BlueObelisk Algorithm ontology
A copy of Blue Obelisk algorithm ontology from http://qsar.svn.sf.net/viewvc/qsar/trunk/qsar-dicts/descriptor-algorithms.owl?revision=212&pathrev=212
descriptor-algorithms.owl
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<?xml version="1.0"?>
<rdf:RDF
xmlns="http://www.w3.org/1998/Math/MathML"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:cvs="https://www.cvshome.org/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:j.0="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:bibtex="http://bibtexml.sf.net/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xml:base="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/">
<owl:Ontology rdf:about="">
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>210</owl:versionInfo>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Descriptor Ontology</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2009-07-19</dc:date>
</owl:Ontology>
<owl:Class rdf:ID="AtomicDescriptor">
<dc:contributor>
<j.0:Contributor rdf:ID="elw">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Egon Willighagen</rdfs:label>
</j.0:Contributor>
</dc:contributor>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Atomic Descriptors</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-11-18</dc:date>
<rdfs:subClassOf>
<owl:Class rdf:ID="Descriptor"/>
</rdfs:subClassOf>
</owl:Class>
<owl:Class rdf:ID="DataFeature">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Data Feature</rdfs:label>
</owl:Class>
<owl:Class rdf:ID="MolecularDescriptor">
<rdfs:subClassOf>
<owl:Class rdf:about="#Descriptor"/>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="#AtomicDescriptor"/>
<owl:disjointWith>
<owl:Class rdf:ID="BondDescriptor"/>
</owl:disjointWith>
<owl:disjointWith>
<owl:Class rdf:ID="ProteinDescriptor"/>
</owl:disjointWith>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Molecular Descriptors</rdfs:label>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-11-18</dc:date>
</owl:Class>
<owl:Class rdf:about="#Descriptor">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Descriptor</rdfs:label>
<rdfs:subClassOf>
<owl:Class rdf:ID="Algorithm"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>
A feature (descriptor) is an algorithm that operates on a chemical
entity (commonly atoms and molecules)
and returns a numerical or nominal (descriptor) value which described
certain information on that entity.
</rdfs:comment>
</owl:Class>
<owl:Class rdf:ID="Implementation">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Implementation</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#Algorithm">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Algorithm</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#BondDescriptor">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2009-07-07</dc:date>
<owl:disjointWith rdf:resource="#AtomicDescriptor"/>
<owl:disjointWith rdf:resource="#MolecularDescriptor"/>
<owl:disjointWith>
<owl:Class rdf:about="#ProteinDescriptor"/>
</owl:disjointWith>
<rdfs:subClassOf rdf:resource="#Descriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Atomic Descriptors</rdfs:label>
<dc:contributor rdf:resource="#elw"/>
</owl:Class>
<owl:Class rdf:ID="DataRepresentation">
<rdfs:subClassOf rdf:resource="#DataFeature"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Data Representation</rdfs:label>
</owl:Class>
<owl:Class rdf:ID="Category">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Category</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#ProteinDescriptor">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Protein Descriptor</rdfs:label>
<rdfs:subClassOf rdf:resource="#Descriptor"/>
<j.0:definition rdf:parseType="Literal">
A descriptor specifically designed for characterizing proteins
</j.0:definition>
<dc:contributor rdf:resource="#rg"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-11-02</dc:date>
<owl:disjointWith rdf:resource="#AtomicDescriptor"/>
<owl:disjointWith rdf:resource="#BondDescriptor"/>
<owl:disjointWith rdf:resource="#MolecularDescriptor"/>
</owl:Class>
<owl:Class rdf:ID="Reference"/>
<owl:Class rdf:ID="DescriptorValue">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Descriptor Value</rdfs:label>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>One or more output values calculated by an Implementation
of a certain Algorithm for a certain molecule.
</rdfs:comment>
</owl:Class>
<owl:Class rdf:ID="Contributor">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Contributor</rdfs:label>
</owl:Class>
<owl:ObjectProperty rdf:ID="isClassifiedAs">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Is Classified As</rdfs:label>
<rdfs:range rdf:resource="#Category"/>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="isA">
<rdfs:range rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Is A</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="requires">
<rdfs:range rdf:resource="#DataFeature"/>
<rdfs:domain rdf:resource="#Algorithm"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Requires</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="instanceOf">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Instance Of</rdfs:label>
<rdfs:domain rdf:resource="#Implementation"/>
<rdfs:range rdf:resource="#Algorithm"/>
</owl:ObjectProperty>
<j.0:MolecularDescriptor rdf:ID="kierHallSmarts">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-09-26</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Kier & Hall SMARTS</rdfs:label>
<dc:contributor>
<j.0:Contributor rdf:ID="rguha">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Rajarshi Guha</rdfs:label>
</j.0:Contributor>
</dc:contributor>
<j.0:isClassifiedAs>
<j.0:Category rdf:ID="topologicalDescriptor">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Topological Descriptor</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<j.0:definition rdf:parseType="Literal">
Descriptor reflecting the molecular connectivity without geometry information.
</j.0:definition>
<j.0:isClassifiedAs>
<j.0:Category rdf:ID="descriptorCategories">
<dc:contributor rdf:resource="#elw"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>DescriptorCategories</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-11-18</dc:date>
</j.0:Category>
</j.0:isClassifiedAs>
<dc:contributor rdf:resource="#elw"/>
</j.0:Category>
</j.0:isClassifiedAs>
<j.0:description rdf:parseType="Literal">
Traditionally, the E-state indices are obtained by identifying a set of
fragments and then evaluating the E-state index from them. However it has
been shown by Butina (Molecules, 2004, 9, 1004-1009) that the frequency
of occurrence of the fragments can lead to QSAR models that perform as well
as those based on the original E-state indices. This descriptor generates
counts for 35 fragments. Descriptor names are prefixed with "khs."
</j.0:description>
<j.0:definition rdf:parseType="Literal">
Counts the number of occurrences of the E-state fragments
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="chiCluster">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Chi Cluster Indices</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:description rdf:parseType="Literal">
Both the simple and valence versions of this descriptor are evaluated
</j.0:description>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-11-13</dc:date>
<j.0:definition rdf:parseType="Literal">
Evaluates the Kier & Hall Chi cluster indices of orders 3,4,5,6 and 7
</j.0:definition>
<dc:contributor rdf:resource="#rguha"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="gravitationalIndex">
<j.0:isClassifiedAs>
<j.0:Category rdf:ID="geometricalDescriptor">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Geometrical Descriptor</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Any descriptor derived from the three-dimensional structure of the molecule.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#descriptorCategories"/>
<dc:contributor rdf:resource="#elw"/>
</j.0:Category>
</j.0:isClassifiedAs>
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor rdf:resource="#elw"/>
<j.0:description rdf:parseType="Literal">
This descriptor is described by Katritzky et al.
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="KAT96"></bibtex:cite>
.
