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Searched refs:getAtomNumber (Results 1 – 25 of 40) sorted by relevance

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/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/
H A DCalculations.java392 minAtoms[ib].atom.getAtomNumber(), in getConstraintList()
415 iVal[0] = atom.atom.getAtomNumber(); in getAtomList()
513 new int[] { minAtoms[c.ia].atom.getAtomNumber(), minAtoms[c.ib].atom.getAtomNumber() }}); in getDebugLineC()
522 new int[] { minAtoms[c.ia].atom.getAtomNumber(), minAtoms[c.ib].atom.getAtomNumber(), in getDebugLineC()
523 minAtoms[c.ic].atom.getAtomNumber()} }); in getDebugLineC()
531 new int[] { minAtoms[c.ia].atom.getAtomNumber(), minAtoms[c.ib].atom.getAtomNumber(), in getDebugLineC()
532 … minAtoms[c.ic].atom.getAtomNumber(), minAtoms[c.id].atom.getAtomNumber(), c.iData[4] } }); in getDebugLineC()
539 new int[] { minAtoms[c.ia].atom.getAtomNumber(), minAtoms[c.ib].atom.getAtomNumber(), in getDebugLineC()
540 minAtoms[c.ic].atom.getAtomNumber(), minAtoms[c.id].atom.getAtomNumber() } }); in getDebugLineC()
545 new int[] { minAtoms[c.ia].atom.getAtomNumber(), minAtoms[c.ib].atom.getAtomNumber() } }); in getDebugLineC()
[all …]
H A DCalculationsMMFF.java247 new int[] { minAtoms[c.ia].atom.getAtomNumber(), minAtoms[c.ib].atom.getAtomNumber(), in getDebugLine()
248 minAtoms[c.ic].atom.getAtomNumber()} }); in getDebugLine()
/dports/science/jmol/jmol-14.32.7/src/org/openscience/jmol/app/janocchio/
H A DNMR_Viewer.java24 public int getAtomNumber(int atomIndex) { in getAtomNumber() method in NMR_Viewer
25 return ms.at[atomIndex].getAtomNumber(); in getAtomNumber()
H A DCoupleTable.java385 String reserve = "" + viewer.getAtomNumber(atomIndex) + " " in getValueAt()
H A DNoeTable.java492 String reserve = "" + viewer.getAtomNumber(atomIndex) + " " in getValueAt()
/dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/
H A DAminoAcid.java148 … if (getNTerminus() != null) clone.setNTerminus(clone.getAtom(getAtomNumber(getNTerminus()))); in clone()
149 … if (getCTerminus() != null) clone.setCTerminus(clone.getAtom(getAtomNumber(getCTerminus()))); in clone()
H A DAtomContainer.java448 public int getAtomNumber(IAtom atom) {
945 int position = getAtomNumber(atom);
1081 int position = getAtomNumber(atom);
/dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/
H A DAminoAcid.java148 … if (getNTerminus() != null) clone.setNTerminus(clone.getAtom(getAtomNumber(getNTerminus()))); in clone()
149 … if (getCTerminus() != null) clone.setCTerminus(clone.getAtom(getAtomNumber(getCTerminus()))); in clone()
H A DAtomContainer.java428 public int getAtomNumber(IAtom atom) {
919 int position = getAtomNumber(atom);
1049 int position = getAtomNumber(atom);
/dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/
H A DMDLRXNReaderTest.java259 …Assert.assertEquals(getAtomNumber(reactionSet, reactionSet.getReaction(0).getMapping(i).getChemObj… in testAsadExamples()
260 … getAtomNumber(reactionSet2, reactionSet2.getReaction(0).getMapping(i).getChemObject(0))); in testAsadExamples()
261 …Assert.assertEquals(getAtomNumber(reactionSet, reactionSet.getReaction(0).getMapping(i).getChemObj… in testAsadExamples()
262 … getAtomNumber(reactionSet2, reactionSet2.getReaction(0).getMapping(i).getChemObject(1))); in testAsadExamples()
274 …private String getAtomNumber(IReactionSet reactionSet, IChemObject chemObject) throws CDKException… in getAtomNumber() method in MDLRXNReaderTest
