The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.
chemical information ontology (cheminf) - information entities about chemical entities
To develop the ontology, you must change the default auto-create settings in Protege 4. Go to file>preferences>New Entities. Change the following: specified URI = http://semanticscience.org/resource/ Followed by '/', End with : AutoID AutoID - digit count = 6, prefix = CHEMINF_
A is_enantiomer_of B if and only if, given any a that instantiates A, has molecular graph ag, there is some b such that b instantiates B, is described by molecular graph bg, such that ca is equal to cb and ag is transformed into bg through a C2 symmetric transform.
A is_tautomer_of B if and only if, given any a which instantiates A and has composition ca and is described by a molecular graph ag, there is some b that instantiates B, has composition cb and is described by a molecular graph bg, such that ca equals cb, ag is different from bg and a derives from b as the result of an intramolecular chemical transformation process (i.e. a chemical transformation process which has only one participant), in which only bonds to hydrogen are broken or formed.
An isotopologue is a molecular entity that differs only in isotopic composition from another molecular entity. (AU:I03351)
Subclass relation between a class that has stereochemistry defined and an otherwise identical class that does not.
Connects a molecule to a normalized counterpart of the same molecule according to an algorithm.
Caution: The number of moieties in the first molecule may be greater than in the second molecule. Example: salts.
Caution: this is not a subclass relation and should not be thought of as such for reasoning purposes.
This connects a molecule to its normalized counterpart according to the OPS specification.
Subclass relation between a class that has isotopes specified, for example D2O or 14C-urea, and an otherwise identical class that does not, for example water or urea.
Connects a molecule to molecule with identical heavy-atom connectivity which is neutral. It is not a subclass relation.
Connects a molecule to an isomer with identical constitution but differing in its arrangement of atoms in space. (AU:S05984)
Connects a molecule to an isomer with identical constitution.
Connects a molecule to a stereoisomer which is not its enantiomer.
This connects a molecule to its normalized counterpart according to the PubChem specification.
This connects entities at different granularities.
Has as member parts (see BFO 2 Graz for more on this) many molecular entities.
This is intended to capture the case where a database has ad hoc relations between molecules that are not necessarily subclass relations.
Connects a molecular entity to another molecular entity according to some specification.
has component with uncharged counterpart
Connects a molecular substance, say a mixture containing ions, with a neutral form of one of the ions.
Connects a molecular entity that is deemed similar to another according to some algorithm.
similar to by PubChem 2D similarity algorithm
Has a Tanimoto score with the counterpart molecular entity of more than 0.9, based on the PubChem fingerprint specification.
similar to by PubChem 3D similarity algorithm
Has a 3D Tanimoto score with the counterpart molecule where the 3D shape similarity for the two is greater than 0.795 and the 3D feature score is greater than 0.495 or there are no features and the 3D shape similarity is greater than 0.925, where the shape similarity ST is calculated by ST=VAB/(VAA+VBB-VAB), where VAA and VBB are self-overlap volume of conformers A and B, and VAB is the common overlap volume between them and the feature score CT is calculated by CT=sum(VfAB)/(sum(VfAA)+sum(VfBB)-sum(VfAB)), where the superscript f indicates any of the six independent fictitious feature atom types, VfAA and VfBB are the respective self-overlap volumes of conformers A and B for feature atom type f, and VfAB is the overlap volume of conformers A and B for feature type f.
A exists in an equilibrium with B at pH 7.4 and physiological temperature and B is the dominant isomer.
is_isotopically_unspecified_parent_of
Superclass relation between a class does not have isotopes specified, such as water or urea, and a class that does, such as D2O or 14C-urea.
is_stereoundefined_parent_of
Superclass relation between a class that does not have stereochemistry defined and another otherwise identical one that does.
is component with uncharged counterpart of
This is here because Open PHACTS has requested an inverse. Use with caution!