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Gravitational Index</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor characterizing the mass distribution of the molecule.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-24</dc:date>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="SALLER">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Gasteiger, J.</bibtex:author>
<bibtex:author>Saller, H.</bibtex:author>
<bibtex:title>
Berechnung der Ladungsverteilung in konjugierten
Systemen durch eine Quantifizierung des
Mesomeriekonzeptes
</bibtex:title>
<bibtex:journal>Angew. Chem.</bibtex:journal>
<bibtex:year>1985</bibtex:year>
<bibtex:volume>97</bibtex:volume>
<bibtex:pages>699-701</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:Reference rdf:ID="ERTL2000">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Ertl, P. and Rohde, B. and Selzer, P.</bibtex:author>
<bibtex:title>Fast Calculation of Molecular Polar Surface Area as a Sum of
Fragment-Based Contributions and Its Application to the Prediction of
Drug Transport Properties
</bibtex:title>
<bibtex:journal>J. Med. Chem.</bibtex:journal>
<bibtex:year>2000</bibtex:year>
<bibtex:volume>43</bibtex:volume>
<bibtex:number>20</bibtex:number>
<bibtex:pages>3714-3717</bibtex:pages>
<bibtex:doi>10.1021/jm000942e</bibtex:doi>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="chiPathCluster">
<dc:contributor rdf:resource="#rguha"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-11-13</dc:date>
<j.0:definition rdf:parseType="Literal">
Evaluates the Kier & Hall Chi path cluster indices of orders 4,5 and 6
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:description rdf:parseType="Literal">
Both the simple and valence versions of this descriptor are evaluated
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Chi Path-Cluster Indices</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="weightedPath">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Weighted path descriptors</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-01-15</dc:date>
<dc:contributor rdf:resource="#rguha"/>
<j.0:definition rdf:parseType="Literal">
The weighted path (molecular ID) descriptors described by Randic. They characterize molecular branching.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="chi1C">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<dc:contributor>
<j.0:Contributor rdf:ID="mf">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Matteo Floris</rdfs:label>
</j.0:Contributor>
</dc:contributor>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates carbon connectivity index (order 1).
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Carbon connectivity index (order 1)</rdfs:label>
<j.0:description rdf:parseType="Literal">
While the atomic connectivity is calculated as the sum of
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>d</mi>
<mi>i</mi>
</msub>
</mrow>
<mrow>
<msub>
<mi>d</mi>
<mi>j</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mi>0.5</mi>
</msup>
</mrow>
</mfrac>
</mrow>
over all bonds between heavy atoms i and j, the carbon connectivity index
takes into account only bonds between carbon atoms.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:BondDescriptor rdf:ID="bondSigmaElectronegativity">
<dc:contributor>
<j.0:Contributor rdf:ID="mrc">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Miguel Rojas</rdfs:label>
</j.0:Contributor>
</dc:contributor>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Bond Sigma Electronegativity</rdfs:label>
<j.0:isClassifiedAs>
<j.0:Category rdf:ID="electronicDescriptor">
<j.0:definition rdf:parseType="Literal">
Descriptor relating to the electronic distribution in a molecule.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Electronic Descriptors</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<j.0:isClassifiedAs rdf:resource="#descriptorCategories"/>
<dc:contributor rdf:resource="#elw"/>
</j.0:Category>
</j.0:isClassifiedAs>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates of bond-Polarizability of a bond.
</j.0:definition>
<j.0:description rdf:parseType="Literal">
Calculation is calculated determining the difference the
Sigma electronegativity on atoms A and B of a bond.
</j.0:description>
</j.0:BondDescriptor>
<j.0:MolecularDescriptor rdf:ID="eccentricConnectivityIndex">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Eccentric Connectivity Index</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-03-19</dc:date>
<j.0:description rdf:parseType="Literal">
The eccentric connectivity index for a hydrogen supressed molecular graph is given by the
expression
<math xmlns="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#" display="block" overflow="scroll">
<msup>
<mi>ξ</mi>
<mi>c</mi>
</msup>
<mo>=</mo>
<munder>
<mo>∑</mo>
<mrow>
<mi>i</mi>
<mo>=</mo>
<mn>1</mn>
</mrow>
</munder>
<mi>n</mi>
<mi>E</mi>
<mo></mo>
<mfenced>
<mi>i</mi>
</mfenced>
<mi>V</mi>
<mo></mo>
<mfenced>
<mi>i</mi>
</mfenced>
</math>
where E(i) is the eccentricity of the i
<sup xmlns="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#">th</sup>
atom (path length from the
i
<sup xmlns="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#">th</sup>
atom to the atom farthest from it) and V(i) is the vertex degree of the
i
<sup xmlns="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#">th</sup>
atom.
</j.0:description>
<j.0:definition rdf:parseType="Literal">
A topological descriptor combining distance and adjacency information.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:contributor rdf:resource="#rguha"/>
</j.0:MolecularDescriptor>
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date"/>
<j.0:Contributor rdf:ID="pmr">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Peter Murray-Rust</rdfs:label>
</j.0:Contributor>
<j.0:MolecularDescriptor rdf:ID="lipinskifailures">
<j.0:isClassifiedAs>
<j.0:Category rdf:ID="constitutionalDescriptor">
<dc:contributor rdf:resource="#elw"/>
<j.0:definition rdf:parseType="Literal">
Descriptor reflecting the molecular composition of a compound without
connectivity and geometry information.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#descriptorCategories"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Constitutional Descriptor</rdfs:label>
</j.0:Category>
</j.0:isClassifiedAs>
<j.0:description rdf:parseType="Literal">
The Rule of 5 got its name from the cutoff values for each of the four parameters that define the potential
of
a drug candidate for good absorption: all of these values are close to five or a multiple of five.
The original definition, given by Christopher A. Lipinski, says that poor absorption (or permeation) is
<em xmlns="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#">more likely</em>
when:
the molecule has more than 5 H-bond donors and more than 10 H-bond acceptors;
its molecular weight is over 500.
its LogP is over 5;
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Lipinski's Rule of Five</rdfs:label>
<j.0:definition rdf:parseType="Literal">
This Class contains a method that returns the number failures of the
Lipinski's Rule Of Five.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
</j.0:MolecularDescriptor>
<j.0:BondDescriptor rdf:ID="bondPartialSigmaCharge">
<j.0:description rdf:parseType="Literal">
Calculation is calculated determining the difference the
Partial Sigma Charge on atoms A and B of a bond. Based in
Gasteiger Charge.
</j.0:description>
<dc:contributor rdf:resource="#mrc"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates bond-sigma Partial charge of a
bond.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Bond Partial Sigma Charge</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:BondDescriptor>
<j.0:AtomicDescriptor rdf:ID="atomHybridizationVSEPR">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Atomic Hybridization VSEPR</rdfs:label>
<j.0:description rdf:parseType="Literal">
The calculation find a SIMPLE WAY the molecular geometry for
following from Valence Shell Electron Pair Repulsion or
VSEPR model and at the same time its hybridization of atoms
in a molecule.
</j.0:description>
<dc:contributor rdf:resource="#mrc"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that returns the hybridization state of an atom.
</j.0:definition>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="chiChain">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-11-12</dc:date>
<j.0:definition rdf:parseType="Literal">
Evaluates the Kier & Hall Chi chain indices of orders 3,4,5 and 6
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:description rdf:parseType="Literal">
Both the simple and valence versions of this descriptor are evaluated
</j.0:description>
<dc:contributor rdf:resource="#rguha"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Chi Chain Indices</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="ringCount">
<j.0:definition rdf:parseType="Literal">
Descriptor that counts the number of rings in the molecules. Optionally,
it counts the number rings with a specified number of ring atoms.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2009-07-23</dc:date>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:contributor rdf:resource="#elw"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Ring Count</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="sigmaElectronegativity">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<j.0:definition rdf:parseType="Literal">
This Class contains a method that returns the sigma electronegativity for a given atom.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
<j.0:description rdf:parseType="Literal">
Sigma electronegativity is given by
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mi>X</mi>
<mo>=</mo>
<mi>a</mi>
<mo>+</mo>
<mi>b</mi>
<mi>q</mi>
<mo>+</mo>
<mi>c</mi>
<mrow>
<mo>(</mo>
<mrow>
<msup>
<mi>q</mi>
<mi>2</mi>
</msup>
</mrow>
<mo>)</mo>
</mrow>
</mrow>
,
where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge.
