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Searched defs:bsAtoms (Results 1 – 25 of 61) sorted by relevance

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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/
H A DBioModelSet.java78 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/dssx/
H A DDSSR1.java107 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
H A DAnnotationParser.java289 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/
H A DUnitCellIterator.java52 Atom[] atoms, BS bsAtoms, float distance) { in set()
110 public void addAtoms(BS bsAtoms) { in addAtoms()
H A DCIPData.java72 BS bsAtoms; field in CIPData
155 public CIPData set(Viewer vwr, BS bsAtoms) { in set()
H A DSymmetry.java100 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/
H A DBondIterator.java31 private BS bsAtoms; field in BondIterator
H A DAtomIterator.java45 private BS bsAtoms; field in AtomIterator
H A DXtalSymmetry.java292 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
/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/
H A DMMConstraint.java26 public void set(int steps, BS bsAtoms, int[] atomMap) { in set()
H A DMinimizer.java80 public BS bsAtoms; field in Minimizer
683 …public void calculatePartialCharges(ModelSet ms, BS bsAtoms, BS bsReport) throws JmolAsyncExceptio… in calculatePartialCharges()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/
H A DTransformManager.java297 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 …]
H A DTransformManager4D.java63 protected void rotateXYBy(float xDelta, float yDelta, BS bsAtoms) { in rotateXYBy()
H A DPropertyManager.java974 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/pymol/
H A DJmolObject.java59 private BS bsAtoms; field in JmolObject
79 JmolObject(int id, String branchNameID, BS bsAtoms, Object info) { in JmolObject()
H A DPyMOLGroup.java17 BS bsAtoms = new BS(); field in PyMOLGroup
/dports/science/jmol/jmol-14.32.7/src/org/jmol/thread/
H A DSpinThread.java49 private BS bsAtoms; field in SpinThread
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/
H A DStateScript.java61 public boolean deleteAtoms(int modelIndex, BS bsBonds, BS bsAtoms) { in deleteAtoms()
H A DModelSet.java296 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 …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapebio/
H A DTrace.java67 private void setPutty(float[] info, BS bsAtoms) { in setPutty()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/renderspecial/
H A DDipolesRenderer.java122 BS bsAtoms = (BS) o[2]; in renderDipoleVector() local
/dports/science/jmol/jmol-14.32.7/src/org/jmol/inchi/
H A DInChIJNI.java109 private static JniInchiStructure newJniInchiStructure(Viewer vwr, BS bsAtoms) { in newJniInchiStructure()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapespecial/
H A DDipoles.java227 BS bsAtoms = (BS) value; in setProperty() local
356 private void getAllMolecularDipoles(BS bsAtoms) { in getAllMolecularDipoles()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/
H A DJmolScriptManager.java61 BS addHydrogensInline(BS bsAtoms, Lst<Atom> vConnections, P3[] pts) throws Exception; in addHydrogensInline()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/cif/
H A DTopoCifParser.java671 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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