor which conforms to the InChI format specification.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: InChIDescriptor

MOLfile descriptor
type: Class
description: A MOLfile descriptor is a structure descriptor which conforms to the MOLfile format specification.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: MOLfileDescriptor

atomic connectivity index
type: Class
description: 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).
subclass of: geometric descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: AtomicConnectivityIndex

Wiener path number
type: Class
description: Half the sum of all the distance matrix entries, topological index of atom-atom distances.
subclass of: topological descriptor
preferred label: WienerPathNumber

formal charge descriptor
type: Class
description: 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]
subclass of: charge descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: FormalChargeDescriptor

partial charge descriptor
type: Class
description: 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]
subclass of: charge descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: PartialChargeDescriptor

electronegativity descriptor
type: Class
description: An electronegativity descriptor is a chemical descriptor that is about the electronegativity quality of an atom.
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: ElectronegativityDescriptor

chemical descriptor
type: Class
description: 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.
subclass of: Restriction
  on property: is about
  some values from: chemical entity
preferred label: ChemicalDescriptor

bond multiplicity descriptor
type: Class
description: 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.
subclass of: electronic descriptor
preferred label: BondMultiplicityDescriptor

charge descriptor
type: Class
description: A charge descriptor is a chemical descriptor which indicates the charge of a chemical entity.
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: ChargeDescriptor

bond length descriptor
type: Class
description: 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.
subclass of: dimensional extent descriptor
preferred label: BondLengthDescriptor

constitutional descriptor
type: Class
subclass of: chemical descriptor
preferred label: ConstitutionalDescriptor

Wiener polarity number descriptor
type: Class
description: Half the sum of all the distance matrix entries with a value of 3
subclass of: topological descriptor
preferred label: WienerPolarityNumberDescriptor

PubChem compound identifier (CID)
type: Class
subclass of: PubChem Identifier
preferred label: PubChemCompoundIdentifier(CID)

PubChem substance identifier (SID)
type: Class
subclass of: PubChem Identifier
preferred label: PubChemSubstanceIdentifier(SID)

topological surface area descriptor
type: Class
subclass of: surface area descriptor
preferred label: TopologicalSurfaceAreaDescriptor

generic SMILES descriptor
type: Class
description: 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).
subclass of: SMILES descriptor
preferred label: GenericSMILESDescriptor

topological polar surface area descriptor
type: Class
subclass of: topological surface area descriptor
preferred label: TopologicalPolarSurfaceAreaDescriptor

charge weighted partial negative surface area
type: Class
description: charge weighted partial negative surface area
short name: PNSA-3
subclass of: surface area descriptor
preferred label: ChargeWeightedPartialNegativeSurfaceArea

DPSA-1
type: Class
description: difference of PPSA-1 and PNSA-1
short name: DPSA-1
subclass of: surface area descriptor
preferred label: DPSAMinus1

DPSA-2
type: Class
description: difference of FPSA-2 and PNSA-2
short name: DPSA-2
subclass of: surface area descriptor
preferred label: DPSAMinus2

DPSA-3
type: Class
description: difference of PPSA-3 and PNSA-3
short name: DPSA-3
subclass of: surface area descriptor
preferred label: DPSAMinus3

FPSA-1
type: Class
description: PPSA-1 / total molecular surface area
short name: FPSA-1
subclass of: surface area descriptor
preferred label: FPSAMinus1

FPSA-2
type: Class
description: PPSA-2 / total molecular surface area
short name: FPSA-2
subclass of: surface area descriptor
preferred label: FPSAMinus2

FPSA-3
type: Class
description: PPSA-3 / total molecular surface area
short name: FPSA-3
subclass of: surface area descriptor
preferred label: FPSAMinus3

FNSA-1
type: Class
description: PNSA-1 / total molecular surface area
short name: FNSA-1
subclass of: surface area descriptor
preferred label: FNSAMinus1

FNSA-2
type: Class
description: PNSA-2 / total molecular surface area
short name: FNSA-2
subclass of: surface area descriptor
preferred label: FNSAMinus2

FNSA-3
type: Class
description: PNSA-3 / total molecular surface area
short name: FNSA-3
subclass of: surface area descriptor
preferred label: FNSAMinus3

WPSA-1
type: Class
description: PPSA-1 * total molecular surface area / 1000
short name: WPSA-1
subclass of: surface area descriptor
preferred label: WPSAMinus1

WPSA-2
type: Class
description: PPSA-2 * total molecular surface area /1000
short name: WPSA-2
subclass of: surface area descriptor
preferred label: WPSAMinus2

WPSA-3
type: Class
description: PPSA-3 * total molecular surface area /1000
short name: WPSA-3
subclass of: surface area descriptor
preferred label: WPSAMinus3

WNSA-1
type: Class
description: PNSA-1 * total molecular surface area /1000
short name: WNSA-1
subclass of: surface area descriptor
preferred label: WNSAMinus1

WNSA-2
type: Class
description: PNSA-2 * total molecular surface area /1000
short name: WNSA-2
subclass of: surface area descriptor
preferred label: WNSAMinus2

WNSA-3
type: Class
description: PNSA-3 * total molecular surface area /1000
short name: WNSA-3
subclass of: surface area descriptor
preferred label: WNSAMinus3

relative positive charge
type: Class
description: most positive charge / total positive charge
short name: RPCG
subclass of: surface area descriptor
preferred label: RelativePositiveCharge

relative negative charge
type: Class
description: most negative charge / total negative charge
short name: RNCG
subclass of: surface area descriptor
preferred label: RelativeNegativeCharge

relative positive charge surface area
type: Class
description: most positive surface area * RPCG
short name: RPCS
subclass of: surface area descriptor
preferred label: RelativePositiveChargeSurfaceArea

relative negative charge surface area
type: Class
description: most negative surface area * RNCG
short name: RNCS
subclass of: surface area descriptor
preferred label: RelativeNegativeChargeSurfaceArea

THSA
type: Class
description: sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2
short name: THSA
subclass of: surface area descriptor

TPSA
type: Class
description: sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2
short name: TPSA
subclass of: surface area descriptor

RHSA
type: Class
description: THSA / total molecular surface area
short name: RHSA
subclass of: surface area descriptor

RPSA
type: Class
description: TPSA / total molecular surface area
short name: RPSA
subclass of: surface area descriptor

collection of 3D coordinates
type: Class
subclass of: structural descriptor
preferred label: CollectionOf3DCoordinates

collection of 3D atomic coordinates
type: Class
subclass of: collection of 3D coordinates
preferred label: CollectionOf3DAtomicCoordinates

molecular polarizability
type: Class
description: Sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens)
short name: BPol
subclass of: charge delocalization descriptor
preferred label: MolecularPolarizability

fragment complexity descriptor
type: Class
description: defined as @cdk.cite{Nilakantan06}
short name: FragmentComplexity
subclass of: complexity descriptor
preferred label: FragmentComplexityDescriptor

vertex adjacency matrix descriptor
type: Class
subclass of: geometric descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: VertexAdjacencyMatrixDescriptor

