| /dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/ |
| H A D | ForceFieldMMFF.java | 269 public boolean setArrays(Atom[] atoms, BS bsAtoms, Bond[] bonds, in setArrays()
682 Atom[] atoms, int[] aTypes, BS bsAtoms, in calculatePartialCharges()
871 private static int[] setAtomTypes(Atom[] atoms, BS bsAtoms, in setAtomTypes()
971 private int[] setBondTypes(Bond[] bonds, int bondCount, BS bsAtoms) { in setBondTypes()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/api/ |
| H A D | SymmetryInterface.java | 133 public BS notInCentroid(ModelSet modelSet, BS bsAtoms, in notInCentroid()
157 BS bsAtoms, in setPointGroup()
229 void calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms); in calculateCIPChiralityForAtoms()
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| H A D | JmolPropertyManager.java | 47 String fixJMEFormalCharges(BS bsAtoms, String s); in fixJMEFormalCharges()
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| H A D | SmilesMatcherInterface.java | 57 public int[][] getMapForJME(String jme, Atom[] at, BS bsAtoms); in getMapForJME()
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| H A D | JmolAnnotationParser.java | 28 String calculateDSSRStructure(Viewer vwr, BS bsAtoms); in calculateDSSRStructure()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/ |
| H A D | ProteinStructure.java | 224 public Monomer findMonomer(BS bsAtoms, boolean isFirst) { in findMonomer()
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| H A D | BioExt.java | 128 int derivType, BS bsAtoms, BS bsSelected, in getPdbData()
251 int derivType, BS bsAtoms, BS bsSelected, boolean isDraw, in getData()
1261 BS bsAtoms = new BS(); in mutateAtom() local
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| H A D | BioModel.java | 220 public boolean getConformation(int conformationIndex0, boolean doSet, BS bsAtoms, BS bsRet) { in getConformation()
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| H A D | BioPolymer.java | 460 public void getRangeGroups(int nResidues, BS bsAtoms, BS bsResult) { in getRangeGroups()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/pymol/ |
| H A D | PyMOLScene.java | 183 private BS bsAtoms; field in PyMOLScene
699 private JmolObject getJmolObject(int id, BS bsAtoms, Object info) { in getJmolObject()
705 private JmolObject addJmolObject(int id, BS bsAtoms, Object info) { in addJmolObject()
771 PyMOLGroup addGroup(Lst<Object> object, String parent, int type, BS bsAtoms) { in addGroup()
1125 BS bsAtoms = htDefinedAtoms.get(objectJmolName); in setAtomMap() local
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| H A D | PyMOLReader.java | 718 BS bsAtoms = null; in processObject() local
917 BS bsAtoms = pymolScene.setAtomMap(atomMap, ac0); in processMolecule() local
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
| H A D | BondCollection.java | 81 public BondIterator getBondIteratorForType(int bondType, BS bsAtoms) { in getBondIteratorForType()
114 public BS getBondsForSelectedAtoms(BS bsAtoms, boolean bondSelectionModeOr) { in getBondsForSelectedAtoms()
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| H A D | Model.java | 142 public final BS bsAtoms = new BS(); field in Model
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| H A D | AtomCollection.java | 1107 public void taintAtoms(BS bsAtoms, int type) { in taintAtoms()
2606 public void getAtomsInFrame(BS bsAtoms) { in getAtomsInFrame()
2648 protected void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsAtoms) { in deleteModelAtoms()
2706 private void deleteAtomTensors(BS bsAtoms) { in deleteAtomTensors()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/util/ |
| H A D | MolWriter.java | 45 public boolean addMolFile(int iModel, SB mol, BS bsAtoms, BS bsBonds, in addMolFile()
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| H A D | JmolMolecule.java | 348 public static BS getBitSetForMF(Atom[] at, BS bsAtoms, String mf) { in getBitSetForMF()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/ |
| H A D | SelectionManager.java | 64 void processDeletedModelAtoms(BS bsAtoms) { in processDeletedModelAtoms()
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| H A D | Viewer.java | 3454 public String calculateStructures(BS bsAtoms, boolean asDSSP, in calculateStructures()
3820 public BS getBondsForSelectedAtoms(BS bsAtoms) { in getBondsForSelectedAtoms()
4327 public void setFrameOffsets(BS bsAtoms, boolean isFull) { in setFrameOffsets()
7692 public Quat[] getAtomGroupQuaternions(BS bsAtoms, int nMax) { in getAtomGroupQuaternions()
8047 boolean isInternal, BS bsAtoms, in moveAtoms()
8629 public int deleteAtoms(BS bsAtoms, boolean fullModels) { in deleteAtoms()
8658 public int deleteModels(int modelIndex, BS bsAtoms) { in deleteModels()
9090 private void setHydrogens(BS bsAtoms) { in setHydrogens()
9250 int deltaZ, BS bsAtoms) { in moveAtomWithHydrogens()
9662 public BS addHydrogens(BS bsAtoms, int flags) { in addHydrogens()
[all …]
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/ |
| H A D | PointGroup.java | 165 private BS bsAtoms; field in PointGroup
212 T3[] atomset, BS bsAtoms, in getPointGroup()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/cif/ |
| H A D | MMTFReader.java | 468 BS bsAtoms = asc.bsAtoms; in addStructureSymmetry() local
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/scriptext/ |
| H A D | CmdExt.java | 1429 BS bsAtoms = null; in configuration() local
4030 BS bsAtoms; in write() local
5785 BS bsAtoms = vwr.getModelUndeletedAtomsBitSet(vwr.am.cmi); in assign() local
5863 private BS expFor(int i, BS bsAtoms) throws ScriptException { in expFor()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/script/ |
| H A D | ScriptManager.java | 739 public BS addHydrogensInline(BS bsAtoms, Lst<Atom> vConnections, P3[] pts) in addHydrogensInline()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/ |
| H A D | SmilesMatcher.java | 567 public int[][] getMapForJME(String jme, Atom[] at, BS bsAtoms) { in getMapForJME()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/quantum/ |
| H A D | NBOParser.java | 551 BS bsAtoms = vwr.ms.getModelAtomBitSetIncludingDeleted(modelIndex, false); in setJmolLewisStructure() local
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/modelkit/ |
| H A D | ModelKitPopup.java | 1105 BS bsAtoms = new BS(); in assignBond() local
1592 BS bsAtoms = assignBond(bondIndex, type); in cmdAssignBond() local
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