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Searched refs:modelSet (Results 1 – 25 of 38) sorted by relevance

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/dports/biology/jalview/jalview/src/jalview/javascript/
H A DMouseOverStructureListener.java79 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/
H A DModelManager.java37 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()
H A DStateManager.java432 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()
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H A DColorManager.java131 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()
H A DSelectionManager.java92 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()
H A DAnimationManager.java209 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/render/
H A DShapeRenderer.java72 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()
H A DRepaintManager.java190 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/
H A DSymmetry.java602 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()
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H A DSymmetryDesc.java65 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/
H A DJmolRepaintManager.java28 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
H A DAtomIndexIterator.java26 …public void setModel(ModelSet modelSet, int modelIndex, int zeroBase, int atomIndex, T3 center, fl… in setModel() argument
H A DSymmetryInterface.java75 …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
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/
H A DAtomIteratorWithinModel.java97 …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()
H A DMeasurementPending.java39 public MeasurementPending set(ModelSet modelSet) { in set() argument
40 return (MeasurementPending) setM(modelSet, null, Float.NaN, (short) 0, in set()
H A DMeasurement.java93 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()
H A DMeasurementData.java193 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()
H A DModel.java158 public Model set(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, in set() argument
160 ms = modelSet; in set()
H A DModelLoader.java1596 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 …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shape/
H A DShape.java121 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()
/dports/math/z3/z3-z3-4.8.13/examples/userPropagator/
H A Dexample.cpp60 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/
H A DBioModel.java80 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()
/dports/math/moab/fathomteam-moab-7bde9dfb84a8/src/
H A DGeomTopoTool.cpp50 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 …]
/dports/games/pioneer/pioneer-20210723/src/
H A DCityOnPlanet.cpp173 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()
/dports/math/moab/fathomteam-moab-7bde9dfb84a8/src/moab/
H A DGeomTopoTool.hpp231 EntityHandle get_root_model_set() { return modelSet; } in get_root_model_set()
300 EntityHandle modelSet; member in moab::GeomTopoTool

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