/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/ |
H A D | BioModelSet.java | 78 BS bsAtoms = bsA; in calcAllRasmolHydrogenBonds() local 174 public String calculateAllStuctures(BS bsAtoms, boolean asDSSP, in calculateAllStuctures() 202 public String getAllDefaultStructures(BS bsAtoms, BS bsModified) { in getAllDefaultStructures() 248 public BS getAllSequenceBits(String specInfo, BS bsAtoms, BS bsResult) { in getAllSequenceBits() 432 public String getFullProteinStructureState(BS bsAtoms, int mode) { in getFullProteinStructureState() 571 public void setAllConformation(BS bsAtoms) { in setAllConformation() 662 BS bsAtoms = new BS(); in getAllBasePairBits() local 813 private BS checkMap(Map<String, BS> map, String key, BS bsAtoms) { in checkMap() 882 private int getStructureLines(BS bsAtoms, SB cmd, in getStructureLines() 994 private BS modelsOf(BS bsAtoms, BS bsAtomsRet) { in modelsOf()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/dssx/ |
H A D | DSSR1.java | 107 public String calculateDSSRStructure(Viewer vwr, BS bsAtoms) { in calculateDSSRStructure() 251 BS bsAtoms = ms.am[modelIndex].bsAtoms; in getBasePairs() local 440 BS bsAtoms = m.bsAtoms; in setGroup1() local 471 ms.getSequenceBits(map.toString(), bsAtoms, bs); in getAtomicDSSRData() local
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H A D | AnnotationParser.java | 289 BS bsAtoms = new BS(); in catalogStructureUnits() local 383 BS bsAtoms = new BS(); in catalogValidations() local 612 float val, BS bsAtoms, int[] modelAtomIndices, in catalogUnit() 886 public String calculateDSSRStructure(Viewer vwr, BS bsAtoms) { in calculateDSSRStructure()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/ |
H A D | UnitCellIterator.java | 52 Atom[] atoms, BS bsAtoms, float distance) { in set() 110 public void addAtoms(BS bsAtoms) { in addAtoms()
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H A D | CIPData.java | 72 BS bsAtoms; field in CIPData 155 public CIPData set(Viewer vwr, BS bsAtoms) { in set()
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H A D | Symmetry.java | 100 BS bsAtoms, in setPointGroup() 602 public BS notInCentroid(ModelSet modelSet, BS bsAtoms, int[] minmax) { in notInCentroid() 730 BS bsAtoms, float radius) { in getIterator() 801 public void calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms) { in calculateCIPChiralityForAtoms()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/ |
H A D | BondIterator.java | 31 private BS bsAtoms; field in BondIterator
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H A D | AtomIterator.java | 45 private BS bsAtoms; field in AtomIterator
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H A D | XtalSymmetry.java | 292 BS bsAtoms = asc.bsAtoms; in applySymmetryLattice() local 618 private void applyAllSymmetry(MSInterface ms, BS bsAtoms) throws Exception { in applyAllSymmetry() 884 BS bsAtoms = (acr.isMolecular ? null : asc.bsAtoms); in symmetryAddAtoms() local 1231 BS bsAtoms = asc.bsAtoms; in applySymmetryBio() local
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/ |
H A D | MMConstraint.java | 26 public void set(int steps, BS bsAtoms, int[] atomMap) { in set()
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H A D | Minimizer.java | 80 public BS bsAtoms; field in Minimizer 683 …public void calculatePartialCharges(ModelSet ms, BS bsAtoms, BS bsReport) throws JmolAsyncExceptio… in calculatePartialCharges()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/ |
H A D | TransformManager.java | 297 protected void rotateXYBy(float degX, float degY, BS bsAtoms) { in rotateXYBy() 313 private void applyRotation(M3 mNew, boolean isInternal, BS bsAtoms, in applyRotation() 326 protected void rotate3DBall(float xDeg, float yDeg, BS bsAtoms) { in rotate3DBall() 341 public synchronized void rotateXRadians(float angleRadians, BS bsAtoms) { in rotateXRadians() 342 applyRotation(matrixTemp3.setAsXRotation(angleRadians), false, bsAtoms, in rotateXRadians() local 346 public synchronized void rotateYRadians(float angleRadians, BS bsAtoms) { in rotateYRadians() 361 private synchronized void rotateAxisAngle2(A4 axisAngle, BS bsAtoms) { in rotateAxisAngle2() 414 BS bsAtoms) { in rotateAxisAngleRadiansFixed() 446 boolean isSpin, BS bsAtoms, in rotateAboutPointsInternal() 519 applyRotation(matrixTemp3.setAA(axisangleT), true, bsAtoms, in rotateAxisAngleRadiansInternal() local [all …]