Connects a neutral molecule with a salt.
is major tautomer at pH 7.4 of
A exists in an equilibrium with B at pH 7.4 and physiological temperature and A is the dominant isomer.
is OPS normalized counterpart of
If A 'is OPS normalized counterpart of' B, then A is the molecular entity corresponding to the connection table obtained by applying OPS normalization to the connection table of B.
is uncharged counterpart of
If A 'is uncharged counterpart of' B, then A is the neutral species corresponding to B. B may itself of course be neutral.
is counterpart with different charge of
If A 'is a counterpart with different charge of' B, then A is an otherwise identical species to B but for charge.
shares OPS normalized parent with
If A 'shares OPS normalized parent with' B, then A 'has OPS normalized counterpart' C and B 'has OPS normalized counterpart' C.
has ChemAxon canonicalised tautomer
If A 'has ChemAxon canonicalised tautomer' B then B is the molecular entity corresponding to the output of ChemAxon's canonical tautomer generation algorithm applied to the connection table of A.
is ChemAxon canonicalised tautomer of
If B 'has ChemAxon canonicalised tautomer' A then B is the molecular entity corresponding to the output of ChemAxon's canonical tautomer generation algorithm applied to the connection table of A.
A chemical entity is any molecular entity or chemical substance.
molecular weight calculated by pipeline pilot
A molecular weight descriptor calculated by a relevant module of the Pipeline Pilot software tool.
Ghose/Crippen ALogP calculation algorithm
Fragment Method used for the calculation of ALogP as defined by Ghose and Crippen. Ghose, A.K., Viswanadhan V.N., and Wendoloski, J.J., Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragment Methods: An Analysis of AlogP and CLogP Methods. J. Phys. Chem. A, 1998, 102, 3762-3772.
Ertl polar surface area calculation algorithm
Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties, Ertl, P., Rohde, B., Selzer, P., J. Med. Chem. 2000, 43, 3714-3717.
polar surface area descriptor calculated by Pipeline Pilot
hydrogen bond acceptor count calculated by pipeline pilot
hydrogen bond donor count calculated by pipeline pilot
rotatable bond count calculated by pipeline pilot
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
Lipinski rule of five violation calculation algorithm
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Deliv. Rev., 1997, 23, 3-25.
rule of five violations calculated by pipeline pilot
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
rule of three passes calculation algorithm
A ‘Rule of Three’ for fragment-based lead discovery? Miles Congreve, Robin Carr, Chris Murray and Harren Jhoti. Drug Discovery Today, 2003,8(19), 876-877
rule of three passes calculated by pipeline pilot
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
medchem friendly descriptor calculated by pipeline pilot
logP calculated by ACD/Labs PhysChem software
octanol-water distribution coefficient calculated at a given pH.
logD calculated at pH 7.4 by ACD/Labs PhysChem software
ACD_LogD(pH7.4) Distribution Coefficient calculated at pH7.4
most acidic pKa calculated by ACD/Labs PhysChem software library
most basic pKa calculated by ACD/Labs PhysChem software library
Molecular Species is a description of the predominant form of the molecule at pH7.4.
molecular species at pH 7.4 calculated by ACD/Labs PhysChem software
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
ACD/Labs PhysChem software library version 12.01
PubChem software library
RDKit software library
RDKit software library version 2015_09_2
number of rule of five violations calculated by RDKit software library version 2015_09_2
hydrogen bond acceptor count calculated by RDKit software library version 2015_09_2
hydrogen bond donor count calculated by RDKit software library version 2015_09_2
logP descriptor calculated by RDKit software library version 2015_09_2
molecular formula calculated by RDKit software library version 2015_09_2
average molecular weight calculated by RDKit software library version 2015_09_2
total polar surface area calculated by RDKit software library version 2015_09_2
PubChem software library version 2.1
molecular weight calculated by the pubchem software library
molecular formula calculated by the pubchem software library
total formal charge calculated by the pubchem software library
monoisotopic mass calculated by the pubchem software library
exact mass calculated by pubchem software library
pubchem depositor-supplied molecular entity name
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.
