/dports/biology/jalview/jalview/src/jalview/javascript/ |
H A D | MouseOverStructureListener.java | 79 String[] modelSet; field in MouseOverStructureListener 86 modelSet = modelList; in MouseOverStructureListener() 87 if (modelSet != null) in MouseOverStructureListener() 89 for (int i = 0; i < modelSet.length; i++) in MouseOverStructureListener() 91 modelSet[i] = resolveModelFile(modelSet[i]); in MouseOverStructureListener() 131 return modelSet; in getStructureFiles() 177 this.getClass().getName() + " modelSet[0]: " + modelSet[0]); in updateColours() 183 SequenceI[][] sequence = new SequenceI[modelSet.length][]; in updateColours() 184 for (int m = 0; m < modelSet.length; m++) in updateColours() 186 StructureMapping[] sm = ssm.getMapping(modelSet[m]); in updateColours() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/ |
H A D | ModelManager.java | 37 ModelSet modelSet; field in ModelManager 56 modelSetName = modelSet.modelSetName; in createModelSet() 80 atomSetCollection, (isAppend ? modelSet : null), bsNew); in createModelSet() 82 if (modelSet.ac == 0 && !modelSet.getMSInfoB("isPyMOL")) in createModelSet() 98 return ModelLoader.createAtomDataSet(vwr, modelSet, tokType, atomSetCollection, in createAtomDataSet()
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H A D | StateManager.java | 432 ModelSet modelSet = vwr.ms; in Connections() local 433 if (modelSet == null) in Connections() 436 bondCount = modelSet.bondCount; in Connections() 438 Bond[] bonds = modelSet.bo; in Connections() 447 ModelSet modelSet = vwr.ms; in restore() local 448 if (modelSet == null) in restore() 450 modelSet.deleteAllBonds(); in restore() 453 int ac = modelSet.ac; in restore() 456 Bond b = modelSet.bondAtoms(modelSet.at[c.atomIndex1], in restore() 461 for (int i = modelSet.bondCount; --i >= 0;) in restore() [all …]
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H A D | ColorManager.java | 131 ModelSet modelSet = vwr.ms; in getColixAtomPalette() local 216 modelSet.getMoleculeIndex(atom.i, true), 0, in getColixAtomPalette() 217 modelSet.getMoleculeCountInModel(atom.mi) - 1, ColorEncoder.ROYGB, in getColixAtomPalette() 224 modelSet.getAltLocIndexInModel(modelIndex, atom.altloc), 0, in getColixAtomPalette() 225 modelSet.getAltLocCountInModel(modelIndex), ColorEncoder.ROYGB, in getColixAtomPalette() 231 modelSet.getInsertionCodeIndexInModel(modelIndex, in getColixAtomPalette() 233 modelSet.getInsertionCountInModel(modelIndex), ColorEncoder.ROYGB, in getColixAtomPalette()
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H A D | SelectionManager.java | 92 void display(ModelSet modelSet, BS bs, int addRemove, boolean isQuiet) { in display() argument 96 BS bsAll = modelSet.getModelAtomBitSetIncludingDeleted(-1, false); in display() 113 modelSet.setBsHidden(bsHidden); in display() 118 void hide(ModelSet modelSet, BS bs, int addRemove, boolean isQuiet) { in hide() argument 123 if (modelSet != null) in hide() 124 modelSet.setBsHidden(bsHidden); in hide()
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H A D | AnimationManager.java | 209 ModelSet modelSet = vwr.ms; in setModel() local 210 int modelCount = (modelSet == null ? 0 : modelSet.mc); in setModel() 252 ModelSet modelSet = vwr.ms; in setBackgroundModelIndex() local 253 if (modelSet == null || modelIndex < 0 || modelIndex >= modelSet.mc) in setBackgroundModelIndex()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/render/ |
H A D | ShapeRenderer.java | 72 public boolean renderShape(JmolRendererInterface g3d, ModelSet modelSet, Shape shape) { in renderShape() argument 73 setup(g3d, modelSet, shape); in renderShape() 80 public void setup(JmolRendererInterface g3d, ModelSet modelSet, Shape shape) { in setup() argument 82 this.ms = modelSet; in setup()
