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Searched refs:nResidues (Results 1 – 25 of 28) sorted by relevance

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/dports/science/mmdb2/mmdb2-2.0.20/mmdb2/
H A Dmmdb_chain.cpp1340 nResidues = 0; in FreeMemory()
1453 return nResidues; in GetNumberOfResidues()
1516 residue[nResidues]->index = nResidues; in GetResidueCreate()
1517 nResidues++; in GetResidueCreate()
1615 nResidues--; in _ExcludeResidue()
1700 nResidues = 0; in DeleteAllResidues()
1741 nResidues = j; in TrimResidueTable()
1865 nResidues++; in InsResidue()
2106 nResidues = chain->nResidues; in Copy()
2149 nResidues = chain->nResidues; in _copy()
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H A Dmmdb_selmngr.cpp976 while (i<chain->nResidues) { in Select()
993 while (i<chain->nResidues) { in Select()
1045 while (i<chain->nResidues) { in Select()
1051 while (i<chain->nResidues) { in Select()
1309 while (i<chain->nResidues) { in Select()
1326 while (i<chain->nResidues) { in Select()
1364 while (i<chain->nResidues) { in Select()
1370 while (i<chain->nResidues) { in Select()
1688 for (r=0;r<chain->nResidues;r++) { in SelectProperty()
1818 for (r=0;r<chain->nResidues;r++) { in SelectUDD()
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H A Dmmdb_model.cpp3012 for (ir=0;ir<chn->nResidues;ir++) in GetNumberOfResidues()
3274 if (chain[i]->nResidues>0) { in TrimChainTable()
3293 if (chn) return chn->nResidues; in GetNumberOfResidues()
3370 int i,j,k,nChns,nResidues; in GetResidueTable() local
3382 NumberOfResidues += nResidues; in GetResidueTable()
3392 for (j=0;j<nResidues;j++) in GetResidueTable()
3409 NumberOfResidues = chn->nResidues; in GetResidueTable()
3491 if (chain[i]->nResidues<=0) { in DeleteSolvent()
4581 for (i=0;i<chn->nResidues;i++) in AddChain()
5019 nres += chain[i]->nResidues; in CalcSecStructure()
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H A Dmmdb_bondmngr.cpp78 for (ir=0;ir<chain->nResidues;ir++) { in MakeBonds()
H A Dmmdb_coormngr.cpp1107 int i,j,k,n,nChains,nResidues; in GetResidueTable() local
1121 NumberOfResidues += nResidues; in GetResidueTable()
1134 for (n=0;n<nResidues;n++) in GetResidueTable()
1155 NumberOfResidues = chain->nResidues; in GetResidueTable()
1347 if (chain) return chain->nResidues; in GetNumberOfResidues()
1387 if (chain) return chain->nResidues; in GetNumberOfResidues()
1621 if ((0<=resNo) && (resNo<chn->nResidues)) in GetAtom()
1662 if ((0<=resNo) && (resNo<chn->nResidues)) in GetAtom()
1797 if ((0<=resNo) && (resNo<chn->nResidues)) in GetAtom()
1840 if ((0<=resNo) && (resNo<chn->nResidues)) in GetAtom()
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H A Dmmdb_root.cpp929 for (k=0;k<crChain0->nResidues;k++) { in PDBCleanup()
960 for (nr=0;(nr<crChain0->nResidues) && (!Solvent);nr++) { in PDBCleanup()
972 for (nr=0;nr<crChain0->nResidues;nr++) { in PDBCleanup()
986 for (nr=0;nr<crChain0->nResidues;nr++) { in PDBCleanup()
1076 for (nr=0;nr<crChain0->nResidues;nr++) { in PDBCleanup()
1155 for (k=0;k<crChain0->nResidues;k++) { in MakeHetAtoms()
1305 for (k=0;k<chain->nResidues;k++) { in FinishStructEdit()
1330 for (k=0;k<chain->nResidues;k++) { in FinishStructEdit()
H A Dmmdb_manager.cpp130 for (i=0;i<crChain->nResidues;i++) in Copy()
H A Dmmdb_atom.cpp1032 int nResidues, nAtoms, i,j,k; in GetChainCalphas() local
1045 chain->GetResidueTable ( res,nResidues ); in GetChainCalphas()
1047 if (nResidues>0) { in GetChainCalphas()
1049 Calphas = new PAtom[nResidues]; in GetChainCalphas()
1053 for (i=0;i<nResidues;i++) { in GetChainCalphas()
1065 for (i=0;i<nResidues;i++) { in GetChainCalphas()
H A Dmmdb_chain.h638 int nResidues; // number of residues variable
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/
H A Dmolecule_identifier.hpp74 unsigned int nResidues; member in MoleculeIdentifier
123 mmdbID(VALUE_NOT_SET), moleculeID(VALUE_NOT_SET), pdbChain(""), gi(VALUE_NOT_SET), nResidues(0) in MoleculeIdentifier()
127 …VALUE_NOT_SET), moleculeID(VALUE_NOT_SET), pdbChain(VALUE_NOT_SET), gi(VALUE_NOT_SET), nResidues(0)
H A Dalignment_manager.cpp418 int nResidues = 0; in RealignAllDependentStructures() local