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Sigma Electronegativity</rdfs:label>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="rotatableBondsCount">
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the number of nonrotatable bonds on a molecule.
</j.0:definition>
<j.0:description rdf:parseType="Literal">
The number of rotatable bonds is given by the SMARTS specified by Daylight on
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="DAY01"></bibtex:cite>
.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Rotatable Bonds Count</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="ip">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-01-15</dc:date>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<dc:contributor rdf:resource="#mr"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Ionization Potential</rdfs:label>
<j.0:description rdf:parseType="Literal">
It should be noted that the descriptor values are obtained using a predictive model
and are not calculated directly from the structure
</j.0:description>
<j.0:definition rdf:parseType="Literal">
Descriptor that evaluates the ionization potential.
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="atomHybridization">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Atomic Hybridization</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor that returns the hybridization state of an atom.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="aromaticAtomsCount">
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Aromatic Atoms Count</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:definition rdf:parseType="Literal">
Descriptor based on the number of aromatic atoms of a molecule.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="WHIM">
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>WHIM</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Holistic descriptors described by Todeschini et al
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="TOD98"></bibtex:cite>
.
</j.0:definition>
<j.0:isClassifiedAs>
<j.0:Category rdf:ID="hybridDescriptor">
<j.0:isClassifiedAs rdf:resource="#descriptorCategories"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Hybrid Descriptor</rdfs:label>
<dc:contributor rdf:resource="#rg"/>
</j.0:Category>
</j.0:isClassifiedAs>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="petitjeanShapeIndex">
<dc:contributor rdf:resource="#rguha"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Petitjean Shape Indices</rdfs:label>
<j.0:definition rdf:parseType="Literal">
The topological and geometric shape indices described Petitjean and Bath et al.
respectively. Both measure the anisotropy in a molecule.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#geometricalDescriptor"/>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-01-15</dc:date>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="TOD98">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Todeschini, R. and Gramatica, P.</bibtex:author>
<bibtex:title>New 3D Molecular Descriptors: The WHIM theory and QAR Applications</bibtex:title>
<bibtex:journal>Persepectives in Drug Discovery and Design</bibtex:journal>
<bibtex:year>1998</bibtex:year>
<bibtex:pages>355-380</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:AtomicDescriptor rdf:ID="covalentRadius">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Covalent Radius</rdfs:label>
<dc:contributor rdf:resource="#mrc"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<j.0:definition rdf:parseType="Literal">
Descriptor that returns the covalent radius of a given atom.
</j.0:definition>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="xlogP">
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>XLogP</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Prediction of logP based on the atom-type method called XLogP.
</j.0:definition>
<j.0:description rdf:parseType="Literal">
For a description of the methodology see
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="WANG97"></bibtex:cite>
.
</j.0:description>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="chi0vC">
<j.0:description rdf:parseType="Literal">
Let
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>=</mo>
<mrow>
<mfrac>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mi>1</mi>
<mo>)</mo>
</mrow>
</mfrac>
</mrow>
</mrow>
,
where
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>p</mi>
<mi>i</mi>
</msub>
</mrow>
is the numbers of valence electrons of atom i,
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
is the number of hydrogens bonded to atom i, and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
is the atomic number of atom i.
While the atomic valence connectivity is calculated as the sum of
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mi>0.5</mi>
</msup>
</mrow>
</mfrac>
</mrow>
over all heavy atoms i with
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
greather than 0,
the carbon valence connectivity index takes into account only carbon atoms with
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
greather than 0.
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Valence carbon connectivity index (order 0)</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates carbon valence connectivity index (order 0).
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="largestChain">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Largest Chain</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Returns the number of atoms in the largest chain
</j.0:definition>
<dc:contributor>
<j.0:Contributor rdf:ID="chhoppe">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Christian Hoppe</rdfs:label>
</j.0:Contributor>
</dc:contributor>
<j.0:description rdf:parseType="Literal">
</j.0:description>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="partialSigmaCharge">
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates sigma partial charges in
sigma-bonded systems (PEOE) of an heavy atom.
</j.0:definition>
<dc:contributor rdf:resource="#mrc"/>
<j.0:description rdf:parseType="Literal">
Calculation is based on Gasteiger Marsili (PEOE)
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="MARSILI"></bibtex:cite>
.
</j.0:description>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Partial Pi Charge</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="NilaComplexity">
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-8-22</dc:date>
<j.0:definition rdf:parseType="Literal">
Class that returns the complexity of a system. The complexity is defined as @cdk.cite{Nilakantan06}
</j.0:definition>
<dc:contributor rdf:resource="#chhoppe"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Fragment Complexity</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="longestAliphaticChain">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Longest Aliphatic Chain</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<j.0:description rdf:parseType="Literal">
</j.0:description>
<j.0:definition rdf:parseType="Literal">
Returns the number of atoms in the longest aliphatic chain
</j.0:definition>
<dc:contributor rdf:resource="#chhoppe"/>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="atomicSoftness">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-04-21</dc:date>
<j.0:description rdf:parseType="Literal">
Inductive atomic softness of an atom in a polyatomic system can be defined
as as charge delocalizing ability.
This descriptor is described by Cherkasov
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="CHER2003"></bibtex:cite>
.
</j.0:description>
<dc:contributor rdf:resource="#mf"/>
<j.0:definition rdf:parseType="Literal">
This class calculates the atomic softness of a given atom.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Inductive atomic softness</rdfs:label>
</j.0:AtomicDescriptor>
<j.0:DataFeature rdf:ID="has2DCoordinates">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>has 2D Coordinates</rdfs:label>
</j.0:DataFeature>
<j.0:MolecularDescriptor rdf:ID="zagrebIndex">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Zagreb Index</rdfs:label>
<j.0:definition rdf:parseType="Literal">
The sum of the squared atom degrees of all heavy atoms.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="mde">
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Molecular Distance Edge</rdfs:label>
<dc:contributor rdf:resource="#rguha"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-09-18</dc:date>
<j.0:description rdf:parseType="Literal">
For a description of the methodology see
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="LIU98"></bibtex:cite>
.
</j.0:description>
<j.0:definition rdf:parseType="Literal">
Evaluate molecular distance edge descriptors for C, N and O
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="atomDegree">
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the number of not-Hs substituents of an atom.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Atomic Degree</rdfs:label>
<dc:contributor rdf:resource="#mf"/>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="chi1v">
<dc:contributor rdf:resource="#mf"/>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:description rdf:parseType="Literal">
Let
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>=</mo>
<mrow>
<mfrac>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mi>1</mi>
<mo>)</mo>
</mrow>
</mfrac>
</mrow>
</mrow>
,
where
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>p</mi>
<mi>i</mi>
</msub>
</mrow>
is the numbers of valence electrons of atom i,
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
is the number of hydrogens bonded to atom i, and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
is the atomic number of atom i.