Petitjean Topological Shape Index
type: Class
description: A measure of the anisotropy in a molecule (as per Petitjean et al)
subclass of: Petitjean Shape Index
preferred label: PetitjeanTopologicalShapeIndex

Petitjean Geometric Shape Index
type: Class
description: A measure of the anisotropy in a molecule (as per Bath et al)
subclass of: Petitjean Shape Index
preferred label: PetitjeanGeometricShapeIndex

Petitjean number
type: Class
description: 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 .
short name: petitjeanNumber
subclass of: topological descriptor
preferred label: PetitjeanNumber

Petitjean Shape Index
type: Class
description: A measure of the anisotropy in a molecule
short name: petitjeanShapeIndex
subclass of: topological descriptor
preferred label: PetitjeanShapeIndex

XLogP descriptor
type: Class
description: 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.
short name: XLogP
subclass of: logP descriptor
preferred label: XLogPDescriptor

MLogP descriptor
type: Class
description: A LogP descriptor based on a simple equation using the number of carbons and hetero atoms.
short name: MannholdLogP
subclass of: logP descriptor
preferred label: MLogPDescriptor

maximal ratio of length to breadth descriptor
type: Class
subclass of: ratio of length to breadth descriptor
preferred label: MaximalRatioOfLengthToBreadthDescriptor

ratio of length to breadth descriptor
type: Class
IAO_0000115: A descriptor characterizing the ratio of the length to the breadth of a given entity.
subclass of: geometric descriptor
preferred label: RatioOfLengthToBreadthDescriptor

minimal ratio of length to breadth descriptor
type: Class
subclass of: ratio of length to breadth descriptor
preferred label: MinimalRatioOfLengthToBreadthDescriptor

ionization energy descriptor
type: Class
IAO_0000115: 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.
IAO_0000118: ionization energy
IAO_0000118: ionization enthalpy
IAO_0000118: ionization potential
subclass of: charge delocalization descriptor
preferred label: IonizationEnergyDescriptor

eccentric connectivity index descriptor
type: Class
short name: EccentricConnectivityIndex
subclass of: topological descriptor
preferred label: EccentricConnectivityIndexDescriptor

equilibrium constant
type: Class
subclass of: electronic descriptor
preferred label: EquilibriumConstant

acid dissociation constant
type: Class
description: 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.
short name: Ka
subclass of: equilibrium constant
preferred label: AcidDissociationConstant

pKa
type: Class
description: the logarithmic measure of the acid dissociation constant (Ka)
short name: pKa
subclass of: equilibrium constant
preferred label: PKa

molecular weight calculated by pipeline pilot
type: Class
IAO_0000115: A molecular weight descriptor calculated by a relevant module of the Pipeline Pilot software tool.
subclass of: average molecular weight descriptor
preferred label: MolecularWeightCalculatedByPipelinePilot

absolute SMILES descriptor
type: Class
description: An absolute SMILES descriptor is an isomeric SMILES descriptor that is produced using a canonicalization algorithm.
subclass of: isomeric SMILES descriptor
preferred label: AbsoluteSMILESDescriptor

tautomer count
type: Class
description: a count descriptor that denotes the number of tautomers.
subclass of: count descriptor
preferred label: TautomerCount

stereocenter count
type: Class
subclass of: count descriptor
preferred label: StereocenterCount

atom stereocenter count
type: Class
subclass of: stereocenter count
disjoint with: bond stereocenter count
preferred label: AtomStereocenterCount

defined atom stereocenter count
type: Class
subclass of: atom stereocenter count
preferred label: DefinedAtomStereocenterCount

formation energy descriptor
type: Class
description: A formation energy descriptor is an energetic descriptor which gives the value for the energy of formation of a chemical entity.
subclass of: energetic descriptor
preferred label: FormationEnergyDescriptor

solvation energy descriptor
type: Class
description: A solvation energy descriptor is a chemical descriptor which gives the value for the energy of dissolving a particular chemical entity in a solvent.
subclass of: energetic descriptor
preferred label: SolvationEnergyDescriptor

count descriptor
type: Class
description: 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.
subclass of: constitutional descriptor
preferred label: CountDescriptor

dissociation energy descriptor
type: Class
description: A dissociation energy descriptor is an energetic descriptor which gives a value for the dissociation energy for a chemical entity.
subclass of: energetic descriptor
preferred label: DissociationEnergyDescriptor

undefined atom stereocenter count
type: Class
subclass of: atom stereocenter count
preferred label: UndefinedAtomStereocenterCount

bond stereocenter count
type: Class
subclass of: stereocenter count
preferred label: BondStereocenterCount

defined bond stereocenter count
type: Class
subclass of: bond stereocenter count
preferred label: DefinedBondStereocenterCount

undefined bond stereocenter count
type: Class
subclass of: bond stereocenter count
preferred label: UndefinedBondStereocenterCount

average molecular weight descriptor
type: Class
description: 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
subclass of: molecular mass descriptor
preferred label: AverageMolecularWeightDescriptor

exact mass descriptor
type: Class
description: 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.
subclass of: molecular mass descriptor
preferred label: ExactMassDescriptor

monoisotopic mass descriptor
type: Class
description: 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.
subclass of: molecular mass descriptor
preferred label: MonoisotopicMassDescriptor

complexity descriptor
type: Class
description: 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 .
subclass of: structural descriptor
preferred label: ComplexityDescriptor

pi-system size
type: Class
description: The integer number of atoms in a pi-orbital system.
short name: LargestPiSystem
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: PiMinussystemSize

bond dissociation Gibbs energy descriptor
type: Class
description: 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.
subclass of: dissociation energy descriptor
preferred label: BondDissociationGibbsEnergyDescriptor

solvation Gibbs energy descriptor
type: Class
description: 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.
subclass of: solvation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: SolvationGibbsEnergyDescriptor

bond charge density descriptor
type: Class
subclass of: charge density descriptor
preferred label: BondChargeDensityDescriptor

surface area descriptor
type: Class
description: A surface area descriptor is a descriptor which describes a measure or calculation of the surface area of a chemical entity.
subclass of: dimensional extent descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: SurfaceAreaDescriptor

charge density descriptor
type: Class
description: A charge density descriptor is a chemical entity descriptor which indicates the distribution of the electric charge over the volume of the chemical entity.
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: ChargeDensityDescriptor

aromatic atom count
type: Class
description: A descriptor that provides the integer count of aromatic atoms in a given molecular entity.
subclass of: atom count
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: AromaticAtomCount

bond count
type: Class
description: A descriptor that specifies the integer count of bonds in a given molecular entity.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: BondCount