A software module is a collection of software methods.
Is this equivalent to IAO 'source code module' (IAO_0000096) on the same level as 'software'? From the textual definition in IAO it seems fairly close. (JH)
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is a programming language implementation of a plan specification which is capable of realizing some objective specification when part of a software application.
A software library is a collection of programming language mplementations (e.g. modules, methods) capable of realizing some objective specification when linked to a application software.
A software application is a programming language implementation of a plan specification capable of realizing some objective specification.
logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01
Octanol-water distribution coefficient calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01.
hydrogen bond acceptor count calculated by ACD/Labs PhysChem software library version 12.01
Hydrogen bond acceptor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
hydrogen bond donor count calculated by ACD/Labs PhysChem software library version 12.01
Hydrogen bond donor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
Boiling point at 760 mmHg pressure calculated by ACD/Labs PhysChem software library version 12.01
The boiling point of a substance at 760 mmHg pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
number of freely rotating bonds calculated by ACD/Labs PhysChem software library version 12.01
Number of freely rotating bonds that has been calculated by ACD/Labs PhysChem software library version 12.01.
polar surface area calculated by ACD/Labs PhysChem software library version 12.01
Polar surface area that has been calculated by ACD/Labs PhysChem software library version 12.01.
molecular weight of the corresponding free base
The molecular weight for the free base chemical structure matching this chemical structure.
molar refractivity calculated by ACD/Labs PhysChem software library version 12.01
Molar refractivity that has been calculated by ACD/Labs PhysChem software library version 12.01.
index of refraction calculated by ACD/Labs PhysChem software library version 12.01
Index of refraction that has been calculated by ACD/Labs PhysChem software library version 12.01.
polarizability calculated by ACD/Labs PhysChem software library version 12.01
Polarizability that has been calculated by ACD/Labs PhysChem software library version 12.01.
execution of ACD/Labs PhysChem software library version 12.01
A parameterized software execution of ACD/Labs PhysChem software library version 12.01. This refers to a particular run of the software.
A parameterized software execution of Pipeline Pilot. This refers to a particular run of the software.
A parameterized software execution of GGA Indigo. This refers to a particular run of the software.
molar volume calculated by ACD/Labs PhysChem software library version 12.01
Molar volume that has been calculated by ACD/Labs PhysChem software library version 12.01.
density calculated by ACD/Labs PhysChem software library version 12.01
Density that has been calculated by ACD/Labs PhysChem software library version 12.01.
flash point calculated by ACD/Labs PhysChem software library version 12.01
Flash point that has been calculated by ACD/Labs PhysChem software library version 12.01.
enthalpy of vaporization calculated by ACD/Labs PhysChem software library version 12.01
Enthalpy of vaporization that has been calculated by ACD/Labs PhysChem software library version 12.01.
vapour pressure calculated by ACD/Labs PhysChem software library version 12.01
Vapour pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
organic carbon adsorption coefficient at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
Organic carbon adsorption coefficient at pH 5.5 that has been calculated by ACD/Labs PhysChem software library version 12.01.
organic carbon adsorption coefficient at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
Organic carbon adsorption coefficient at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
bioconcentration factor at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
bioconcentration factor at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01
Number of rule of five violations for a chemical structure that has been calculated by ACD/Labs PhysChem software library version 12.01.
surface tension calculated by ACD/Labs PhysChem software library version 12.01
Surface tension, in dyne per centimetre, that has been calculated by ACD/Labs PhysChem software library version 12.01.
covalent unit count generated by pubchem software library
defined atom stereocenter count generated by the pubchem software library
defined bond stereocenter count generated by pubchem software library
isotope atom count generated by pubchem software library
heavy atom count generated by pubchem software library
undefined atom stereocenter count generated by the pubchem software library
undefined bond stereocenter count generated by the pubchem software library
canonical smiles generated by OEChem
OEChem software library
OEChem software library version 1.9.0
isomeric SMILES generated by OEChem
cycle count
A descriptor that specifies the integer count of cycles in a given molecular entity.
aromatic cycle count
A descriptor that specifies the integer count of aromatic cycles in a given molecular entity.