Valence connectivity is calculated as the sum of
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mrow>
<msub>
<mi>v</mi>
<mi>j</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mi>0.5</mi>
</msup>
</mrow>
</mfrac>
</mrow>
over all bonds between heavy atoms i and j.
</j.0:description>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates atomic valence connectivity index (order 1).
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Valence connectivity index (order 1)</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="vAdjMa">
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:description rdf:parseType="Literal">
The values is given by
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mn>1</mn>
<mo>+</mo>
<mo>log</mo>
<mn>2</mn>
<mo>*</mo>
<mn>m</mn>
</mrow>
,
where m is the number of heavy-heavy bonds.
If m is zero, then zero is returned.
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Vertex adjacency information magnitude</rdfs:label>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the vertex adjacency information of a molecule.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="gravitationalIndex_SquareAndCubeRoots">
<j.0:description rdf:parseType="Literal">
This descriptor is described by Wessel et al.
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="WES98"></bibtex:cite>
.
</j.0:description>
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor rdf:resource="#elw"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Gravitational Index (Square and Cube Roots)</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-25</dc:date>
<j.0:definition rdf:parseType="Literal">
Descriptor characterizing the mass distribution of the molecule as the square
or cube root of the gravitational index.
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="chi0v">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Valence connectivity index (order 0)</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates atomic valence connectivity index (order 0).
</j.0:definition>
<j.0:description rdf:parseType="Literal">
Let
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>=</mo>
<mrow>
<mfrac>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mi>1</mi>
<mo>)</mo>
</mrow>
</mfrac>
</mrow>
</mrow>
,
where
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>p</mi>
<mi>i</mi>
</msub>
</mrow>
is the numbers of valence electrons of atom i,
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
is the number of hydrogens bonded to atom i, and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
is the atomic number of atom i.
Valence connectivity is calculated as the sum of
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mi>0.5</mi>
</msup>
</mrow>
</mfrac>
</mrow>
over all heavy atoms i with
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
greather than 0.
</j.0:description>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="MARSILI">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Gasteiger, J.</bibtex:author>
<bibtex:author>Marsili, M.</bibtex:author>
<bibtex:title>
Iterative Partial Equalization of Orbital
Electronegativity- A Rapid Access to Atomic Charges
</bibtex:title>
<bibtex:journal>Tetrahedron</bibtex:journal>
<bibtex:year>1980</bibtex:year>
<bibtex:volume>36</bibtex:volume>
<bibtex:pages>3219-3228</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:AtomicDescriptor rdf:ID="partialPiCharge">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Partial Pi Charge</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<j.0:description rdf:parseType="Literal">
Calculation is based on Gasteiger H.Saller (PEPE)
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="SALLER"></bibtex:cite>
.
</j.0:description>
<dc:contributor rdf:resource="#mrc"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates pi partial charges in pi-bonded
systems of an heavy atom.
</j.0:definition>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="chiPath">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-11-12</dc:date>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:contributor rdf:resource="#rguha"/>
<j.0:description rdf:parseType="Literal">
Both the simple and valence versions of this descriptor are evaluated
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Chi Path Indices</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Evaluates the Kier & Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="period">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Period of an atom</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that returns the period in the periodic table of an atom belonging to an atom container
</j.0:definition>
</j.0:AtomicDescriptor>
<j.0:Reference rdf:ID="PEA99">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Pearlman, R.S. and Smith, K.M.</bibtex:author>
<bibtex:title>Metric Validation and the Receptor-Relevant Subspace Concept</bibtex:title>
<bibtex:journal>J. Chem. Inf. Comput. Sci.</bibtex:journal>
<bibtex:year>1999</bibtex:year>
<bibtex:volume>39</bibtex:volume>
<bibtex:number>1</bibtex:number>
<bibtex:pages>28-35</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:AtomicDescriptor rdf:ID="partialTChargeMMFF94">
<j.0:description rdf:parseType="Literal">
Calculation is based on MMFF94.
</j.0:description>
<dc:contributor rdf:resource="#mrc"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates total partial charges of an heavy
atom.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Partial Total Charge (MMFF94)</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:AtomicDescriptor>
<j.0:Reference rdf:ID="PL96">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Patani, G. A. and LaVoie, E. J.</bibtex:author>
<bibtex:title>Bioisosterism: A Rational Approach in Drug Design</bibtex:title>
<bibtex:journal>Chem. Rev.</bibtex:journal>
<bibtex:year>1996</bibtex:year>
<bibtex:volume>96</bibtex:volume>
<bibtex:pages>3147-3176</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:Descriptor rdf:ID="piContact">
<dc:contributor rdf:resource="#mf"/>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Pi-contact of two atoms</rdfs:label>
<j.0:definition rdf:parseType="Literal">
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).
</j.0:definition>
</j.0:Descriptor>
<j.0:MolecularDescriptor rdf:ID="autoCorrelationMass">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Moreau-Broto Autocorrelation (mass) descriptors</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-01-15</dc:date>
<j.0:definition rdf:parseType="Literal">
The Moreau-Broto autocorrelation descriptors using atomic weight
</j.0:definition>
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor>
<j.0:Contributor rdf:ID="fm">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Federico Marighetti</rdfs:label>
</j.0:Contributor>
</dc:contributor>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="petitjeanNumber">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the Petitjean Number of a molecule.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<j.0:description rdf:parseType="Literal">
According to the Petitjean definition, 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
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>r</mi>
<mi>i</mi>
</msub>
</mrow>
is the largest matrix entry in row i of the distance matrix D, then the radius
is defined as the smallest of the
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>r</mi>
<mi>i</mi>
</msub>
</mrow>
.
The graph diameter D is defined as the largest vertex eccentricity in the graph.
Petitjean Number is the value of
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mrow>
<mo>(</mo>
<ci>diameter</ci>
<mo>-</mo>
<ci>radius</ci>
<mo>)</mo>
</mrow>
<ci>diameter</ci>
</mfrac>
</mrow>
.
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Petitjean Number</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:Descriptor rdf:ID="distanceToAtom">
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the 3D distance between two atoms.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<j.0:isClassifiedAs rdf:resource="#geometricalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Distance to Atom</rdfs:label>
</j.0:Descriptor>
<j.0:Reference rdf:ID="TC00">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Todeschini, R. and Consonni, V.</bibtex:author>
<bibtex:title>Handbook of Molecular Descriptors</bibtex:title>
<bibtex:year>2000</bibtex:year>
<bibtex:isbn>3-52-29913-0</bibtex:isbn>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="apol">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Atomic Polarizabilities</rdfs:label>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<j.0:description rdf:parseType="Literal">
Polarizabilities derive from periodic tables.
</j.0:description>
<j.0:requires>
<j.0:DataRepresentation rdf:ID="GraphRepresentation">
<owl:differentFrom>
<j.0:DataRepresentation rdf:ID="DietzRepresentation">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Dietz Representation</rdfs:label>
<owl:differentFrom rdf:resource="#GraphRepresentation"/>
</j.0:DataRepresentation>
</owl:differentFrom>
<j.0:description rdf:parseType="Literal">
Representation in which atoms are represented by graph nodes and
bonds by graph edges. Consequently, bonds are always localized
between two atoms.
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Graph Representation</rdfs:label>
</j.0:DataRepresentation>
</j.0:requires>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the sum of the atomic polarizabilities (including implicit hydrogens).