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H A D | TransformManager4D.java | 63 protected void rotateXYBy(float xDelta, float yDelta, BS bsAtoms) { in rotateXYBy()
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H A D | PropertyManager.java | 974 BS bsAtoms = vwr.getAtomBitSet(atomExpression); in getMoleculeInfo() local 1059 BS bsAtoms = vwr.getAtomBitSet(atomExpression); in getLigandInfo() local 1192 BS bsAtoms = BSUtil.copy(bs); in getModelExtract() local 1361 private static BS getCovalentBondsForAtoms(Bond[] bonds, int bondCount, BS bsAtoms) { in getCovalentBondsForAtoms() 1776 BS bsAtoms = vwr.getAtomBitSet(atomExpression); in getAnnotationInfo() local 2105 BS bsAtoms = null; in getPdbData() local 2270 BS bsAtoms = new BS(); in getModelCml() local 2329 public String fixJMEFormalCharges(BS bsAtoms, String jme) { in fixJMEFormalCharges()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/pymol/ |
H A D | JmolObject.java | 59 private BS bsAtoms; field in JmolObject 79 JmolObject(int id, String branchNameID, BS bsAtoms, Object info) { in JmolObject()
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H A D | PyMOLGroup.java | 17 BS bsAtoms = new BS(); field in PyMOLGroup
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/thread/ |
H A D | SpinThread.java | 49 private BS bsAtoms; field in SpinThread
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
H A D | StateScript.java | 61 public boolean deleteAtoms(int modelIndex, BS bsBonds, BS bsAtoms) { in deleteAtoms()
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H A D | ModelSet.java | 296 public String getModelDataBaseName(BS bsAtoms) { in getModelDataBaseName() 361 public P3[] getFrameOffsets(BS bsAtoms, boolean isFull) { in getFrameOffsets() 483 public String calculatePointGroup(BS bsAtoms) { in calculatePointGroup() 489 public Map<String, Object> getPointGroupInfo(BS bsAtoms) { in getPointGroupInfo() 494 public String getPointGroupAsString(BS bsAtoms, String type, in getPointGroupAsString() 573 public String getDefaultStructure(BS bsAtoms, BS bsModified) { in getDefaultStructure() 3493 public Object getBoundBoxOrientation(int type, BS bsAtoms) { in getBoundBoxOrientation() 3871 public float[] getCellWeights(BS bsAtoms) { in getCellWeights() 4020 public String getProteinStructureState(BS bsAtoms, int mode) { in getProteinStructureState() 4025 public String calculateStructures(BS bsAtoms, boolean asDSSP, in calculateStructures() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapebio/ |
H A D | Trace.java | 67 private void setPutty(float[] info, BS bsAtoms) { in setPutty()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/renderspecial/ |
H A D | DipolesRenderer.java | 122 BS bsAtoms = (BS) o[2]; in renderDipoleVector() local
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/inchi/ |
H A D | InChIJNI.java | 109 private static JniInchiStructure newJniInchiStructure(Viewer vwr, BS bsAtoms) { in newJniInchiStructure()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapespecial/ |
H A D | Dipoles.java | 227 BS bsAtoms = (BS) value; in setProperty() local 356 private void getAllMolecularDipoles(BS bsAtoms) { in getAllMolecularDipoles()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/ |
H A D | JmolScriptManager.java | 61 BS addHydrogensInline(BS bsAtoms, Lst<Atom> vConnections, P3[] pts) throws Exception; in addHydrogensInline()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/cif/ |
H A D | TopoCifParser.java | 671 BS bsAtoms = new BS(); // atoms that are associated or connected; in finalizeSymmetry() local 705 static BS shiftBits(BS bsAtoms, BS bs) { in shiftBits() 732 private int processAssociations(BS bsConnected, BS bsAtoms) { in processAssociations() 1107 BS bsAtoms = null; field in TopoCifParser.TNode 1334 BS bsAtoms; field in TopoCifParser.TLink
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