| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ |
| H A D | RotatableBondsCountDescriptor.java | 217 List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom); in getConnectedHCount() local
|
| H A D | CarbonTypesDescriptor.java | 158 List<IAtom> connectedAtoms = container.getConnectedAtomsList(atom); in calculate() local
|
| H A D | TPSADescriptor.java | 270 List<IAtom> connectedAtoms = ac.getConnectedAtomsList(atom); in calculate() local
|
| H A D | ALOGPDescriptor.java | 1057 private int getHAtomType(IAtom atom, List connectedAtoms) { in getHAtomType()
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/tools/ |
| H A D | CDKUtilities.java | 250 List<IAtom> connectedAtoms = m.getConnectedAtomsList(a); in fixSulphurH() local
|
| /dports/science/cdk/cdk-cdk-2.3/misc/extra/src/main/java/org/openscience/cdk/geometry/ |
| H A D | AtomTools.java | 67 List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom); in add3DCoordinates1() local
181 List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(refAtom); in calculate3DCoordinatesForLigands() local
|
| /dports/science/cdk/cdk-cdk-2.3/tool/group/src/main/java/org/openscience/cdk/group/ |
| H A D | AtomRefinable.java | 223 List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom); in setupConnectionTable() local
|
| /dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ |
| H A D | AtomTetrahedralLigandPlacer3D.java | 819 IAtomContainer connectedAtoms = atom.getBuilder().newInstance(IAtomContainer.class); in getPlacedAtomsInAtomContainer() local
840 IAtomContainer connectedAtoms = atom.getBuilder().newInstance(IAtomContainer.class); in getUnsetAtomsInAtomContainer() local
|
| H A D | AtomPlacer3D.java | 561 IAtomContainer connectedAtoms = molecule.getBuilder().newInstance(IAtomContainer.class); in getPlacedHeavyAtoms() local
|
| H A D | ModelBuilder3D.java | 464 IAtomContainer connectedAtoms = molecule.getBuilder().newInstance(IAtomContainer.class); in searchAndPlaceBranches() local
|
| /dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/geometry/ |
| H A D | BondTools.java | 62 List<IAtom> connectedAtoms = container.getConnectedAtomsList(bond.getBegin()); in isValidDoubleBondConfiguration() local
|
| H A D | GeometryUtil.java | 1364 List<IAtom> connectedAtoms; in getBondLengthRMSD() local
1429 … List<IAtom> connectedAtoms = firstAtomContainer.getConnectedAtomsList(centerAtomfirstAC); in getAngleRMSD() local
|
| /dports/science/jmol/jmol-14.32.7/src/org/jmol/shape/ |
| H A D | Mesh.java | 282 public int[] connectedAtoms; field in Mesh
|
| /dports/science/cdk/cdk-cdk-2.3/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/ |
| H A D | AbstractBondTest.java | 202 IAtom[] connectedAtoms = b.getConnectedAtoms(atoms[1]); in testGetConnectedAtoms_IAtom() local
|
| /dports/science/molsketch/Molsketch-0.7.2/libmolsketch/ |
| H A D | molecule.cpp | 292 QSet<Atom*> connectedAtoms = {startAtom}; in getConnectedAtoms() local
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/geometry/ |
| H A D | GeometryTools.java | 1394 List<IAtom> connectedAtoms; in getBondLengthRMSD() local
1458 … List<IAtom> connectedAtoms = firstAtomContainer.getConnectedAtomsList(centerAtomfirstAC); in getAngleRMSD() local
|
| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/atomtype/ |
| H A D | CDKAtomTypeMatcher.java | 889 int connectedAtoms = connectedBonds.size() in perceiveNitrogens() local
2369 private int countAttachedDoubleBonds(List<IBond> connectedAtoms, IAtom atom, String symbol) { in countAttachedDoubleBonds()
2491 int connectedAtoms = connectedBonds.size(); in isAcceptable() local
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smsd/filters/ |
| H A D | ChemicalFilters.java | 374 List<IAtom> connectedAtoms = ac1.getConnectedAtomsList(atoms); in makeBondMapsOfAtomMaps() local
|