/dports/science/jmol/jmol-14.32.7/src/org/jmol/util/
H A DNode.java74 public int getAtomNumber(); in getAtomNumber() method
/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/
H A DQueryAtomContainer.java586 public int getAtomNumber(IAtom atom) {
1125 int position = getAtomNumber(atom);
1284 int position = getAtomNumber(atom);
1533 newAtoms[j] = clone.getAtom(getAtomNumber(bond.getAtom(j)));
1544 newLp.setAtom(clone.getAtom(getAtomNumber(lp.getAtom())));
1554 newSe.setAtom(clone.getAtom(getAtomNumber(se.getAtom())));
/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/
H A DChimeMessenger.java71 + a.getAtomNumber() in getInfoXYZ()
H A DPropertyManager.java1423 s = "" + a.getAtomNumber(); in getChimeInfoA()
1960 int iThis = a.getAtomNumber(); in getPdbAtomData()
1969 int iOther = a2.getAtomNumber(); in getPdbAtomData()
2205 .append(PT.formatStringI("%5i", "i", atomLast.getAtomNumber())) in getPdbData()
2206 .append(PT.formatStringI("%5i", "i", a.getAtomNumber())) in getPdbData()
2212 new Object[] { Integer.valueOf(a.getAtomNumber()), in getPdbData()
2218 new Object[] { Integer.valueOf(a.getAtomNumber()), in getPdbData()
2224 new Object[] { Integer.valueOf(a.getAtomNumber()), in getPdbData()
/dports/science/cdk/cdk-cdk-2.3/base/interfaces/src/main/java/org/openscience/cdk/interfaces/
H A DIAtomContainer.java205 int getAtomNumber(IAtom atom); in getAtomNumber() method
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/
H A DAtom.java630 public int getAtomNumber() { in getAtomNumber() method in Atom
938 info.appendI(getAtomNumber()); in getIdentity()
949 info.appendI(getAtomNumber()); in getIdentity()
1114 return getAtomNumber(); in atomPropertyInt()
H A DAtomCollection.java322 if (atom != null && atom.getAtomNumber() == atomNumber && bsVisibleFrames.get(atom.mi)) in getFirstAtomIndexFromAtomNumber()
843 if (doTaint && atomno == at[atomIndex].getAtomNumber()) in setAtomNumber()
2223 if (at[i] != null && at[i].getAtomNumber() == iSpec) in getAtomBitsMDa()
2695 info.put("atomno", Integer.valueOf(at[i].getAtomNumber())); in getAtomIdentityInfo()
2863 if (at[i].getAtomNumber() != atomNumber) in getAtomsFromAtomNumberInFrame()
/dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/graph/
H A DAllPairsShortestPaths.java249 … public int getAtomNumber(IAtom atom) {
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shape/
H A DMeasures.java495 Integer.valueOf(atoms[atomIndex].getAtomNumber())) : (Object) m in defineAll()
692 … atomInfo.put("atomno", Integer.valueOf(atomIndex < 0 ? -1 : atoms[atomIndex].getAtomNumber())); in getInfo()
/dports/biology/jalview/jalview/src/jalview/ext/jmol/
H A DJmolParser.java247 curAtom.number = atom.getAtomNumber(); in convertSignificantAtoms()
/dports/science/cdk/cdk-cdk-2.3/base/datadebug/src/main/java/org/openscience/cdk/debug/
H A DDebugPolymer.java182 public int getAtomNumber(IAtom atom) { in getAtomNumber() method in DebugPolymer
H A DDebugMonomer.java180 public int getAtomNumber(IAtom atom) { in getAtomNumber() method in DebugMonomer
H A DDebugAminoAcid.java180 public int getAtomNumber(IAtom atom) { in getAtomNumber() method in DebugAminoAcid
H A DDebugStrand.java182 public int getAtomNumber(IAtom atom) { in getAtomNumber() method in DebugStrand
/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/
H A DSmilesAtom.java366 public int getAtomNumber() { in getAtomNumber() method in SmilesAtom

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