Searched refs:bioPolymers (Results 1 – 6 of 6) sorted by relevance
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/ |
H A D | BioModel.java | 75 public BioPolymer[] bioPolymers; field in BioModel 93 if (bioPolymers.length == 0) in addBioPolymer() 95 if (bioPolymerCount == bioPolymers.length) in addBioPolymer() 96 bioPolymers = (BioPolymer[])AU.doubleLength(bioPolymers); in addBioPolymer() 98 bioPolymers[bioPolymerCount++] = polymer; in addBioPolymer() 117 BioPolymer b = bioPolymers[i]; in addStructureByBS() 128 if (bioPolymers[i].isNucleic()) in calculateDssx() 152 bioPolymers[i].clearStructures(); in calculateStructures() 162 bioPolymers = new BioPolymer[8]; in clearBioPolymers() 175 bioPolymers = (BioPolymer[])AU.arrayCopyObject(bioPolymers, bioPolymerCount); in freeze() [all …]
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H A D | BioModelSet.java | 114 m.bioPolymers[j].calcSelectedMonomersCount(bsSelected); in calcSelectedMonomersCount() 243 last = m.bioPolymers[ip].getPolymerPointsAndVectors(last, bs, vList, in getAllPolymerPointsAndVectors() 260 String sequence = m.bioPolymers[ip].getSequence(); in getAllSequenceBits() 263 m.bioPolymers[ip].getPolymerSequenceAtoms(j, lenInfo, bsAtoms, in getAllSequenceBits() 497 m.bioPolymers[i].getRangeGroups(nResidues, bs, bsResult); in getGroupsWithinAll() 578 m.bioPolymers[j].setConformation(bsAtoms); in setAllConformation() 631 m.bioPolymers = (BioPolymer[]) AU.arrayCopyObject(m.bioPolymers, in setAllStructureList() 634 BioPolymer bp = m.bioPolymers[i]; in setAllStructureList()
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H A D | BioExt.java | 56 BioPolymer bp = m.bioPolymers[ip]; in getAllPolymerInfo() 119 getPdbData(m.bioPolymers[p], 'S', qtype, mStep, 2, null, null, false, in calculateStraightnessAll() 657 getPdbData(m.bioPolymers[p], ctype, qtype, mStep, derivType, m.bsAtoms, in getPdbDataM()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/dssx/ |
H A D | DSSP.java | 199 private BioPolymer[] bioPolymers; field in DSSP 231 bioPolymers = (BioPolymer[]) objBioPolymers; in calculateDssp() 240 if (bioPolymers[i] instanceof AminoPolymer) in calculateDssp() 245 Model m = bioPolymers[0].model; in calculateDssp() 384 if (!(bioPolymers[i] instanceof AminoPolymer)) in getDualHydrogenBondArray() 386 int n = bioPolymers[i].monomerCount; in getDualHydrogenBondArray() 398 bioPolymers[i].calcRasmolHydrogenBonds(bioPolymers[j], null, null, in getDualHydrogenBondArray() 424 Atom[] atoms = bioPolymers[0].model.ms.at; in getBridges() 429 if (bioPolymers[p1] instanceof AminoPolymer) { in getBridges() 539 for (int i = bioPolymers.length; --i >= 0;) { in getSheetStructures() [all …]
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H A D | DSSR1.java | 283 BioPolymer bp = m.bioPolymers[i]; in setBioPolymers()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapebio/ |
H A D | BioShapeCollection.java | 227 BioPolymer bp = ((BioModel) models[i]).bioPolymers[j]; in initialize()
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