PubChem conformer identifier
type: Class
subclass of: PubChem compound identifier (CID)
preferred label: PubChemConformerIdentifier

bond aromaticity descriptor
type: Class
description: 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.
subclass of: aromaticity descriptor
subclass of: Restriction
  on property: has value
  some values from: boolean
preferred label: BondAromaticityDescriptor

formation Gibbs energy descriptor
type: Class
description: 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.
subclass of: formation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: FormationGibbsEnergyDescriptor

size of largest aliphatic chain
type: Class
description: 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.
subclass of: size of largest chain
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: SizeOfLargestAliphaticChain

formation enthalpy descriptor
type: Class
IAO_0000118: enthalpy of formation
IAO_0000118: heat of formation
description: 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.
subclass of: formation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: FormationEnthalpyDescriptor

volume descriptor
type: Class
description: A volume descriptor is a descriptor which describes a measure or calculation of the volume of a chemical entity.
subclass of: dimensional extent descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: VolumeDescriptor

aromatic bond count
type: Class
description: A descriptor that provides the integer count of aromatic bonds in a given molecular entity.
subclass of: bond count
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: AromaticBondCount

hydrogen bond donor count
type: Class
description: 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.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: HydrogenBondDonorCount

hydrogen bond acceptor count
type: Class
description: 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.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: HydrogenBondAcceptorCount

size of largest chain
type: Class
description: 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.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: SizeOfLargestChain

solvation entropy descriptor
type: Class
description: 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.
subclass of: solvation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: SolvationEntropyDescriptor

solvation enthalpy descriptor
type: Class
description: 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.
subclass of: solvation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: SolvationEnthalpyDescriptor

logP descriptor
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: LogPDescriptor

bond dissociation enthalpy descriptor
type: Class
description: 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.
subclass of: dissociation energy descriptor
preferred label: BondDissociationEnthalpyDescriptor

refractive index descriptor
type: Class
description: 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]
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: RefractiveIndexDescriptor

rotatable bond count
type: Class
description: 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.
short name: RotatableBondsCount
subclass of: bond count
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: RotatableBondCount

melting point descriptor
type: Class
comment: Melting point descriptor specifies the temperature at which a chemical substance undergoes the transition from solid to liquid state under standard conditions.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: MeltingPointDescriptor

boiling point descriptor
type: Class
comment: The boiling point descriptor indicates the temperature at which a chemical substance undergoes a state transition from liquid to gas, at standard conditions.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: BoilingPointDescriptor

formation entropy descriptor
type: Class
description: 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.
subclass of: formation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: FormationEntropyDescriptor

relative permittivity descriptor
type: Class
description: 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 ]
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: RelativePermittivityDescriptor

atom count
type: Class
description: A descriptor that specifies the integer count of atoms in a given molecular entity.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: AtomCount

atomic charge density descriptor
type: Class
subclass of: charge density descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: AtomicChargeDensityDescriptor

bond dissociation entropy descriptor
type: Class
description: 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.
subclass of: dissociation energy descriptor
preferred label: BondDissociationEntropyDescriptor

chemical substance
type: Class
comment: Chemical substance constitutes matter of constant composition, that may contain a collection of molecular entities. [IUPAC: http://goldbook.iupac.org/C01039.html]
subclass of: chemical entity
preferred label: ChemicalSubstance

effective rotor count
type: Class
description: A count descriptor that takes into account flexibility of rings and rotatable bonds.
subclass of: count descriptor
preferred label: EffectiveRotorCount

total formal charge descriptor
type: Class
description: A charge descriptor that gives the total charge for a molecule
subclass of: charge descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: TotalFormalChargeDescriptor

conformer volume descriptor
type: Class
subclass of: volume descriptor
preferred label: ConformerVolumeDescriptor

amino acid count
type: Class
description: a count of the number of amino acid residues.
subclass of: count descriptor
preferred label: AminoAcidCount

alanine count
type: Class
subclass of: amino acid count
preferred label: AlanineCount

arginine count
type: Class
subclass of: amino acid count
preferred label: ArginineCount

asparagine count
type: Class
subclass of: amino acid count
preferred label: AsparagineCount

aspartate count
type: Class
subclass of: amino acid count
preferred label: AspartateCount

cysteine count
type: Class
subclass of: amino acid count
preferred label: CysteineCount

phenylalanine count
type: Class
subclass of: amino acid count
preferred label: PhenylalanineCount

glutamate count
type: Class
subclass of: amino acid count
preferred label: GlutamateCount

glutamine count
type: Class
subclass of: amino acid count
preferred label: GlutamineCount

glycine count
type: Class
subclass of: amino acid count
preferred label: GlycineCount

histidine count
type: Class
description: The number of covalent units (molecule / ion) in a chemical structure
label: covalent unit count
subclass of: count descriptor
subclass of: amino acid count
preferred label: CovalentUnitCount
preferred label: HistidineCount

isoleucine count
type: Class
subclass of: amino acid count
preferred label: IsoleucineCount

proline count
type: Class
subclass of: amino acid count
preferred label: ProlineCount

leucine count
type: Class
subclass of: amino acid count
preferred label: LeucineCount

lysine count
type: Class
subclass of: amino acid count
preferred label: LysineCount

methionine count
type: Class
subclass of: amino acid count
preferred label: MethionineCount

serine count
type: Class
subclass of: amino acid count
preferred label: SerineCount

threonine count
type: Class
subclass of: amino acid count
preferred label: ThreonineCount

tyrosine count
type: Class
subclass of: amino acid count
preferred label: TyrosineCount

valine count
type: Class
subclass of: amino acid count
preferred label: ValineCount

tryptophan count
type: Class
subclass of: amino acid count
preferred label: TryptophanCount

Highest Occupied Molecular Orbital Energy
type: Class
description: A descriptor that the energy of the highest occupied 'molecular' orbital of the chemical entity.
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical entity
preferred label: HighestOccupiedMolecularOrbitalEnergy

Lowest Unoccupied Molecular Orbital Energy
type: Class
description: A descriptor that the energy of the lowest unoccupied 'molecular' orbital of the chemical entity.
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical entity
preferred label: LowestUnoccupiedMolecularOrbitalEnergy

acidic group count
type: Class
description: A descriptor that specifies the integer count of acidic groups in a given molecular entity.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: AcidicGroupCount

basic group count
type: Class
description: A descriptor that specifies the integer count of basic groups in a given molecular entity.
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
preferred label: BasicGroupCount

ALogP descriptor
type: Class
description: The ALogP descriptor described by Ghose and Crippen in 1986 and 1987.
short name: ALogP
subclass of: logP descriptor
preferred label: ALogPDescriptor

hybridization descriptor (VSEPR)
type: Class
subclass of: hybridization descriptor
preferred label: HybridizationDescriptor(VSEPR)

inductive atomic hardness
type: Class
subclass of: electronic descriptor
preferred label: InductiveAtomicHardness

TPSA (fragments)
type: Class
subclass of: topological polar surface area descriptor
preferred label: TPSA(fragments)

VABC volume descriptor
type: Class
subclass of: volume descriptor
preferred label: VABCVolumeDescriptor

heavy atom count
type: Class
description: The number of non-hydrogen atoms
subclass of: atom count
preferred label: HeavyAtomCount

isotope atom count
type: Class
description: The sum of all atoms enriched with respect to a particular atom isotope
subclass of: atom count
preferred label: IsotopeAtomCount

PubChem Identifier
type: Class
subclass of: chemical database identifier
preferred label: PubChemIdentifier