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H A D | RepaintManager.java | 190 public void render(GData gdata, ModelSet modelSet, boolean isFirstPass, in render() argument 221 && getRenderer(i).renderShape(g3d, modelSet, shape)) in render() 247 public String renderExport(GData gdata, ModelSet modelSet, in renderExport() argument 272 getRenderer(i).renderShape(exporter3D, modelSet, shape); in renderExport()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/ |
H A D | Symmetry.java | 602 public BS notInCentroid(ModelSet modelSet, BS bsAtoms, int[] minmax) { in notInCentroid() argument 606 JmolMolecule[] molecules = modelSet.getMolecules(); in notInCentroid() 608 Atom[] atoms = modelSet.at; in notInCentroid() 609 …boolean isOneMolecule = (molecules[moleculeCount - 1].firstAtomIndex == modelSet.am[atoms[iAtom0].… in notInCentroid() 662 private SymmetryDesc getDesc(ModelSet modelSet) { in getDesc() argument 664 "org.jmol.symmetry.SymmetryDesc", modelSet.vwr, "eval"))) : desc).set(modelSet); in getDesc() 668 public Object getSymmetryInfoAtom(ModelSet modelSet, int iatom, String xyz, in getSymmetryInfoAtom() argument 670 return getDesc(modelSet).getSymopInfo(iatom, xyz, op, translation, pt, in getSymmetryInfoAtom() 675 …public Map<String, Object> getSpaceGroupInfo(ModelSet modelSet, String sgName, int modelIndex, boo… in getSpaceGroupInfo() argument 678 Map<String, Object> info = modelSet.getModelAuxiliaryInfo(modelSet.vwr.am.cmi); in getSpaceGroupInfo() [all …]
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H A D | SymmetryDesc.java | 65 private ModelSet modelSet; field in SymmetryDesc 71 public SymmetryDesc set(ModelSet modelSet) { in set() argument 72 this.modelSet = modelSet; in set() 112 int iModel = modelSet.at[iAtom].mi; in getSymopInfo() 113 SymmetryInterface uc = modelSet.am[iModel].biosymmetry; in getSymopInfo() 114 if (uc == null && (uc = modelSet.getUnitCell(iModel)) == null) in getSymopInfo() 155 : modelSet.vwr.am.cmi); in getSpaceGroupInfo() 229 modelSet.setInfo(modelIndex, "spaceGroupInfo", info); in getSpaceGroupInfo() 1291 pt = modelSet.at[iatom]; in getSymmetryInfo() 1382 modelSet.getAtomBitsMDa(T.elemno, in getAtom() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/ |
H A D | JmolRepaintManager.java | 28 void render(GData gdata, ModelSet modelSet, boolean isFirstPass, int[] navMinMax); in render() argument 30 String renderExport(GData gdata, ModelSet modelSet, Map<String, Object> params); in renderExport() argument
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H A D | AtomIndexIterator.java | 26 …public void setModel(ModelSet modelSet, int modelIndex, int zeroBase, int atomIndex, T3 center, fl… in setModel() argument
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H A D | SymmetryInterface.java | 75 …public Map<String, Object> getSpaceGroupInfo(ModelSet modelSet, String spaceGroup, int modelIndex,… in getSpaceGroupInfo() argument 133 public BS notInCentroid(ModelSet modelSet, BS bsAtoms, in notInCentroid() argument
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
H A D | AtomIteratorWithinModel.java | 97 …public void setModel(ModelSet modelSet, int modelIndex, int firstModelAtom, int atomIndex, T3 cent… in setModel() argument 112 atoms = modelSet.at; in setModel() 113 vwr = modelSet.vwr; in setModel()
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H A D | MeasurementPending.java | 39 public MeasurementPending set(ModelSet modelSet) { in set() argument 40 return (MeasurementPending) setM(modelSet, null, Float.NaN, (short) 0, in set()
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H A D | Measurement.java | 93 public Measurement setM(ModelSet modelSet, Measurement m, float value, short colix, in setM() argument 96 this.ms = modelSet; in setM() 98 this.vwr = modelSet.vwr; in setM() 121 isTrajectory = modelSet.isTrajectoryMeasurement(countPlusIndices); in setM() 129 public Measurement setPoints(ModelSet modelSet, int[] indices, Point3fi[] points, in setPoints() argument 132 this.ms = modelSet; in setPoints() 136 vwr = modelSet.vwr; in setPoints()
