/dports/science/mmdb2/mmdb2-2.0.20/mmdb2/ |
H A D | mmdb_chain.cpp | 1340 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() [all …]
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H A D | mmdb_selmngr.cpp | 976 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() [all …]
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H A D | mmdb_model.cpp | 3012 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() [all …]
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H A D | mmdb_bondmngr.cpp | 78 for (ir=0;ir<chain->nResidues;ir++) { in MakeBonds()
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H A D | mmdb_coormngr.cpp | 1107 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() [all …]
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H A D | mmdb_root.cpp | 929 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()
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H A D | mmdb_manager.cpp | 130 for (i=0;i<crChain->nResidues;i++) in Copy()
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H A D | mmdb_atom.cpp | 1032 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()
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H A D | mmdb_chain.h | 638 int nResidues; // number of residues variable
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/ |
H A D | molecule_identifier.hpp | 74 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)
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H A D | alignment_manager.cpp | 418 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() [all …]
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H A D | molecule_identifier.cpp | 87 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()
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H A D | molecule.cpp | 110 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()
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H A D | residue.hpp | 65 int nResidues, int moleculeType);
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H A D | molecule.hpp | 136 int GetAlphaCoords(int nResidues, const int *seqIndexes, const Vector * *coords) const;
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H A D | messenger.cpp | 326 …if (indexFrom > indexTo || indexFrom >= identifier->nResidues || indexTo >= identifier->nResidues)… in ToggleHighlights() 333 highlights[identifier].resize(identifier->nResidues, false); in ToggleHighlights()
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H A D | residue.cpp | 144 int nResidues, int moleculeType) : in Residue() argument 200 !(nResidues == 1 && in Residue()
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H A D | style_manager.cpp | 1647 residueFlags.resize(identifier->nResidues, false); in ExtractObjectLocation()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/ |
H A D | BioPolymer.java | 460 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()
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H A D | BioModelSet.java | 490 public BS getGroupsWithinAll(int nResidues, BS bs) { in getGroupsWithinAll() argument 497 m.bioPolymers[i].getRangeGroups(nResidues, bs, bsResult); in getGroupsWithinAll()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/ |
H A D | tngio.cpp | 1474 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()
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/dports/math/gap/gap-4.11.0/pkg/FactInt-1.6.3/lib/ |
H A D | pplus1.gi | 96 "p+1 for n = ",n,"\nResidues : ",Residues,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/struct_dp/ |
H A D | block_align.cpp | 69 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()
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ |
H A D | DirectionalREL.bf | 297 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…
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/pdb/ |
H A D | PdbReader.java | 1617 int nResidues = parseIntRange(line, 15, 17); in site() local 1623 htSite.put("nResidues", Integer.valueOf(nResidues)); in site()
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