IUPAC Name generated by LexiChem
LexiChem
LexiChem version 2.2.0
Cactvs software library
Cactvs software library version 3.408
hydrogen bond donor count calculated by cactvs
hydrogen bond acceptor count calculated by cactvs
rotatable bond count calculated by cactvs
structure complexity calculated by cactvs
tautomer count calculated by cactvs
TPSA calculated by cactvs
XLogP3 software library
XLogP3 software library version 3.0
xlogp3 calculated by the xlogp3 software
InChI calculated by library version 1.0.4
InChI software library
InChI software library version 1.0.4
InChIKey generated by software version 1.0.4
OEChem software library version 1.7.6
structural alert count
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.
weighted quantitative estimate of drug-likeness
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.
freezing point descriptor
A descriptor that indicates the temperature at which a chemical substance undergoes a state transition from gas or liquid to solid, under standard conditions.
Henry's Law constant
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.
atmospheric OH rate constant
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.
upper explosive limit descriptor
A physical descriptor for the upper explosive limit of the entity in air as a percentage by volume at room temperature.
lower explosive limit descriptor
A physical descriptor for the lower explosive limit in air as a percentage by volume at room temperature
minimum explosive concentration descriptor
A physical descriptor for the minimum explosive concentration.
specific gravity descriptor
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.
relative density descriptor
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.
vapor density descriptor
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.
odor detection threshold descriptor
A physical descriptor for the lowest concentration of an odorant chemical entity that is perceivable by the human sense of smell.
pH descriptor
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.
evaporation rate descriptor
A physical descriptor of the rate of evaporation of a liquid under standard conditions.
autoignition temperature descriptor
A physical descriptor of the lowest temperature at a substance will spontaneously ignite in a normal atmosphere without an external source of ignition.
soil half-life descriptor
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.
metal atom count
A descriptor that specifies the integer count of metal atoms in a given chemical entity.
oxygen atom count
A descriptor that specifies the integer count of oxygen atoms in a given chemical entity.
software module to calculate a molecular descriptor
A software module to calculate a molecular descriptor is software module that implements an algorithm which calculates a descriptor value for a molecular entity.
An identifying descriptor which is used within a particular database system to identify a chemical system.
A preferred name in ChemSpider by virtue of having been validated by a curator.
A molecular entity name in the ChemSpider database which has not been validated by a curator.
A chemical database identifier which has been validated by a curator.
A role inhering in a person which is realized when they perform a curation task.
A planned process in which a person bearing a curator role confirms an association between a CRID and an information content entity.
A planned process in which a person bearing a curator role marks an association between a chemical name and an information content entity as unconfirmed.
A planned process in which a person bearing a curator role modifies a CRID registry.
A planned process in which a person bearing a curator role confirms an association between a chemical name and an information content entity.
A planned process in which a person bearing a curator role deprecates an association between a chemical name and an information content entity.
A planned process in which an association between a CRID and an information content entity is deprecated.
This can be done automatically; it does not need a person bearing a curator role.
A planned process in which an association between a CRID and an information content entity is marked as unconfirmed.
A ChemSpider validated synonym that has been identified as a title by the ChemSpider software.
average molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01
monoisotopic molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01
energy band gap
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]
metal element mass descriptor
A descriptor describing the mass of the metal element component of a composite substance.
molecular formula calculated by ACD/Labs PhysChem software library version 12.01
Molecular formula for a chemical structure as calculated by ACD/Labs PhysChem software library version 12.01.
partition coefficient
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.
A parameter data item is a data item that plays the role of a parameter to a software method.
A numeric data item is a data item which has a value which is numeric.