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="WANG97">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Wang, R., Fu, Y., and Lai, L.</bibtex:author>
<bibtex:title>A New Atom-Additive Method for Calculating Partition Coefficients</bibtex:title>
<bibtex:journal>Journal of Chemical Information and Computer
Sciences
</bibtex:journal>
<bibtex:year>1997</bibtex:year>
<bibtex:volume>37</bibtex:volume>
<bibtex:pages>615-621</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:AtomicDescriptor rdf:ID="piElectronegativity">
<j.0:definition rdf:parseType="Literal">
This algorithm contains a method that returns the pi
electronegativity for a given atom.
</j.0:definition>
<dc:contributor rdf:resource="#mrc"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Pi Electronegativity</rdfs:label>
<j.0:description rdf:parseType="Literal">
Pi electronegativity is given by
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mi>X</mi>
<mo>=</mo>
<mi>a</mi>
<mo>+</mo>
<mi>b</mi>
<mi>q</mi>
<mo>+</mo>
<mi>c</mi>
<mrow>
<mo>(</mo>
<mrow>
<msup>
<mi>q</mi>
<mi>2</mi>
</msup>
</mrow>
<mo>)</mo>
</mrow>
</mrow>
, where a, b and c are Gasteiger Marsili parameters, and q
is the sigma charge.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="hBondAcceptorsDonorsBoehmKlebe">
<dc:contributor>
<j.0:Contributor rdf:ID="jkw">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Joerg Kurt Wegner</rdfs:label>
</j.0:Contributor>
</dc:contributor>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-09-08</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Acceptors or Donors Field Atoms (Boehm,Klebe)</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:description rdf:parseType="Literal">
Force field based definition of hydrogen bond acceptors or donors <bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="BK02"></bibtex:cite>.
This rule covers amino and hydroxy groups.
</j.0:description>
<j.0:definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>
Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe.
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="chi1vC">
<j.0:description rdf:parseType="Literal">
Let
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>=</mo>
<mrow>
<mfrac>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mrow>
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
<mo>-</mo>
<mi>1</mi>
<mo>)</mo>
</mrow>
</mfrac>
</mrow>
</mrow>
,
where
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>p</mi>
<mi>i</mi>
</msub>
</mrow>
is the numbers of valence electrons of atom i,
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>h</mi>
<mi>i</mi>
</msub>
</mrow>
is the number of hydrogens bonded to atom i, and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>z</mi>
<mi>i</mi>
</msub>
</mrow>
is the atomic number of atom i.
While the valence connectivity is calculated as the sum of
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<mrow>
<msub>
<mi>v</mi>
<mi>i</mi>
</msub>
</mrow>
<mrow>
<msub>
<mi>v</mi>
<mi>j</mi>
</msub>
</mrow>
<mo>)</mo>
</mrow>
<mi>0.5</mi>
</msup>
</mrow>
</mfrac>
</mrow>
over all bonds between heavy atoms i and j, the carbon valence
connectivity index takes into account only bonds between carbon atoms.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates carbon valence connectivity index (order 1).
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Valence carbon connectivity index (order 1)</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<dc:contributor rdf:resource="#mf"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="autoCorrelationPolarizability">
<j.0:definition rdf:parseType="Literal">
The Moreau-Broto autocorrelation descriptors using polarizability
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Moreau-Broto Autocorrelation (polarizability) descriptors</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-01-15</dc:date>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor rdf:resource="#fm"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="largestPiSystem">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<j.0:description rdf:parseType="Literal">
</j.0:description>
<j.0:definition rdf:parseType="Literal">
Returns the number of atoms in the largest pi chain
</j.0:definition>
<dc:contributor rdf:resource="#chhoppe"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Largest Pi Chain</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="hBondacceptors">
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the number of hydrogen bond acceptors.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Hydrogen Bond Acceptors</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="isProtonInConjugatedPiSystem">
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
<j.0:definition rdf:parseType="Literal">
This Class contains a method that returns true if the protons is directly bonded to a pi system.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Proton belonging to a pi-system</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
</j.0:AtomicDescriptor>
<j.0:DataFeature rdf:ID="hasFractionalUnitCellCoordinatesCoordinates">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>has Fractional Unit Cell Coordinates Coordinates</rdfs:label>
</j.0:DataFeature>
<j.0:ProteinDescriptor rdf:ID="aminoAcidsCount">
<dc:contributor rdf:resource="#elw"/>
<j.0:definition rdf:parseType="Literal">
Returns the number of amino acids found in the system
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Amino Acid Count</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-01-15</dc:date>
<j.0:description rdf:parseType="Literal">
</j.0:description>
</j.0:ProteinDescriptor>
<j.0:MolecularDescriptor rdf:ID="ALOGP">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>ALogP</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Calculates atom additive logP and molar refractivity values as described by Ghose and Crippen
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="GHOSE1986"></bibtex:cite> and <bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="GHOSE1987"></bibtex:cite>
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<dc:contributor>
<j.0:Contributor rdf:ID="tm">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Todd Martin</rdfs:label>
</j.0:Contributor>
</dc:contributor>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="CPSA">
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:isClassifiedAs rdf:resource="#geometricalDescriptor"/>
<j.0:definition rdf:parseType="Literal">
A variety of descriptors combining surface area and partial charge information
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-05-16</dc:date>
<dc:contributor rdf:resource="#rguha"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Charged Partial Surface Areas</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:BondDescriptor rdf:ID="bondPartialTCharge">
<dc:contributor rdf:resource="#mrc"/>
<j.0:description rdf:parseType="Literal">
Calculation is calculated determining the difference the
Partial Total Charge on atoms A and B of a bond. Based in
Gasteiger Charge.
</j.0:description>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Bond Partial Total Charge</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates bond-total Partial charge of a
bond.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:BondDescriptor>
<j.0:Reference rdf:ID="LIU98">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Liu, S. and Cao, C. and Li, Z.
</bibtex:author>
<bibtex:title>Approach to Estimation and Prediction for Normal
Boiling Point (NBP) of Alkanes Based on a Novel Molecular
Distance Edge (MDE) Vector, lambda
</bibtex:title>
<bibtex:journal>Journal of Chemical Information and Computer Sciences</bibtex:journal>
<bibtex:year>i1998</bibtex:year>
<bibtex:volume>38</bibtex:volume>
<bibtex:pages>387-394</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="hBondacceptorsDaylight">
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<j.0:definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>
Descriptor that calculates the number of hydrogen bond acceptors.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:description rdf:parseType="Literal">
As defined by Daylight website, <bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="DAY01"></bibtex:cite>, a H-bond acceptor is a heteroatom with no positive charge, note that negatively
charged oxygen or sulphur are included. Excluded are halogens, including F,
heteroaromatic oxygen, sulphur and pyrrole N. Higher oxidation levels of N,P,S are excluded.
Note P(III) is currently included. Zeneca's work would imply that (O=S=O) shoud also be excluded.
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Hydrogen Bond Acceptors (Daylight)</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="atomicHardness">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-04-21</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Inductive atomic hardness</rdfs:label>
<j.0:description rdf:parseType="Literal">
Inductive atomic hardness of an atom in a polyatomic system can be defined
as the resistance to a change of the atomic charge.
This descriptor is described by Cherkasov
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="CHER2003"></bibtex:cite>
.