GenBank Protein Identifier
type: Class
subclass of: chemical database identifier
preferred label: GenBankProteinIdentifier

GenBank Nucleotide Identifier
type: Class
subclass of: chemical database identifier
preferred label: GenBankNucleotideIdentifier

ALogP calculated by Pipeline Pilot
type: Class
subclass of: ALogP descriptor
preferred label: ALogPCalculatedByPipelinePilot

polar surface area descriptor
type: Class
subclass of: surface area descriptor
preferred label: PolarSurfaceAreaDescriptor

polar surface area descriptor calculated by Pipeline Pilot
type: Class
subclass of: polar surface area descriptor
preferred label: PolarSurfaceAreaDescriptorCalculatedByPipelinePilot

hydrogen bond acceptor count calculated by pipeline pilot
type: Class
subclass of: hydrogen bond acceptor count
preferred label: HydrogenBondAcceptorCountCalculatedByPipelinePilot

hydrogen bond donor count calculated by pipeline pilot
type: Class
subclass of: hydrogen bond donor count
preferred label: HydrogenBondDonorCountCalculatedByPipelinePilot

rotatable bond count calculated by pipeline pilot
type: Class
subclass of: rotatable bond count
preferred label: RotatableBondCountCalculatedByPipelinePilot

rule of five violations descriptor
type: Class
IAO_0000115: 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
subclass of: physical descriptor
preferred label: RuleOfFiveViolationsDescriptor

rule of five violations calculated by pipeline pilot
type: Class
subclass of: rule of five violations descriptor
preferred label: RuleOfFiveViolationsCalculatedByPipelinePilot

rule of three passes descriptor
type: Class
IAO_0000115: 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
subclass of: physical descriptor
preferred label: RuleOfThreePassesDescriptor

rule of three passes calculated by pipeline pilot
type: Class
subclass of: rule of three passes descriptor
preferred label: RuleOfThreePassesCalculatedByPipelinePilot

medchem friendly descriptor
type: Class
IAO_0000115: 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
subclass of: physical descriptor
preferred label: MedchemFriendlyDescriptor

medchem friendly descriptor calculated by pipeline pilot
type: Class
subclass of: medchem friendly descriptor
preferred label: MedchemFriendlyDescriptorCalculatedByPipelinePilot

logP calculated by ACD/Labs PhysChem software
type: Class
subclass of: logP descriptor
preferred label: LogPCalculatedByACDLabsPhysChemSoftware

logD descriptor
type: Class
IAO_0000115: octanol-water distribution coefficient calculated at a given pH.
subclass of: physical descriptor
preferred label: LogDDescriptor

logD calculated at pH 7.4 by ACD/Labs PhysChem software
type: Class
IAO_0000115: ACD_LogD(pH7.4) Distribution Coefficient calculated at pH7.4
subclass of: logD descriptor

most acidic pKa calculated by ACD/Labs PhysChem software library
type: Class
IAO_0000115: Most acidic pKa of the molecule
subclass of: pKa
preferred label: MostAcidicPKaCalculatedByACDLabsPhysChemSoftwareLibrary

most basic pKa calculated by ACD/Labs PhysChem software library
type: Class
IAO_0000115: Most basic pKa of the molecule
subclass of: pKa
preferred label: MostBasicPKaCalculatedByACDLabsPhysChemSoftwareLibrary

molecular species at pH 7.4 descriptor
type: Class
IAO_0000115: Molecular Species is a description of the predominant form of the molecule at pH7.4.
subclass of: physical descriptor
preferred label: MolecularSpeciesAtPH7.4Descriptor

molecular species at pH 7.4 calculated by ACD/Labs PhysChem software
type: Class
IAO_0000115: 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
subclass of: molecular species at pH 7.4 descriptor

molecular weight calculated by the pubchem software library
type: Class
subclass of: average molecular weight descriptor
preferred label: MolecularWeightCalculatedByThePubchemSoftwareLibrary

molecular formula calculated by the pubchem software library
type: Class
subclass of: molecular formula
preferred label: MolecularFormulaCalculatedByThePubchemSoftwareLibrary

total formal charge calculated by the pubchem software library
type: Class
subclass of: total formal charge descriptor
preferred label: TotalFormalChargeCalculatedByThePubchemSoftwareLibrary

monoisotopic mass calculated by the pubchem software library
type: Class
subclass of: monoisotopic mass descriptor
preferred label: MonoisotopicMassCalculatedByThePubchemSoftwareLibrary

exact mass calculated by pubchem software library
type: Class
subclass of: exact mass descriptor
preferred label: ExactMassCalculatedByPubchemSoftwareLibrary

pubchem depositor-supplied molecular entity name
type: Class
IAO_0000115: 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.
subclass of: molecular entity name
preferred label: PubchemDepositorMinussuppliedMolecularEntityName

logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01
type: Class
description: Octanol-water distribution coefficient calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01.
subclass of: logD descriptor

hydrogen bond acceptor count calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Hydrogen bond acceptor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: hydrogen bond acceptor count

hydrogen bond donor count calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Hydrogen bond donor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: hydrogen bond donor count

Boiling point at 760 mmHg pressure calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: The boiling point of a substance at 760 mmHg pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: boiling point descriptor

number of freely rotating bonds calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Number of freely rotating bonds that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: rotatable bond count

polar surface area calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Polar surface area that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: polar surface area descriptor

molecular weight of the corresponding free base
type: Class
description: The molecular weight for the free base chemical structure matching this chemical structure.
subclass of: average molecular weight descriptor
preferred label: MolecularWeightOfTheCorrespondingFreeBase

molar refractivity calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Molar refractivity that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: molar refractivity

index of refraction calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Index of refraction that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: refractive index descriptor

molar volume calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Molar volume that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: molar volume descriptor

density calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Density that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: density descriptor

flash point calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Flash point that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: flash point descriptor

enthalpy of vaporization calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Enthalpy of vaporization that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: enthalpy of vaporization descriptor

vapour pressure calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Vapour pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: vapour pressure descriptor

organic carbon adsorption coefficient at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Organic carbon adsorption coefficient at pH 5.5 that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: organic carbon adsorption descriptor

organic carbon adsorption coefficient at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Organic carbon adsorption coefficient at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: organic carbon adsorption descriptor

bioconcentration factor at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: bioconcentration factor descriptor

bioconcentration factor at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: bioconcentration factor descriptor

number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Number of rule of five violations for a chemical structure that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: rule of five violations descriptor

surface tension calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Surface tension, in dyne per centimetre, that has been calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: surface tension descriptor

covalent unit count generated by pubchem software library
type: Class
subclass of: histidine count
preferred label: CovalentUnitCountGeneratedByPubchemSoftwareLibrary

defined atom stereocenter count generated by the pubchem software library
type: Class
subclass of: defined atom stereocenter count
preferred label: DefinedAtomStereocenterCountGeneratedByThePubchemSoftwareLibrary

defined bond stereocenter count generated by pubchem software library
type: Class
subclass of: defined bond stereocenter count
preferred label: DefinedBondStereocenterCountGeneratedByPubchemSoftwareLibrary

