| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/molxyz/ |
| H A D | XyzReader.java | 57 int modelAtomCount = parseIntStr(line); in checkLine() local
58 if (modelAtomCount == Integer.MIN_VALUE) { in checkLine()
71 readAtoms(modelAtomCount); in checkLine()
79 skipAtomSet(modelAtomCount); in checkLine()
91 private void skipAtomSet(int modelAtomCount) throws Exception { in skipAtomSet() argument
93 for (int i = modelAtomCount; --i >= 0;) in skipAtomSet()
97 private void readAtoms(int modelAtomCount) throws Exception { in readAtoms() argument
98 for (int i = 0; i < modelAtomCount; ++i) { in readAtoms()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/spartan/ |
| H A D | SpartanInputReader.java | 43 protected int modelAtomCount; field in SpartanInputReader
63 if (modelAtomCount > 1) { in readInputRecords()
108 modelAtomCount = 0; in readInputAtoms()
113 modelAtomCount++; in readInputAtoms()
120 int atom0 = asc.ac - modelAtomCount; in readAtomNames()
123 for (int i = 0; i < modelAtomCount; i++) { in readAtomNames()
131 int nAtoms = modelAtomCount; in readBonds()
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| H A D | SpartanArchive.java | 54 private int modelAtomCount = 0; field in SpartanArchive
68 this.modelAtomCount = smolAtomCount; in SpartanArchive()
82 modelAtomCount = setInfo(infoLine); in readArchive()
123 return modelAtomCount; in readArchive()
143 modelAtomCount = parseInt(tokens[0]); in setInfo()
156 return modelAtomCount; in setInfo()
160 for (int i = 0; i < modelAtomCount; i++) { in readAtoms()
163 : r.asc.atoms[ac0 - modelAtomCount + i]); in readAtoms()
187 for (int i = modelAtomCount; i < tokens.length;) { in addBonds()
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| H A D | SpartanSmolReader.java | 253 modelAtomCount = spartanArchive.readArchive(line, false, asc.ac, false); in readArchive()
271 if (modelAtomCount == 0) { in readProperties()
277 modelAtomCount); in readProperties()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/quantum/ |
| H A D | MoldenReader.java | 43 protected int modelAtomCount; field in MoldenReader
73 modelAtomCount = asc.getAtomSetAtomCount(0);
528 for (int i = 0; i < modelAtomCount; i++) { in readFreqsAndModes()
585 readLines(modelAtomCount); in readGeometryOptimization()
611 modelAtomCount = asc.getLastAtomSetAtomCount(); in readAtomSet()
616 for (int i = 0; i < modelAtomCount; i++) in readAtomSet()
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| H A D | QCJSONReader.java | 101 modelAtomCount = coords.length / 3; in readSteps()
128 for (int i = 0, pt = 0; i < modelAtomCount; i++) { in readSteps()
168 for (int j = 0, pt = 0; j < modelAtomCount; j++) { in readFreqsAndModes()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/ |
| H A D | GromacsReader.java | 66 int modelAtomCount = parseIntStr(rd()); in readAtoms() local
67 for (int i = 0; i < modelAtomCount; ++i) { in readAtoms()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/simple/ |
| H A D | FoldingXyzReader.java | 81 int modelAtomCount = parseIntStr(token); in checkLine() local
88 boolean readLine = readAtoms(modelAtomCount + 1, addAtoms); // Some Tinker files are one off! in checkLine()
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| /dports/science/jmol/jmol-14.32.7/src/org/openscience/jmol/app/janocchio/ |
| H A D | NMR_JmolPanel.java | 1002 int modelAtomCount = getFrameAtomCount(); in notifyFrameChanged() local
1003 … if (labelSetter.getLabelArray() == null || modelAtomCount != labelSetter.getLabelArray().length) { in notifyFrameChanged()
1004 labelSetter.allocateLabelArray(modelAtomCount); in notifyFrameChanged()
1006 noeTable.allocateLabelArray(modelAtomCount); in notifyFrameChanged()
1007 noeTable.allocateExpNoes(modelAtomCount); in notifyFrameChanged()
1008 coupleTable.allocateLabelArray(modelAtomCount); in notifyFrameChanged()
1009 coupleTable.allocateExpCouples(modelAtomCount); in notifyFrameChanged()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/xtal/ |
| H A D | CrystalReader.java | 1606 int modelAtomCount = -1; in readFrequencies() local
1628 modelAtomCount = asc.getLastAtomSetAtomCount(); in readFrequencies()
1638 fillFrequencyData(iAtom0, freqAtomCount, modelAtomCount, ignore, false, in readFrequencies()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/ |
| H A D | AtomSetCollectionReader.java | 1457 protected void fillFrequencyData(int iAtom0, int ac, int modelAtomCount, in fillFrequencyData() argument
1462 boolean withSymmetry = (ac != 0 && modelAtomCount != ac && data == null); in fillFrequencyData()
1496 iAtom += iAtom0 + modelAtomCount * j++; in fillFrequencyData()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
| H A D | ModelLoader.java | 1161 int modelAtomCount = 0; in initializeBonding() local
1179 modelAtomCount = models[i].bsAtoms.cardinality(); in initializeBonding()
1198 || modelBondCount < modelAtomCount / 2) in initializeBonding()
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