</j.0:description>
<dc:contributor rdf:resource="#mf"/>
<j.0:definition rdf:parseType="Literal">
This class calculates the atomic hardness of a given atom.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:AtomicDescriptor>
<j.0:AtomicDescriptor rdf:ID="effectivePolarizability">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Effective Polarizability</rdfs:label>
<j.0:description rdf:parseType="Literal">
Polarizabilities are assigned to the heavy atom by Polarizability class.
</j.0:description>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the effective polarizability of a given heavy atom.
</j.0:definition>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="bpol">
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:description rdf:parseType="Literal">
Polarizabilities derive from periodic tables.
</j.0:description>
<j.0:definition rdf:parseType="Literal">
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).
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Bond Polarizabilities</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="autoCorrelationCharge">
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-01-15</dc:date>
<j.0:definition rdf:parseType="Literal">
The Moreau-Broto autocorrelation descriptors using partial charges
</j.0:definition>
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor rdf:resource="#fm"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Moreau-Broto Autocorrelation (charge) descriptors</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="lengthOverBreadth">
<j.0:definition rdf:parseType="Literal">
Calculates the ratio of length to breadth.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-09-26</dc:date>
<j.0:description rdf:parseType="Literal">
The descriptor has two values
indicating the maximum and minimumn value of LoB. Note that this method does not
perform any orientation.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#geometricalDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Length Over Breadth</rdfs:label>
<dc:contributor rdf:resource="#rguha"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="tpsa">
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Topological Polar Surface Area</rdfs:label>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<j.0:definition rdf:parseType="Literal">
Calculation of topological polar surface area based on fragment
contributions
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="ERTL2000"></bibtex:cite>
.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="TRI92">
<bibtex:entry rdf:parseType="Literal">
<bibtex:book xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Trinijastic, N.</bibtex:author>
<bibtex:title>Chemical Graph Theory</bibtex:title>
<bibtex:publisher>CRC Press</bibtex:publisher>
<bibtex:year>1992</bibtex:year>
<bibtex:isbn>0-8493-4256-2</bibtex:isbn>
</bibtex:book>
</bibtex:entry>
</j.0:Reference>
<j.0:Reference rdf:ID="WES98">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Wessel, M.D. and Jurs, P.C. and Tolan, J.W. and Muskal, S.M.
</bibtex:author>
<bibtex:title>Prediction of Human Intestinal Absorption of Drug Compounds
From Molecular Structure
</bibtex:title>
<bibtex:journal>Journal of Chemical Information and Computer
Sciences
</bibtex:journal>
<bibtex:year>1998</bibtex:year>
<bibtex:volume>38</bibtex:volume>
<bibtex:pages>726-735</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="weight">
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Molecular Weight</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor based on the weight of atoms of a certain element type.
If no element is specified, the returned value is the Molecular Weight
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="BCUT">
<j.0:definition rdf:parseType="Literal">
Eigenvalue based descriptor noted for its utility in chemical diversity
described by Pearlman et al.
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="PEA99"></bibtex:cite>
.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>BCUT</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#hybridDescriptor"/>
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="PET92">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Petitjean, M.
</bibtex:author>
<bibtex:title>Applications of the radius-diameter diagram to the classification of topological and
geometrical shapes of chemical compounds
</bibtex:title>
<bibtex:journal>Journal of Chemical Information and Computer Science</bibtex:journal>
<bibtex:year>1992</bibtex:year>
<bibtex:volume>32</bibtex:volume>
<bibtex:pages>331-337</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:AtomicDescriptor rdf:ID="atomValence">
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the valence of an atom.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Atomic Valence</rdfs:label>
<dc:contributor rdf:resource="#mf"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="hBondAcceptorsBoehmKlebe">
<j.0:definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>
Counts the number of acceptor field atoms for a carbonyl oxygen probe.
</j.0:definition>
<j.0:description rdf:parseType="Literal">
Force field based definition of hydrogen bond acceptors <bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="BK02"></bibtex:cite>
This rule covers nitril, carbonyl, ether, and amin nitrogens.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Acceptor Field Atoms (Boehm,Klebe)</rdfs:label>
<dc:contributor rdf:resource="#jkw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-09-08</dc:date>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="vdwradius">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Van der Waals radius</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<dc:contributor rdf:resource="#mf"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that returns the VdW radius of a given atom.
</j.0:definition>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="hBondDonorsDaylight">
<j.0:definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>
Descriptor that calculates the number of hydrogen bond donors.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:description rdf:parseType="Literal">
As defined by Daylight website, <bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="DAY01"></bibtex:cite>, a H-bond acceptor
must have an N-H bond, an O-H bond, or a F-H bond
</j.0:description>
<dc:contributor rdf:resource="#mf"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Hydrogen Bond Donors (Daylight)</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="aromaticBondsCount">
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Aromatic Bonds Count</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor based on the number of aromatic bonds of a molecule.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
</j.0:MolecularDescriptor>
<j.0:AtomicDescriptor rdf:ID="protonPartialCharge">
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates partial charges of an heavy atom and its protons.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<j.0:description rdf:parseType="Literal">
Calculation is based on Gasteiger Marsili (PEOE)
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Proton Total Partial Charge</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="hBondDonors">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Hydrogen Bond Donors</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the number of hydrogen bond donors.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
</j.0:MolecularDescriptor>
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
<owl:AnnotationProperty rdf:ID="description"/>
<owl:AnnotationProperty rdf:ID="definition"/>
<j.0:MolecularDescriptor rdf:ID="kierValues">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<dc:contributor rdf:resource="#mf"/>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:description rdf:parseType="Literal">
Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular
graphs.
First kappa shape index is given by
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mrow>
<msup>
<mrow>
<ci>n</ci>
<mo>(</mo>
<ci>n</ci>
<mo>-</mo>
<ci>1</ci>
<mo>)</mo>
</mrow>
<ci>2</ci>
</msup>
</mrow>
<mrow>
<msup>
<mi>m</mi>
<mi>2</mi>
</msup>
</mrow>
</mfrac>
</mrow>
,
second kappa shape index is given by
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mrow>
<mrow>
<mo>(</mo>
<ci>n</ci>
<mo>-</mo>
<ci>1</ci>
<mo>)</mo>
</mrow>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<ci>n</ci>
<mo>-</mo>
<ci>2</ci>
<mo>)</mo>
</mrow>
<mi>2</mi>
</msup>
</mrow>
</mrow>
<mrow>
<msup>
<msub>
<ci>p</ci>
<ci>2</ci>
</msub>
<mi>2</mi>
</msup>
</mrow>
</mfrac>
</mrow>
and third kappa shape index is given by
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mrow>
<mrow>
<mo>(</mo>
<ci>n</ci>
<mo>-</mo>
<ci>1</ci>
<mo>)</mo>
</mrow>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<ci>n</ci>
<mo>-</mo>
<ci>3</ci>
<mo>)</mo>
</mrow>
<mi>2</mi>
</msup>
</mrow>
</mrow>
<mrow>
<msup>
<msub>
<ci>p</ci>
<ci>3</ci>
</msub>
<mi>2</mi>
</msup>
</mrow>
</mfrac>
</mrow>
for odd n and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mrow>
<mrow>
<mo>(</mo>
<ci>n</ci>
<mo>-</mo>
<ci>3</ci>
<mo>)</mo>
</mrow>
<mrow>
<msup>
<mrow>
<mo>(</mo>
<ci>n</ci>
<mo>-</mo>
<ci>2</ci>
<mo>)</mo>
</mrow>
<mi>2</mi>
</msup>
</mrow>
</mrow>
<mrow>
<msup>
<msub>
<ci>p</ci>
<ci>3</ci>
</msub>
<mi>2</mi>
</msup>
</mrow>
</mfrac>
</mrow>
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
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Kier and Hall kappa molecular shape indices</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates Kier and Hall kappa molecular shape indices.