isotope atom count generated by pubchem software library
type: Class
subclass of: isotope atom count
preferred label: IsotopeAtomCountGeneratedByPubchemSoftwareLibrary

heavy atom count generated by pubchem software library
type: Class
subclass of: heavy atom count
preferred label: HeavyAtomCountGeneratedByPubchemSoftwareLibrary

undefined atom stereocenter count generated by the pubchem software library
type: Class
subclass of: undefined atom stereocenter count
preferred label: UndefinedAtomStereocenterCountGeneratedByThePubchemSoftwareLibrary

undefined bond stereocenter count generated by the pubchem software library
type: Class
subclass of: undefined bond stereocenter count
preferred label: UndefinedBondStereocenterCountGeneratedByThePubchemSoftwareLibrary

canonical smiles generated by OEChem
type: Class
subclass of: canonical SMILES descriptor
preferred label: CanonicalSmilesGeneratedByOEChem

isomeric SMILES generated by OEChem
type: Class
subclass of: isomeric SMILES descriptor
preferred label: IsomericSMILESGeneratedByOEChem

cycle count
type: Class
IAO_0000115: A descriptor that specifies the integer count of cycles in a given molecular entity.
subclass of: count descriptor
preferred label: CycleCount

aromatic cycle count
type: Class
IAO_0000115: A descriptor that specifies the integer count of aromatic cycles in a given molecular entity.
IAO_0000118: aromatic rings
subclass of: cycle count
preferred label: AromaticCycleCount

IUPAC Name generated by LexiChem
type: Class
subclass of: IUPAC name
preferred label: IUPACNameGeneratedByLexiChem

hydrogen bond donor count calculated by cactvs
type: Class
subclass of: hydrogen bond donor count
preferred label: HydrogenBondDonorCountCalculatedByCactvs

hydrogen bond acceptor count calculated by cactvs
type: Class
subclass of: hydrogen bond acceptor count
preferred label: HydrogenBondAcceptorCountCalculatedByCactvs

rotatable bond count calculated by cactvs
type: Class
subclass of: rotatable bond count
preferred label: RotatableBondCountCalculatedByCactvs

structure complexity calculated by cactvs
type: Class
subclass of: complexity descriptor
preferred label: StructureComplexityCalculatedByCactvs

tautomer count calculated by cactvs
type: Class
subclass of: tautomer count
preferred label: TautomerCountCalculatedByCactvs

TPSA calculated by cactvs
type: Class
subclass of: TPSA
preferred label: TPSACalculatedByCactvs

xlogp3 calculated by the xlogp3 software
type: Class
subclass of: XLogP descriptor
preferred label: Xlogp3CalculatedByTheXlogp3Software

InChI calculated by library version 1.0.4
type: Class
subclass of: InChI descriptor
preferred label: InChICalculatedByLibraryVersion1.0.4

InChIKey generated by software version 1.0.4
type: Class
subclass of: InChIKey
preferred label: InChIKeyGeneratedBySoftwareVersion1.0.4

chemical graph
type: Class
description: 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.
subclass of: structural descriptor
preferred label: ChemicalGraph

ChemSpider identifier
type: Class
description: Database identifier used by ChemSpider.
subclass of: chemical database identifier
preferred label: ChemSpiderIdentifier

DrugBank identifier
type: Class
description: Database identifier used by DrugBank.
subclass of: chemical database identifier
preferred label: DrugBankIdentifier

ChEBI identifier
type: Class
description: Database identifier used by ChEBI.
subclass of: chemical database identifier
preferred label: ChEBIIdentifier

HMDB identifier
type: Class
description: Database identifier used by Human Metabolome Database.
subclass of: chemical database identifier
preferred label: HMDBIdentifier

KEGG identifier
type: Class
description: Database identifier used by KEGG.
subclass of: chemical database identifier
preferred label: KEGGIdentifier

Reactome identifier
type: Class
description: Database identifier used by Reactome.
subclass of: chemical database identifier
preferred label: ReactomeIdentifier

ChEMBL identifier
type: Class
description: Identifier used by the ChEMBL database for compounds, assays, target, etc.
subclass of: chemical database identifier
preferred label: ChEMBLIdentifier

organic carbon adsorption descriptor
type: Class
IAO_0000117: Colin Batchelor
description: 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.
subclass of: physical descriptor
preferred label: OrganicCarbonAdsorptionDescriptor

bioconcentration factor descriptor
type: Class
IAO_0000117: Colin Batchelor
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: BioconcentrationFactorDescriptor

molar volume descriptor
type: Class
IAO_0000117: Colin Batchelor
description: A descriptor of the volume occupied by one mole of the given substance at a given temperature and pressure.
subclass of: physical descriptor
preferred label: MolarVolumeDescriptor

density descriptor
type: Class
IAO_0000117: Colin Batchelor
description: A descriptor of the density of a given substance at a given temperature and pressure.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: DensityDescriptor

flash point descriptor
type: Class
IAO_0000117: Colin Batchelor
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: FlashPointDescriptor

enthalpy of vaporization descriptor
type: Class
IAO_0000117: Colin Batchelor
description: A descriptor of the energy taken in by a chemical substance on vaporization at a given temperature and pressure.
subclass of: physical descriptor
preferred label: EnthalpyOfVaporizationDescriptor

vapour pressure descriptor
type: Class
IAO_0000117: Colin Batchelor
description: A descriptor of the pressure exerted by the vapour phase of a chemical substance on its condensed phase at a given temperature and pressure.
subclass of: physical descriptor
preferred label: VapourPressureDescriptor

surface tension descriptor
type: Class
IAO_0000117: Colin Batchelor
description: A descriptor of the disposition of a portion of liquid to resist a force.
subclass of: physical descriptor
preferred label: SurfaceTensionDescriptor

structural alert count
type: Class
IAO_0000115: 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.
subclass of: count descriptor
preferred label: StructuralAlertCount

weighted quantitative estimate of drug-likeness
type: Class
IAO_0000115: 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.
IAO_0000118: QED weighted
subclass of: physical descriptor
preferred label: WeightedQuantitativeEstimateOfDrugMinuslikeness

freezing point descriptor
type: Class
description: A descriptor that indicates the temperature at which a chemical substance undergoes a state transition from gas or liquid to solid, under standard conditions.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: FreezingPointDescriptor

Henry's Law constant
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: Henry'sLawConstant

atmospheric OH rate constant
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: AtmosphericOHRateConstant

upper explosive limit descriptor
type: Class
description: A physical descriptor for the upper explosive limit of the entity in air as a percentage by volume at room temperature.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: UpperExplosiveLimitDescriptor

lower explosive limit descriptor
type: Class
description: A physical descriptor for the lower explosive limit in air as a percentage by volume at room temperature
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: LowerExplosiveLimitDescriptor

minimum explosive concentration descriptor
type: Class
description: A physical descriptor for the minimum explosive concentration.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: MinimumExplosiveConcentrationDescriptor

specific gravity descriptor
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: SpecificGravityDescriptor

relative density descriptor
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: RelativeDensityDescriptor

vapor density descriptor
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: VaporDensityDescriptor

odor detection threshold descriptor
type: Class
description: A physical descriptor for the lowest concentration of an odorant chemical entity that is perceivable by the human sense of smell.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: OdorDetectionThresholdDescriptor

pH descriptor
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: PHDescriptor

evaporation rate descriptor
type: Class
description: A physical descriptor of the rate of evaporation of a liquid under standard conditions.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: EvaporationRateDescriptor

autoignition temperature descriptor
type: Class
IAO_0000118: kindling point
description: A physical descriptor of the lowest temperature at a substance will spontaneously ignite in a normal atmosphere without an external source of ignition.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: AutoignitionTemperatureDescriptor

soil half-life descriptor
type: Class
description: 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.
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: SoilHalfMinuslifeDescriptor

