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Searched refs:bioPolymers (Results 1 – 6 of 6) sorted by relevance

/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/
H A DBioModel.java75 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()
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H A DBioModelSet.java114 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()
H A DBioExt.java56 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/dssx/
H A DDSSP.java199 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()
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H A DDSSR1.java283 BioPolymer bp = m.bioPolymers[i]; in setBioPolymers()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapebio/
H A DBioShapeCollection.java227 BioPolymer bp = ((BioModel) models[i]).bioPolymers[j]; in initialize()