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:ProteinDescriptor rdf:ID="taeAminoAcid">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-08-23</dc:date>
<dc:contributor rdf:resource="#rguha"/>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:definition rdf:parseType="Literal">
The TAE RECON descriptors for amino acid sequences. Uses precalculated quantum mechanical
parameters to generate a set of 147 descriptors for a given sequence
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>TAE RECON descriptors for amino acid sequences</rdfs:label>
</j.0:ProteinDescriptor>
<j.0:Reference rdf:ID="BK02">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Böhm, M. and Klebe, G.</bibtex:author>
<bibtex:title>Development of New Hydrogen-Bond Descriptors and Their {A}pplication to Comparative Molecular Field Analyses</bibtex:title>
<bibtex:journal>J. Med. Chem.</bibtex:journal>
<bibtex:year>2002</bibtex:year>
<bibtex:volume>45</bibtex:volume>
<bibtex:pages>1585-1597</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="carbonTypes">
<dc:contributor rdf:resource="#rguha"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-09-26</dc:date>
<j.0:definition rdf:parseType="Literal">
Characterizes the carbon connectivity in terms of hybridization
</j.0:definition>
<j.0:description rdf:parseType="Literal">
This is a port of the ADAPT CTYPES routine and is a count of
carbon atom in different hybridization states and environments
</j.0:description>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Carbon Types</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="BAT95">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Bath, P.A. and Poirette, A.R. and Willet, P. and Allen, F.H.
</bibtex:author>
<bibtex:title>The Extent of the Relationship between the Graph-Theoretical and the Geometrical Shape
Coefficients of Chemical Compounds
</bibtex:title>
<bibtex:journal>Journal of Chemical Information and Computer Science</bibtex:journal>
<bibtex:year>1995</bibtex:year>
<bibtex:volume>35</bibtex:volume>
<bibtex:pages>714-716</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:Reference rdf:ID="RAN84">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Randic, M.
</bibtex:author>
<bibtex:title>On molecular identification numbers</bibtex:title>
<bibtex:journal>Journal of Chemical Information and Computer Science</bibtex:journal>
<bibtex:year>1984</bibtex:year>
<bibtex:volume>24</bibtex:volume>
<bibtex:pages>164-175</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="atomCount">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Element Count</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor based on the number of atoms of a certain element type.
</j.0:definition>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
</j.0:MolecularDescriptor>
<j.0:DataFeature rdf:ID="has3DCoordinates">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>has 3D Coordinates</rdfs:label>
</j.0:DataFeature>
<j.0:MolecularDescriptor rdf:ID="bondCount">
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<j.0:definition rdf:parseType="Literal">
Descriptor based on the number of bonds of a certain bond order.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<dc:contributor rdf:resource="#elw"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Bond Count</rdfs:label>
</j.0:MolecularDescriptor>
<j.0:MolecularDescriptor rdf:ID="momentOfInertia">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-02-07</dc:date>
<j.0:isClassifiedAs rdf:resource="#geometricalDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Moments of Inertia</rdfs:label>
<dc:contributor rdf:resource="#rguha"/>
<dc:contributor rdf:resource="#elw"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the principal moments of inertia and ratios
of the principal moments. Als calculates the radius of gyration.
</j.0:definition>
</j.0:MolecularDescriptor>
<j.0:Descriptor rdf:ID="bondsToAtom">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Bonds to Atom</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor based on the number of bonds on the shortest path between two atoms.
</j.0:definition>
<dc:contributor rdf:resource="#mf"/>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
</j.0:Descriptor>
<j.0:Reference rdf:ID="KAT96">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Katritzky, A.R. and Mu, L. and Lobanov, V.S. and Karelson, M.</bibtex:author>
<bibtex:title>Correlation of Boiling Points With Molecular Structure. 1. A Training Set of 298 Diverse
Organics and a Test Set of 9 Simple Inorganics
</bibtex:title>
<bibtex:journal>J. Phys. Chem.</bibtex:journal>
<bibtex:year>1996</bibtex:year>
<bibtex:volume>100</bibtex:volume>
<bibtex:pages>10400-10407</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="rdfProtonCalculatedValues">
<j.0:description rdf:parseType="Literal">
A given proton is represented by 5 different descriptors.
The first one has the form
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq></eq>
<apply>
<msub>
<ci>g</ci>
<ci>H</ci>
</msub>
<ci>r</ci>
</apply>
<apply>
<sum></sum>
<mrow>
<msub>
<ci>p</ci>
<ci>i</ci>
</msub>
<msup>
<ci>e</ci>
<mrow>
<mo>-</mo>
<ci>B</ci>
<msup>
<mrow>
<mo>(</mo>
<ci>r</ci>
<mo>-</mo>
<msub>
<ci>r</ci>
<ci>i</ci>
</msub>
<mo>)</mo>
</mrow>
<ci>2</ci>
</msup>
</mrow>
</msup>
</mrow>
</apply>
</apply>
</mrow>
where i denotes an atom up to four not rotatable bonds away from the target proton,
p is the partial atomic charge of the atom i, B is a smoothing parameter,
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>r</mi>
<mi>i</mi>
</msub>
</mrow>
is the
3D distance between proton and atom i, and r is a running variable.
The second one is a topological form of the first one, where i is an atom up to the fifth sphere,
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>p</mi>
<mi>i</mi>
</msub>
</mrow>
is the
partial atomic charge of atom i, and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>r</mi>
<mi>i</mi>
</msub>
</mrow>
is now the sum of bond length on the shortest path between the proton and atom i.
The third one has the form
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq></eq>
<apply>
<msub>
<ci>g</ci>
<ci>D</ci>
</msub>
<ci>r</ci>
</apply>
<apply>
<sum></sum>
<mrow>
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<msub>
<mi>r</mi>
<mi>D,i</mi>
</msub>
<mi>2</mi>
</msup>
</mrow>
</mfrac>
<msup>
<ci>e</ci>
<mrow>
<mo>-</mo>
<ci>B</ci>
<msup>
<mrow>
<mo>(</mo>
<ci>r</ci>
<mo>-</mo>
<msub>
<ci>a</ci>
<ci>D,i</ci>
</msub>
<mo>)</mo>
</mrow>
<ci>2</ci>
</msup>
</mrow>
</msup>
</mrow>
</apply>
</apply>
</mrow>
where i denotes a double bond up to the seventh sphere of nonrotatable bonds centered on the target proton,
and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>r</mi>
<mi>D</mi>
</msub>
</mrow>
and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>a</mi>
<mi>D</mi>
</msub>
</mrow>
are
geometric variables.
The fourth one has the form
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq></eq>
<apply>
<msub>
<ci>g</ci>
<ci>S</ci>
</msub>
<ci>r</ci>
</apply>
<apply>
<sum></sum>
<mrow>
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<msub>
<mi>r</mi>
<mi>S,i</mi>
</msub>
<mi>2</mi>
</msup>
</mrow>
</mfrac>
<msup>
<ci>e</ci>
<mrow>
<mo>-</mo>
<ci>B</ci>
<msup>
<mrow>
<mo>(</mo>
<ci>r</ci>
<mo>-</mo>
<msub>
<ci>a</ci>
<ci>S,i</ci>
</msub>
<mo>)</mo>
</mrow>
<ci>2</ci>
</msup>
</mrow>
</msup>
</mrow>
</apply>
</apply>
</mrow>
where i denotes a single bond up to the seventh sphere of nonrotatable bonds centered on the target proton,
and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>r</mi>
<mi>S</mi>
</msub>
</mrow>
and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>a</mi>
<mi>S</mi>
</msub>
</mrow>
are
geometric variables.