CAS registry number
type: Class
description: Identifier used by the Chemical Abstracts Service database.
subclass of: chemical database identifier
preferred label: CASRegistryNumber

EC number
type: Class
description: A seven-digit identifier for chemical substances for regulatory purposes within the European Union.
label: EINECS No
label: European Community number
subclass of: chemical database identifier
preferred label: ECNumber
preferred label: EINECSNo
preferred label: EuropeanCommunityNumber

metal atom count
type: Class
IAO_0000115: A descriptor that specifies the integer count of metal atoms in a given chemical entity.
subclass of: atom count
preferred label: MetalAtomCount

oxygen atom count
type: Class
IAO_0000115: A descriptor that specifies the integer count of oxygen atoms in a given chemical entity.
subclass of: atom count
preferred label: OxygenAtomCount

chemical database identifier
type: Class
IAO_0000115: An identifying descriptor which is used within a particular database system to identify a chemical system.
IAO_0000117: Person: Colin Batchelor
subclass of: identifying descriptor
preferred label: ChemicalDatabaseIdentifier

ChemSpider validated synonym
type: Class
IAO_0000115: A preferred name in ChemSpider by virtue of having been validated by a curator.
IAO_0000117: Person: Colin Batchelor
subclass of: preferred name
preferred label: ChemSpiderValidatedSynonym

ChemSpider unvalidated synonym
type: Class
IAO_0000115: A molecular entity name in the ChemSpider database which has not been validated by a curator.
IAO_0000117: Person: Colin Batchelor
subclass of: molecular entity name
preferred label: ChemSpiderUnvalidatedSynonym

validated chemical database identifier
type: Class
IAO_0000115: A chemical database identifier which has been validated by a curator.
IAO_0000117: Person: Colin Batchelor
subclass of: chemical database identifier
preferred label: ValidatedChemicalDatabaseIdentifier

ChemSpider title
type: Class
IAO_0000115: A ChemSpider validated synonym that has been identified as a title by the ChemSpider software.
subclass of: ChemSpider validated synonym
preferred label: ChemSpiderTitle

average molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01
type: Class
IAO_0000117: Person: Colin Batchelor
subclass of: average molecular weight descriptor

monoisotopic molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01
type: Class
IAO_0000117: Person: Colin Batchelor
subclass of: monoisotopic mass descriptor

energy band gap
type: Class
IAO_0000115: 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]
IAO_0000118: band gap
IAO_0000118: energy gap
subclass of: energetic descriptor
preferred label: EnergyBandGap

metal element mass descriptor
type: Class
IAO_0000115: A descriptor describing the mass of the metal element component of a composite substance.
IAO_0000118: metal element mass
subclass of: mass descriptor
preferred label: MetalElementMassDescriptor

molecular formula calculated by ACD/Labs PhysChem software library version 12.01
type: Class
description: Molecular formula for a chemical structure as calculated by ACD/Labs PhysChem software library version 12.01.
subclass of: molecular formula

partition coefficient
type: Class
IAO_0000115: 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.
subclass of: physical descriptor
preferred label: PartitionCoefficient

numeric chemical descriptor
type: Class
subclass of: chemical descriptor
preferred label: NumericChemicalDescriptor

textual chemical descriptor
type: Class
subclass of: chemical descriptor
preferred label: TextualChemicalDescriptor

chemical substance descriptor
type: Class
subclass of: chemical descriptor
preferred label: ChemicalSubstanceDescriptor

group of an atom
type: Class
description: Descriptor that returns the group in the periodic table of a given atom.
subclass of: constitutional descriptor
preferred label: GroupOfAnAtom

NInChI descriptor
type: Class
description: An InChI-like descriptor for nanomaterials.
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
preferred label: NInChIDescriptor

TUCAN descriptor
type: Class
description: TUCAN is an identifier based on a canonicalization and serialization algorithm that is independent of domain-specific concepts of structure and bonding.
subclass of: identifying descriptor
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: polyatomic entity
preferred label: TUCANDescriptor

absolute configuration stereochemical descriptor
type: Class
creator: http://orcid.org/0000-0002-4378-6061
date: 2022-07-11T08:01:45+00:00
description: The spatial arrangement of the atoms of a chiral molecular entity (or group) and its stereochemical description e.g. R or S.
source: https://doi.org/10.1351/goldbook.A00020
subclass of: stereochemical descriptor
preferred label: AbsoluteConfigurationStereochemicalDescriptor

relative configuration stereochemical descriptor
type: Class
creator: http://orcid.org/0000-0002-4378-6061
date: 2022-07-11T08:04:08+00:00
description: 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.
source: https://doi.org/10.1351/goldbook.R05260
subclass of: stereochemical descriptor
preferred label: RelativeConfigurationStereochemicalDescriptor

ACD/Labs index name
type: Class
IAO_0000118: index name
creator: http://orcid.org/0000-0002-4378-6061
date: 2022-07-11T08:20:10+00:00
description: A molecular entity name that represents the name of a molecular structure determined by the naming algorithms developed by ACD/Labs.
source: https://www.acdlabs.com/products/name/
subclass of: molecular entity name
preferred label: ACDLabsIndexName

InChI with fixedH layer
type: Class
creator: http://orcid.org/0000-0002-4378-6061
date: 2022-07-11T08:22:02+00:00
description: 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.
source: https://doi.org/10.1186%2Fs13321-015-0068-4
subclass of: InChI descriptor
preferred label: InChIWithFixedHLayer

ChEBI name
type: Class
IAO_0000115: 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.
subclass of: preferred name
preferred label: ChEBIName

drug trade name
type: Class
IAO_0000115: Trade name of a drug compound.
subclass of: molecular entity name
preferred label: DrugTradeName

International Non-proprietary Name
type: Class
IAO_0000115: International Non-proprietary Name, defined by the WHO.
short name: INN
subclass of: molecular entity name
preferred label: InternationalNonMinusproprietaryName

Unique Ingredient Identifier
type: Class
description: Identifier used by the USA Food and Drug Administration.
short name: UNII
subclass of: chemical database identifier
preferred label: UniqueIngredientIdentifier

LipidMaps identifier
type: Class
description: Identifier used by the LipidMaps database, http://www.lipidmaps.org/.
subclass of: chemical database identifier
preferred label: LipidMapsIdentifier