420 nResidues += (*b)->width; in RealignAllDependentStructures()
421 if (nResidues == 0) { in RealignAllDependentStructures()
433 int *masterSeqIndexes = new int[nResidues], *dependentSeqIndexes = new int[nResidues]; in RealignAllDependentStructures()
443 double *weights = new double[nResidues]; in RealignAllDependentStructures()
447 CVP *masterCoords = new CVP[nResidues], *dependentCoords = new CVP[nResidues]; in RealignAllDependentStructures()
472 for (int j=0; j<nResidues; ++j) { in RealignAllDependentStructures()
978 int nResidues; member
1058 modList.front().nResidues = u->first->width; in CreateNewPairwiseAlignmentsByBlockExtension()
1066 totalShifts += e->nResidues; in CreateNewPairwiseAlignmentsByBlockExtension()
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H A Dmolecule_identifier.cpp87 if (identifier->nResidues == 0) in GetIdentifier()
88 identifier->nResidues = molecule->residues.size(); in GetIdentifier()
89 else if (identifier->nResidues != molecule->residues.size()) in GetIdentifier()
130 if (identifier->nResidues == 0) in GetIdentifier()
131 identifier->nResidues = sequence->Length(); in GetIdentifier()
132 else if (identifier->nResidues != sequence->Length()) in GetIdentifier()
H A Dmolecule.cpp110 int nResidues = 0; in Molecule() local
117 ++nResidues; in Molecule()
121 if (residue->id != nResidues) in Molecule()
246 int Molecule::GetAlphaCoords(int nResidues, const int *seqIndexes, const Vector * *coords) const in GetAlphaCoords() argument
256 for (int i=0; i<nResidues; ++i) { in GetAlphaCoords()
H A Dresidue.hpp65 int nResidues, int moleculeType);
H A Dmolecule.hpp136 int GetAlphaCoords(int nResidues, const int *seqIndexes, const Vector * *coords) const;
H A Dmessenger.cpp326 …if (indexFrom > indexTo || indexFrom >= identifier->nResidues || indexTo >= identifier->nResidues)… in ToggleHighlights()
333 highlights[identifier].resize(identifier->nResidues, false); in ToggleHighlights()
H A Dresidue.cpp144 int nResidues, int moleculeType) : in Residue() argument
200 !(nResidues == 1 && in Residue()
H A Dstyle_manager.cpp1647 residueFlags.resize(identifier->nResidues, false); in ExtractObjectLocation()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/
H A DBioPolymer.java460 public void getRangeGroups(int nResidues, BS bsAtoms, BS bsResult) { in getRangeGroups() argument
465 bsTemp.setBits(Math.max(0, i - nResidues), i + nResidues + 1); in getRangeGroups() local
466 i += nResidues - 1; in getRangeGroups()
H A DBioModelSet.java490 public BS getGroupsWithinAll(int nResidues, BS bs) { in getGroupsWithinAll() argument
497 m.bioPolymers[i].getRangeGroups(nResidues, bs, bsResult); in getGroupsWithinAll()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/
H A Dtngio.cpp1474 int64_t nMolecules, nChains, nResidues, nAtoms, nFramesRead; in gmx_print_tng_molecule_system() local
1518 tng_chain_num_residues_get(input, chain, &nResidues); in gmx_print_tng_molecule_system()
1519 for (int64_t k = 0; k < nResidues; k++) in gmx_print_tng_molecule_system()
1541 tng_molecule_num_residues_get(input, molecule, &nResidues); in gmx_print_tng_molecule_system()
1542 if (nResidues > 0) in gmx_print_tng_molecule_system()
1544 for (int64_t k = 0; k < nResidues; k++) in gmx_print_tng_molecule_system()
/dports/math/gap/gap-4.11.0/pkg/FactInt-1.6.3/lib/
H A Dpplus1.gi96 "p+1 for n = ",n,"\nResidues : ",Residues,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/struct_dp/
H A Dblock_align.cpp69 Matrix(unsigned int nBlocks, unsigned int nResidues) : grid(nBlocks + 1) in Matrix() argument
70 { for (unsigned int i=0; i<nBlocks; ++i) grid[i].resize(nResidues + 1); } in Matrix()
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/
H A DDirectionalREL.bf297 fprintf (stdout, "\nResidues (and p-values) for which there is evidence of directional selection…
298 fprintf (summaryPath, "\nResidues (and p-values) for which there is evidence of directional selecti…
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/pdb/
H A DPdbReader.java1617 int nResidues = parseIntRange(line, 15, 17); in site() local
1623 htSite.put("nResidues", Integer.valueOf(nResidues)); in site()

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