A textual data item is a data item which has a value that has at least some non-numeric characters included in it.
A numeric data format specification is a data format specification for data items which are numeric, that is, they contain only numeric values.
A textual data format specification is a specification of the format of data items which are textual, that is, they consist of character data.
specific surface area
A property of solids which is the total surface area of a material per unit of mass, solid or bulk volume, or cross-sectional area.
group of an atom
Descriptor that returns the group in the periodic table of a given atom.
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.
algorithm to interpret a connection table
An algorithm that specifies how to take a connection table and convert it into a representation of a molecule.
structural standardization error
An error message produced in the execution of a structural standardiation algorithm.
structural standardization warning
connection table interpretation warning
connection table interpretation error
information data item
A software message data item which is merely intended to convey information and not a warning or an error.
connection table interpretation information data item
structural standardization information data item
structural validation information data item
International Non-proprietary Name, defined by the WHO.
Identifier used by the USA Food and Drug Administration.
Identifier used by the LipidMaps database, http://www.lipidmaps.org/.
Identifier used by the Cancer Chemotherapy National Service Center.
Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).
In publications of chemical reseach the chemical structure descriptors, e.g. chamical graphs, are often labeled with short names, the local chemical structure symbols, to be more easily referenced in other sections of the publication or supplementary data.
A symbol that is used within a particular local context to denote the descriptor, e.g. a chemical graph, that is used within this context to refer to a specific chemical structure.
local chemical structure symbol
The letter-code and number in your lab journal, used to denote a sample.
A symbol that is used to denote a chemical sample within a local context.
local chemical sample symbol
BCUT
Eigenvalue based descriptor noted for its utility in chemical diversity.
bond partial pi charge
Descriptor that calculates bond-pi Partial charge of a bond by determining the difference the Partial Pi Charge on atoms A and B of a bond (based in Gasteiger Charge).
bond partial sigma charge
Descriptor that calculates bond-sigma Partial charge of a bond.
bond partial total charge
Descriptor that calculates bond-total Partial charge of a bond.
bond sigma electronegativity
Descriptor that calculates of bond-Polarizability of a bond by determining the difference the Sigma electronegativity on atoms A and B of a bond.
bonds to Atom
Descriptor based on the number of bonds on the shortest path between two atoms (topological distance).
This is the shortest distance between a pair of atoms in a graph, defined as the number of edges in the shortest path between the atom pair in the molecular graph.
chi chain indices
Evluates the simple and valence chi chain descriptors (Kier and Hall) of orders 3, 4, 5, 6 and 7.
It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
chi cluster indices
Evluates the simple and valence chi cluster descriptors (Kier and Hall) of orders 3, 4,5 and 6.
chi path indices
Evaluates the Kier and Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7.
chi path-cluster indices
Evaluates the Kier and Hall Chi path cluster indices of orders 4,5 and 6.
gravitational index
Descriptor characterizing the mass distribution of the molecule.
gravitational index (square and cube roots)
Descriptor characterizing the mass distribution of the molecule as the square or cube root of the gravitational index.
acceptor field atoms (Boehm,Klebe)
Counts the number of acceptor field atoms for a carbonyl oxygen probe using force field based definition.
hydrogen bond acceptors (Daylight)
SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
Descriptor that calculates the number of hydrogen bond acceptors (by Daylight).
acceptors or donors field atoms (Boehm,Klebe)
Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe.
donor field atoms (Boehm,Klebe)
Counts the number of donor field atoms for an amino hydrogen probe.
hydrogen bond donors (Daylight)
Descriptor that calculates the number of hydrogen bond donors (by Daylight).
proton belonging to an aromatic system
Descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions.
proton belonging to a pi-system
Descriptor returns true if the protons is directly bonded to a pi system.