National Service Center number
type: Class
description: Identifier used by the Cancer Chemotherapy National Service Center.
short name: NSC number
subclass of: chemical database identifier
preferred label: NationalServiceCenterNumber

RTECS identifier
type: Class
description: Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).
subclass of: chemical database identifier
preferred label: RTECSIdentifier

European Registry of Materials identifier
type: Class
description: Identifier used by the European Registry of Materials (https://nanocommons.github.io/identifiers/).
subclass of: chemical database identifier
preferred label: EuropeanRegistryOfMaterialsIdentifier

SwissLipids identifier
type: Class
subclass of: chemical database identifier
preferred label: SwissLipidsIdentifier

MolMeDB identifier
type: Class
subclass of: chemical database identifier
preferred label: MolMeDBIdentifier

PDB ligand identifier
type: Class
subclass of: chemical database identifier
preferred label: PDBLigandIdentifier

PDB structure identifier
type: Class
short name: PDB identifier
subclass of: chemical database identifier
preferred label: PDBStructureIdentifier

number of rule of five violations calculated by RDKit software library version 2015_09_2
type: Class
subclass of: rule of five violations descriptor

hydrogen bond acceptor count calculated by RDKit software library version 2015_09_2
type: Class
subclass of: hydrogen bond acceptor count

hydrogen bond donor count calculated by RDKit software library version 2015_09_2
type: Class
subclass of: hydrogen bond donor count

logP descriptor calculated by RDKit software library version 2015_09_2
type: Class
subclass of: logP descriptor

molecular formula calculated by RDKit software library version 2015_09_2
type: Class
subclass of: molecular formula

average molecular weight calculated by RDKit software library version 2015_09_2
type: Class
subclass of: average molecular weight descriptor

total polar surface area calculated by RDKit software library version 2015_09_2
type: Class
subclass of: polar surface area descriptor

Bond Polarizabilities
type: Class
description: 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).
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
preferred label: BondPolarizabilities

oxidation state
type: Class
description: 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]
subclass of: electronic descriptor
subclass of: AtomicDescriptor
subclass of: Restriction
  on property: is about
  some values from: atom
preferred label: OxidationState
source: https://doi.org/10.1351/goldbook.O04365

connectivity SMILES descriptor
type: Class
description: A connectivity SMILES descriptor is a SMILES descriptor that does not include any stereochemical or isotopic information.
subclass of: SMILES descriptor
preferred label: ConnectivitySMILESDescriptor

BCUT
type: Class
description: Eigenvalue based descriptor noted for its utility in chemical diversity.
doi: http://dx.doi.org/10.1021/ci980137x
short name: BCUT
subclass of: topological descriptor

bond partial pi charge
type: Class
description: 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).
short name: bondPartialPiCharge
subclass of: electronic descriptor
preferred label: BondPartialPiCharge

bond partial sigma charge
type: Class
description: Descriptor that calculates bond-sigma Partial charge of a bond.
short name: bondPartialSigmaCharge
subclass of: electronic descriptor
preferred label: BondPartialSigmaCharge

bond partial total charge
type: Class
description: Descriptor that calculates bond-total Partial charge of a bond.
short name: bondPartialTCharge
subclass of: electronic descriptor
preferred label: BondPartialTotalCharge

bond sigma electronegativity
type: Class
description: Descriptor that calculates of bond-Polarizability of a bond by determining the difference the Sigma electronegativity on atoms A and B of a bond.
short name: bondSigmaElectronegativity
subclass of: electronic descriptor
preferred label: BondSigmaElectronegativity

bonds to Atom
type: Class
description: Descriptor based on the number of bonds on the shortest path between two atoms (topological distance).
short name: bondsToAtom
comment: 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.
subclass of: topological descriptor
preferred label: BondsToAtom

chi chain indices
type: Class
description: Evluates the simple and valence chi chain descriptors (Kier and Hall) of orders 3, 4, 5, 6 and 7.
short name: chiChain
comment: It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
subclass of: topological descriptor
preferred label: ChiChainIndices

chi cluster indices
type: Class
description: Evluates the simple and valence chi cluster descriptors (Kier and Hall) of orders 3, 4,5 and 6.
short name: chiCluster
comment: It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
subclass of: topological descriptor
preferred label: ChiClusterIndices

chi path indices
type: Class
description: Evaluates the Kier and Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7.
short name: chiPath
comment: It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
subclass of: topological descriptor
preferred label: ChiPathIndices

chi path-cluster indices
type: Class
description: Evaluates the Kier and Hall Chi path cluster indices of orders 4,5 and 6.
short name: chiPathCluster
comment: It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
subclass of: topological descriptor
preferred label: ChiPathMinusclusterIndices

gravitational index
type: Class
description: Descriptor characterizing the mass distribution of the molecule.
doi: http://dx.doi.org/10.1021/jp953224q
short name: gravitationalIndex
subclass of: geometric descriptor
preferred label: GravitationalIndex

gravitational index (square and cube roots)
type: Class
description: Descriptor characterizing the mass distribution of the molecule as the square or cube root of the gravitational index.
doi: http://dx.doi.org/10.1021/ci980029a
short name: gravitationalIndex_SquareAndCubeRoots
subclass of: gravitational index
preferred label: GravitationalIndex(squareAndCubeRoots)

acceptor field atoms (Boehm,Klebe)
type: Class
description: Counts the number of acceptor field atoms for a carbonyl oxygen probe using force field based definition.
doi: http://dx.doi.org/10.1021/jm011039x
short name: hBondAcceptorsBoehmKlebe
subclass of: electronic descriptor
preferred label: AcceptorFieldAtoms(Boehm,Klebe)

hydrogen bond acceptors (Daylight)
type: Class
description: Descriptor that calculates the number of hydrogen bond acceptors (by Daylight).
short name: hBondacceptorsDaylight
comment: SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
subclass of: electronic descriptor
preferred label: HydrogenBondAcceptors(Daylight)

acceptors or donors field atoms (Boehm,Klebe)
type: Class
description: Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe.
doi: http://dx.doi.org/10.1021/jm011039x
short name: hBondAcceptorsDonorsBoehmKlebe
subclass of: electronic descriptor
preferred label: AcceptorsOrDonorsFieldAtoms(Boehm,Klebe)

donor field atoms (Boehm,Klebe)
type: Class
description: Counts the number of donor field atoms for an amino hydrogen probe.
doi: http://dx.doi.org/10.1021/jm011039x
short name: hBondDonorsBoehmKlebe
subclass of: electronic descriptor
preferred label: DonorFieldAtoms(Boehm,Klebe)

hydrogen bond donors (Daylight)
type: Class
description: Descriptor that calculates the number of hydrogen bond donors (by Daylight).
short name: hBondDonorsDaylight
comment: SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
subclass of: electronic descriptor
preferred label: HydrogenBondDonors(Daylight)

proton belonging to an aromatic system
type: Class
description: 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.
short name: isProtonInAromaticSystem
subclass of: constitutional descriptor
preferred label: ProtonBelongingToAnAromaticSystem

proton belonging to a pi-system
type: Class
description: Descriptor returns true if the protons is directly bonded to a pi system.
short name: isProtonInConjugatedPiSystem
subclass of: constitutional descriptor
preferred label: ProtonBelongingToAPiMinussystem

