| /dports/science/lammps/lammps-stable_29Sep2021/tools/msi2lmp/frc_files/ |
| H A D | pcff_templates.dat | 73 aromaticity:NON_AROMATIC
83 aromaticity:NON_AROMATIC
93 aromaticity:NON_AROMATIC
103 aromaticity:NON_AROMATIC
394 aromaticity:AROMATIC
416 aromaticity:AROMATIC
432 aromaticity:AROMATIC
529 aromaticity:AROMATIC
534 aromaticity:AROMATIC
709 aromaticity:AROMATIC
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smiles/smarts/ |
| H A D | SMARTSQueryTool.java | 24 import org.openscience.cdk.aromaticity.Aromaticity;
25 import org.openscience.cdk.aromaticity.ElectronDonation;
180 private Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), field in SMARTSQueryTool
286 public void setAromaticity(Aromaticity aromaticity) { in setAromaticity() argument
287 this.aromaticity = checkNotNull(aromaticity, "aromaticity was not provided"); in setAromaticity()
437 aromaticity.apply(atomContainer); in initializeMolecule()
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| H A D | SmartsPattern.java | 26 import org.openscience.cdk.aromaticity.Aromaticity;
27 import org.openscience.cdk.aromaticity.ElectronDonation;
|
| /dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/main/java/org/openscience/cdk/fingerprint/ |
| H A D | LingoFingerprinter.java | 26 import org.openscience.cdk.aromaticity.Aromaticity;
27 import org.openscience.cdk.aromaticity.ElectronDonation;
60 private final Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), field in LingoFingerprinter
93 aromaticity.apply(atomContainer); in getRawFingerprint()
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| /dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/ |
| H A D | QueryAtomContainerCreator.java | 151 …c static QueryAtomContainer createAnyAtomContainer(IAtomContainer container, boolean aromaticity) { in createAnyAtomContainer() argument
152 if (aromaticity) in createAnyAtomContainer()
176 …c QueryAtomContainer createAnyAtomAnyBondContainer(IAtomContainer container, boolean aromaticity) { in createAnyAtomAnyBondContainer() argument
177 if (aromaticity) in createAnyAtomAnyBondContainer()
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| /dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/test/java/org/openscience/cdk/smarts/ |
| H A D | DfSubstructureTest.java | 27 import org.openscience.cdk.aromaticity.Aromaticity;
28 import org.openscience.cdk.aromaticity.ElectronDonation;
|
| /dports/biology/py-biopython/biopython-1.79/Bio/SeqUtils/ |
| H A D | ProtParam.py | 131 def aromaticity(self): member in ProteinAnalysis
140 aromaticity = sum(aa_percentages[aa] for aa in aromatic_aas)
142 return aromaticity
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| /dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/main/java/org/openscience/cdk/smarts/ |
| H A D | SmartsPattern.java | 27 import org.openscience.cdk.aromaticity.Aromaticity;
28 import org.openscience.cdk.aromaticity.ElectronDonation;
|
| /dports/science/cdk/cdk-cdk-2.3/misc/extra/src/main/java/org/openscience/cdk/tools/ |
| H A D | AtomTypeTools.java | 23 import org.openscience.cdk.aromaticity.Aromaticity;
85 …public IRingSet assignAtomTypePropertiesToAtom(IAtomContainer molecule, boolean aromaticity) throw… in assignAtomTypePropertiesToAtom() argument
95 if (aromaticity) { in assignAtomTypePropertiesToAtom()
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ |
| H A D | XLogPDescriptorTest.java | 26 import org.openscience.cdk.aromaticity.Aromaticity;
27 import org.openscience.cdk.aromaticity.ElectronDonation;
296 Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.all()); in testAromaticBenzene() local
297 aromaticity.apply(mol); in testAromaticBenzene()
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book_jp/ |
| H A D | terminology_jp.rst | 35 | | aromaticity flag | 芳香族性フラグ …
251 | | MDL aromaticity model | MDL芳香属性モデル …
361 | | simple aromaticity model | 単純芳香族性モデル …
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| /dports/science/cdk/cdk-cdk-2.3/base/testdata/src/test/resources/data/mdl/ |
| H A D | bug716259.mol | 1 Bug [ 716259 ] Wrong aromaticity detection
|
| /dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/aromaticity/ |
| H A D | ElectronDonation.java | 25 package org.openscience.cdk.aromaticity;
|
| H A D | PiBondModel.java | 25 package org.openscience.cdk.aromaticity;
|
| /dports/biology/paml/paml4.9j/dat/ |
| H A D | g1974a.dat | 25 aromaticity ( data from Xuhua Xia): d_ij=|d_i - d_j|
|
| H A D | grantham.dat | 28 c p v aromaticity (from Xuhua Xia)
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/aromaticity/ |
| H A D | AromaticityCalculatorTest.java | 19 package org.openscience.cdk.aromaticity;
|
| /dports/science/p5-Chemistry-Pattern/Chemistry-Pattern-0.27/ |
| H A D | Changes | 5 - Change the default bond matching test to account for aromaticity.
|
| H A D | README | 10 - Change the default bond matching test to account for aromaticity.
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/aromaticity/ |
| H A D | AromaticityCalculator.java | 24 package org.openscience.cdk.aromaticity;
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/tools/ |
| H A D | IonizationPotentialToolTest.java | 25 import org.openscience.cdk.aromaticity.Aromaticity;
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/IFG/ |
| H A D | README | 32 Cause RDKit and Peter tool can have distinct aromaticity dectection behaviours, list
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smiles/smarts/ |
| H A D | SMARTSQueryToolTest.java | 32 import org.openscience.cdk.aromaticity.Aromaticity;
33 import org.openscience.cdk.aromaticity.ElectronDonation;
|
| /dports/science/p5-Chemistry-File-MDLMol/Chemistry-File-MDLMol-0.21/ |
| H A D | Changes | 6 - Added a new default test subroutine for bonds, that takes aromaticity
|
| H A D | README | 14 - Added a new default test subroutine for bonds, that takes aromaticity
|