Kier Hall SMARTS
Counts the number of occurrences of the E-state fragments.
molecular distance edge
Evaluate molecular distance edge descriptors for C, N and O.
moments of inertia
Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration.
partial total charge (MMFF94)
Descriptor that calculates total partial charges of an heavy atom.
period of an atom
Descriptor that returns the period in the periodic table of an atom belonging to an atom container.
pi-contact of two atoms
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).
proton total partial charge
Descriptor that calculates partial charges of an heavy atom and its protons based on Gasteiger Marsili (PEOE).
RDF proton descriptor
This is a mixed descriptor: topological, geometrical and electronic descriptor.
TAE RECON descriptors for amino acid sequences
Descriptors are derived from pre-calculated quantum mechanical parameters by using the paramaters for amino acids and evaluating a set of 147 descriptors for peptide sequences.
{@cdk.cite BREN1995} {@cdk.cite BREN1997} {@cdk.cite WHITE2003}
weighted path
The weighted path (molecular ID) descriptors were described by Randic and they characterize molecular branching.
WHIM
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.
Holistic descriptors described by Todeschini et al.
Moreau-Broto Autocorrelation (charge) descriptors
The Moreau-Broto autocorrelation descriptors using partial charges.
Moreau-Broto autocorrelation (mass) descriptors
The Moreau-Broto autocorrelation descriptors using atomic weight.
Moreau-Broto autocorrelation (polarizability) descriptors
The Moreau-Broto autocorrelation descriptors using polarizability.
carbon types
Characterizes the carbon connectivity in terms of hybridization
C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3, C4SP3
carbon connectivity index (order 0)
Descriptor that calculates the carbon connectivity index (order 0).
valence connectivity index (order 0)
Descriptor that calculates atomic valence connectivity index (order 0).
valence carbon connectivity index (order 0)
Descriptor that calculates carbon valence connectivity index (order 0).
carbon connectivity index (order 1)
Descriptor that calculates carbon connectivity index (order 1).
valence connectivity index (order 1)
Descriptor that calculates atomic valence connectivity index (order 1).
valence carbon connectivity index (order 1)
Descriptor that calculates carbon valence connectivity index (order 1).
distance to atom
Descriptor that calculates the 3D distance between two atoms.
effective polarizability
EffectiveAtomPolarizabilityDescriptor, effAtomPol
Descriptor that calculates the effective polarizability of a given heavy atom.
hybridization ratio
Characterizes molecular complexity in terms of carbon hybridization states.
It reports the fraction of sp3 carbons to sp2 carbons as Nsp3/ (Nsp3 + Nsp2). The original form of the descriptor (i.e., simple ratio) has been used to characterize molecular complexity, especially in the are of natural products , which usually have a high value of the sp3 to sp2 ratio. Other short names: HybridizationRatio, HybRatio.
Kier and Hall kappa molecular shape indices
Descriptor that calculates Kier and Hall kappa molecular shape indices.
Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs. First kappa shape index is given by n ( n - 1 ) 2 m 2 , second kappa shape index is given by ( n - 1 ) ( n - 2 ) 2 p 2 2 and third kappa shape index is given by ( n - 1 ) ( n - 3 ) 2 p 3 2 for odd n and ( n - 3 ) ( n - 2 ) 2 p 3 2 for enev n, where n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3. Other short names: KappaShapeIndices, Kier1, Kier2, Kier3.
partial pi charge
Descriptor that calculates pi partial charges in pi-bonded systems of an heavy atom based on based on Gasteiger H.Saller (PEPE).
partial sigma charge
Descriptor that calculates sigma partial charges in sigma-bonded systems (PEOE) of an heavy atom based on Gasteiger Marsili.
pi electronegativity
Descriptor that returns the pi electronegativity for a given atom.
Pi electronegativity is given by X = a + b q + c ( q 2 ) , where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge. Other short_name: elecPiA.
SwissLipids identifier
MolMeDB identifier
PDB ligand identifier
PDB structure identifier
NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community.
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.
A descriptor characterizing the ratio of the length to the breadth of a given entity.