Kier Hall SMARTS
type: Class
description: Counts the number of occurrences of the E-state fragments.
doi: http://dx.doi.org/10.3390/91201004
short name: kierHallSmarts
subclass of: topological descriptor
preferred label: KierHallSMARTS

molecular distance edge
type: Class
description: Evaluate molecular distance edge descriptors for C, N and O.
doi: http://dx.doi.org/10.1021/ci970109z
short name: mde
subclass of: topological descriptor
preferred label: MolecularDistanceEdge

moments of inertia
type: Class
description: Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration.
short name: momentOfInertia
subclass of: geometric descriptor
preferred label: MomentsOfInertia

partial total charge (MMFF94)
type: Class
description: Descriptor that calculates total partial charges of an heavy atom.
short name: partialTChargeMMFF94
subclass of: electronic descriptor
preferred label: PartialTotalCharge(MMFF94)

period of an atom
type: Class
description: Descriptor that returns the period in the periodic table of an atom belonging to an atom container.
short name: period
subclass of: constitutional descriptor
preferred label: PeriodOfAnAtom

pi-contact of two atoms
type: Class
description: 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).
short name: piContact
subclass of: constitutional descriptor
preferred label: PiMinuscontactOfTwoAtoms

proton total partial charge
type: Class
description: Descriptor that calculates partial charges of an heavy atom and its protons based on Gasteiger Marsili (PEOE).
short name: protonPartialCharge
subclass of: electronic descriptor
preferred label: ProtonTotalPartialCharge

RDF proton descriptor
type: Class
description: Calculation of RDF proton descriptor.
doi: http://dx.doi.org/10.1021/ac010737m
short name: rdfProtonCalculatedValues
comment: This is a mixed descriptor: topological, geometrical and electronic descriptor.
subclass of: topological descriptor
preferred label: RDFProtonDescriptor

TAE RECON descriptors for amino acid sequences
type: Class
description: 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.
doi: http://dx.doi.org/10.1016/0097-8485(94)00052-G
short name: taeAminoAcid
comment: {@cdk.cite BREN1995} {@cdk.cite BREN1997} {@cdk.cite WHITE2003}
subclass of: electronic descriptor
preferred label: TAERECONDescriptorsForAminoAcidSequences

weighted path
type: Class
description: The weighted path (molecular ID) descriptors were described by Randic and they characterize molecular branching.
short name: weightedPath
subclass of: topological descriptor
preferred label: WeightedPath

WHIM
type: Class
description: Holistic descriptors described by Todeschini et al.
short name: WHIM
comment: 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.
subclass of: topological descriptor

Moreau-Broto Autocorrelation (charge) descriptors
type: Class
description: The Moreau-Broto autocorrelation descriptors using partial charges.
short name: autoCorrelationCharge
comment: ATSc1 - ATSc5
subclass of: topological descriptor

Moreau-Broto autocorrelation (mass) descriptors
type: Class
description: The Moreau-Broto autocorrelation descriptors using atomic weight.
short name: autoCorrelationMass
comment: ATSm1 - ATSm5
subclass of: topological descriptor

Moreau-Broto autocorrelation (polarizability) descriptors
type: Class
description: The Moreau-Broto autocorrelation descriptors using polarizability.
short name: autoCorrelationPolarizability
comment: ATSp1 - ATSp5
subclass of: topological descriptor

carbon types
type: Class
description: Characterizes the carbon connectivity in terms of hybridization
short name: carbonTypes
comment: C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3, C4SP3
subclass of: topological descriptor
preferred label: CarbonTypes

carbon connectivity index (order 0)
type: Class
description: Descriptor that calculates the carbon connectivity index (order 0).
short name: chi0C
subclass of: topological descriptor
preferred label: CarbonConnectivityIndex(order0)

valence connectivity index (order 0)
type: Class
description: Descriptor that calculates atomic valence connectivity index (order 0).
short name: chi0v
subclass of: topological descriptor
preferred label: ValenceConnectivityIndex(order0)

valence carbon connectivity index (order 0)
type: Class
description: Descriptor that calculates carbon valence connectivity index (order 0).
short name: chi0vC
subclass of: topological descriptor
preferred label: ValenceCarbonConnectivityIndex(order0)

carbon connectivity index (order 1)
type: Class
description: Descriptor that calculates carbon connectivity index (order 1).
short name: chi1C
subclass of: topological descriptor
preferred label: CarbonConnectivityIndex(order1)

valence connectivity index (order 1)
type: Class
description: Descriptor that calculates atomic valence connectivity index (order 1).
short name: chi1v
subclass of: topological descriptor
preferred label: ValenceConnectivityIndex(order1)

valence carbon connectivity index (order 1)
type: Class
description: Descriptor that calculates carbon valence connectivity index (order 1).
short name: chi1vC
subclass of: topological descriptor
preferred label: ValenceCarbonConnectivityIndex(order1)

distance to atom
type: Class
description: Descriptor that calculates the 3D distance between two atoms.
short name: distanceToAtom
subclass of: geometric descriptor
preferred label: DistanceToAtom

effective polarizability
type: Class
description: Descriptor that calculates the effective polarizability of a given heavy atom.
short name: effectivePolarizability
comment: EffectiveAtomPolarizabilityDescriptor, effAtomPol
subclass of: electronic descriptor
preferred label: EffectivePolarizability

hybridization ratio
type: Class
description: Characterizes molecular complexity in terms of carbon hybridization states.
short name: hybratio
comment: 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.
subclass of: topological descriptor
preferred label: HybridizationRatio

Kier and Hall kappa molecular shape indices
type: Class
description: Descriptor that calculates Kier and Hall kappa molecular shape indices.
short name: kierValues
comment: 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.
subclass of: topological descriptor
preferred label: KierAndHallKappaMolecularShapeIndices

partial pi charge
type: Class
description: Descriptor that calculates pi partial charges in pi-bonded systems of an heavy atom based on based on Gasteiger H.Saller (PEPE).
doi: http://dx.doi.org/10.1002/ange.19850970818
short name: partialPiCharge
comment: Other short_name: pepe.
subclass of: electronic descriptor
preferred label: PartialPiCharge

partial sigma charge
type: Class
description: Descriptor that calculates sigma partial charges in sigma-bonded systems (PEOE) of an heavy atom based on Gasteiger Marsili.
doi: http://dx.doi.org/10.1016/0040-4020(80)80168-2
short name: partialSigmaCharge
subclass of: electronic descriptor
preferred label: PartialSigmaCharge

pi electronegativity
type: Class
description: Descriptor that returns the pi electronegativity for a given atom.
short name: piElectronegativity
comment: 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.
subclass of: electronic descriptor
preferred label: PiElectronegativity

The CHEMINF module of PINK Annotation Schema
type: Ontology
abstract: The CHEMINF module of PINK Annotation Schema providing a taxonomy for chemical descriptors.
version IRI: cheminf
introduction: 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).