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H A D | MeasurementData.java | 193 public void define(JmolMeasurementClient client, ModelSet modelSet) { in define() argument 195 atoms = modelSet.at; in define() 212 Measurement m = new Measurement().setPoints(modelSet, indices, pts, null); in define()
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H A D | Model.java | 158 public Model set(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, in set() argument 160 ms = modelSet; in set()
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H A D | ModelLoader.java | 1596 Atom[] atoms = modelSet.at; in createAtomDataSet() 1598 if (modelSet.unitCells != null) in createAtomDataSet() 1623 modelSet.setAtomCoord(i, xyz.x, xyz.y, xyz.z); in createAtomDataSet() 1627 BS bs = BS.newN(modelSet.ac); in createAtomDataSet() 1628 modelSet.getAtomsWithin(tolerance, pt, bs, -1); in createAtomDataSet() 1647 modelSet.setAtomCoords(bs, T.vibxyz, vib); in createAtomDataSet() 1651 modelSet.setAtomProperty(bs, tokType, 0, iterAtom.getOccupancy(), null, null, in createAtomDataSet() 1656 modelSet.setAtomProperty(bs, tokType, 0, iterAtom.getPartialCharge(), null, in createAtomDataSet() 1661 modelSet.setAtomProperty(bs, tokType, 0, iterAtom.getBfactor(), null, null, null); in createAtomDataSet() 1674 modelSet.recalculateLeadMidpointsAndWingVectors(-1); in createAtomDataSet() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/shape/ |
H A D | Shape.java | 121 final public void initializeShape(Viewer vwr, ModelSet modelSet, in initializeShape() argument 126 setModelSet(modelSet); in initializeShape() 166 public void setModelSet(ModelSet modelSet) { in setModelSet() argument 167 this.ms = modelSet; in setModelSet()
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/dports/math/z3/z3-z3-4.8.13/examples/userPropagator/ |
H A D | example.cpp | 60 std::unordered_set<model, model_hash_function> modelSet; member in user_propagator 74 if (modelSet.find(currentModel) != modelSet.end()) { in final() 86 modelSet.insert(currentModel); in final()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/ |
H A D | BioModel.java | 80 BioModel(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, in BioModel() argument 82 vwr = modelSet.vwr; in BioModel() 83 set(modelSet, modelIndex, trajectoryBaseIndex, jmolData, properties, auxiliaryInfo); in BioModel() 86 vwr.getJBR().getBioModelSet(modelSet); in BioModel() 88 modelSet.am[modelIndex] = this; in BioModel()
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/dports/math/moab/fathomteam-moab-7bde9dfb84a8/src/ |
H A D | GeomTopoTool.cpp | 50 modelSet(modelRootSet), updated(false), in GeomTopoTool() 110 if (modelSet) in dimension() 112 if(!mdbImpl->contains_entities(modelSet, &this_set, 1 )) in dimension() 138 if (modelSet) in global_id() 140 if(!mdbImpl->contains_entities(modelSet, &this_set, 1 )) in global_id() 1121 if (mdbImpl->contains_entities(modelSet, &wrt_ent, 1)) in get_senses() 1257 if (modelSet) in add_geo_set() 1259 result = mdbImpl->add_entities(modelSet, &set, 1); in add_geo_set() 1700 if (modelSet==0) in duplicate_model() 1702 rval = mdbImpl->create_meshset(MESHSET_SET, modelSet); in duplicate_model() [all …]
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/dports/games/pioneer/pioneer-20210723/src/ |
H A D | CityOnPlanet.cpp | 173 ModelSet modelSet; in SetCityModelPatterns() local 177 modelSet.insert(m); in SetCityModelPatterns() 182 for (TSetIter it = modelSet.begin(), itEnd = modelSet.end(); it != itEnd; ++it) { in SetCityModelPatterns()
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/dports/math/moab/fathomteam-moab-7bde9dfb84a8/src/moab/ |
H A D | GeomTopoTool.hpp | 231 EntityHandle get_root_model_set() { return modelSet; } in get_root_model_set() 300 EntityHandle modelSet; member in moab::GeomTopoTool
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