The last one has the form
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq></eq>
<apply>
<msub>
<ci>g</ci>
<ci>3</ci>
</msub>
<ci>r</ci>
</apply>
<apply>
<sum></sum>
<mrow>
<msup>
<ci>e</ci>
<mrow>
<mo>-</mo>
<ci>B</ci>
<msup>
<mrow>
<mo>(</mo>
<ci>r</ci>
<mo>-</mo>
<msub>
<ci>a</ci>
<ci>3,i</ci>
</msub>
<mo>)</mo>
</mrow>
<ci>2</ci>
</msup>
</mrow>
</msup>
</mrow>
</apply>
</apply>
</mrow>
where i denotes an atom three nonrotatable bonds away from the target proton and belonging to a
six-membered ring, and
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<msub>
<mi>a</mi>
<mi>3</mi>
</msub>
</mrow>
is
a dihedral angle in radian units.
Each values is returned as atom property.
</j.0:description>
<dc:contributor rdf:resource="#mf"/>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<j.0:definition rdf:parseType="Literal">
Calculation of RDF proton descriptor based on
<bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="GAST2002"></bibtex:cite>
.
</j.0:definition>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:isClassifiedAs rdf:resource="#geometricalDescriptor"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>RDF Proton Descriptor</rdfs:label>
<dc:contributor rdf:resource="#elw"/>
</j.0:MolecularDescriptor>
<j.0:DataFeature rdf:ID="hasPartialAtomicCharges">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>has Partial Atomic Charges</rdfs:label>
</j.0:DataFeature>
<j.0:AtomicDescriptor rdf:ID="isProtonInAromaticSystem">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Proton belonging to an aromatic system</rdfs:label>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<j.0:isClassifiedAs rdf:resource="#constitutionalDescriptor"/>
<dc:contributor rdf:resource="#mf"/>
<j.0:definition rdf:parseType="Literal">
This Class contains a method that 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 0 for other positions.
</j.0:definition>
</j.0:AtomicDescriptor>
<j.0:MolecularDescriptor rdf:ID="hBondDonorsBoehmKlebe">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-09-08</dc:date>
<j.0:description rdf:parseType="Literal">
Force field based definition of hydrogen bond donors <bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="BK02"></bibtex:cite>.
This rule covers amino groups, chloro, bromo and iodo atoms <bibtex:cite xmlns:bibtex="http://bibtexml.sf.net/" ref="PL96"></bibtex:cite>.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>
Counts the number of donor field atoms for an amino hydrogen probe.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Donor Field Atoms (Boehm,Klebe)</rdfs:label>
<dc:contributor rdf:resource="#jkw"/>
</j.0:MolecularDescriptor>
<j.0:Reference rdf:ID="CHER2003">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Cherkasov, A.</bibtex:author>
<bibtex:title>Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial
Charges
</bibtex:title>
<bibtex:journal>J. Chem. Inf. Comput. Sci.</bibtex:journal>
<bibtex:year>2003</bibtex:year>
<bibtex:volume>43</bibtex:volume>
<bibtex:pages>2039-2047</bibtex:pages>
<bibtex:doi>10.1021/ci034147w</bibtex:doi>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="chi0C">
<dc:contributor rdf:resource="#mf"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Carbon connectivity index (order 0)</rdfs:label>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates the carbon connectivity index (order 0).
</j.0:definition>
<j.0:description rdf:parseType="Literal">
While the atomic connectivity is calculated as the sum of
<mrow xmlns="http://www.w3.org/1998/Math/MathML">
<mfrac>
<mi>1</mi>
<mrow>
<msup>
<msub>
<mi>d</mi>
<mi>i</mi>
</msub>
<mi>0.5</mi>
</msup>
</mrow>
</mfrac>
</mrow>
over all heavy atoms i with degree greather than zero, carbon connectivity index
takes into account only carbon atoms with degree greather than zero.
</j.0:description>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2004-11-26</dc:date>
</j.0:MolecularDescriptor>
<j.0:BondDescriptor rdf:ID="bondPartialPiCharge">
<dc:contributor rdf:resource="#mrc"/>
<j.0:definition rdf:parseType="Literal">
Descriptor that calculates bond-pi Partial charge of a bond.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Bond Partial Pi Charge</rdfs:label>
<j.0:isClassifiedAs rdf:resource="#electronicDescriptor"/>
<j.0:description rdf:parseType="Literal">
Calculation is calculated determining the difference the
Partial Pi Charge on atoms A and B of a bond. Based in
Gasteiger Charge.
</j.0:description>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2006-05-08</dc:date>
</j.0:BondDescriptor>
<j.0:Reference rdf:ID="GAST2002">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J.</bibtex:author>
<bibtex:title>Prediction of 1H NMR Chemical Shifts Using Neural Networks</bibtex:title>
<bibtex:journal>Anal. Chem.</bibtex:journal>
<bibtex:year>2002</bibtex:year>
<bibtex:volume>74</bibtex:volume>
<bibtex:number>1</bibtex:number>
<bibtex:pages>80-90</bibtex:pages>
<bibtex:doi>10.1021/ac010737m</bibtex:doi>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<j.0:Reference rdf:ID="GWB98">
<bibtex:entry rdf:parseType="Literal">
<bibtex:article xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Gillet, J. and Willett, P. and Bradshaw, J.</bibtex:author>
<bibtex:title>Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms</bibtex:title>
<bibtex:journal>J. Chem. Inf. Comput. Sci.</bibtex:journal>
<bibtex:year>1998</bibtex:year>
<bibtex:volume>38</bibtex:volume>
<bibtex:pages>165-179</bibtex:pages>
</bibtex:article>
</bibtex:entry>
</j.0:Reference>
<owl:AnnotationProperty rdf:about="http://bibtexml.sf.net/entry"/>
<j.0:Reference rdf:ID="DAY01">
<bibtex:entry rdf:parseType="Literal">
<bibtex:misc xmlns:bibtex="http://bibtexml.sf.net/">
<bibtex:author>Daylight</bibtex:author>
<bibtex:title>SMILES on-line tutorial</bibtex:title>
<bibtex:url>http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html</bibtex:url>
</bibtex:misc>
</bibtex:entry>
</j.0:Reference>
<j.0:MolecularDescriptor rdf:ID="wienerNumbers">
<dc:contributor rdf:resource="#mf"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>2005-01-27</dc:date>
<j.0:isClassifiedAs rdf:resource="#topologicalDescriptor"/>
<j.0:definition rdf:parseType="Literal">
This class calculates Wiener path number and Wiener polarity number.
</j.0:definition>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Wiener Numbers</rdfs:label>
<j.0:description rdf:parseType="Literal">
Wiener path number: half the sum of all the distance matrix entries.
Wiener polarity number: half the sum of all the distance matrix entries with a value of 3.
</j.0:description>
</j.0:MolecularDescriptor>
</rdf:RDF>
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