/dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/ |
H A D | residuetypes.cpp | 63 residueName(rName), in ResidueTypeEntry() 68 std::string residueName; member 119 return gmx::equalCaseInsensitive(residueName, old.residueName); in findResidueEntryWithName() 124 bool ResidueType::nameIndexedInResidueTypes(const std::string& residueName) in nameIndexedInResidueTypes() argument 126 return findResidueEntryWithName(impl_->entry, residueName).has_value(); in nameIndexedInResidueTypes() 131 if (auto foundIt = findResidueEntryWithName(impl_->entry, residueName)) in addResidue() 143 impl_->entry.emplace_back(residueName, residueType); in addResidue() 149 auto foundIt = findResidueEntryWithName(impl_->entry, residueName); in namedResidueHasType() 169 return impl_->entry[index].residueName; in nameFromResidueIndex() 179 auto foundIt = findResidueEntryWithName(impl_->entry, residueName); in typeOfNamedDatabaseResidue() [all …]
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H A D | atomprop.cpp | 76 residueName(rName), in BaseEntry() 84 std::string residueName; member 165 const std::string& residueName, in findPropertyIndex() argument 171 bool bProtein = restype->namedResidueHasType(residueName, "Protein"); in findPropertyIndex() 172 bool bProtWild = residueName == "AAA"; in findPropertyIndex() 177 int rlen = compareToDatabase(residueName, ap->entry[i].residueName); in findPropertyIndex() 180 if ((ap->entry[i].residueName == "*") || (ap->entry[i].residueName == "???")) in findPropertyIndex() 184 else if (ap->entry[i].residueName == "AAA") in findPropertyIndex() 233 const std::string& residueName, in addProperty() argument 243 ap->entry.emplace_back(BaseEntry(atomName, residueName)); in addProperty() [all …]
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H A D | residuetypes.h | 65 bool nameIndexedInResidueTypes(const std::string& residueName); 72 void addResidue(const std::string& residueName, const std::string& residueType); 80 bool namedResidueHasType(const std::string& residueName, const std::string& residueType); 87 int indexFromResidueName(const std::string& residueName) const; 101 std::string typeOfNamedDatabaseResidue(const std::string& residueName); 108 std::optional<std::string> optionalTypeOfNamedDatabaseResidue(const std::string& residueName);
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H A D | mtop_lookup.h | 206 const char** residueName, in mtopGetAtomAndResidueName() argument 233 if (residueName != nullptr) in mtopGetAtomAndResidueName() 235 *residueName = *(atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].name); in mtopGetAtomAndResidueName() 250 const char** residueName, in mtopGetAtomAndResidueName() argument 254 residueName, globalResidueIndex); in mtopGetAtomAndResidueName()
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/dports/science/gromacs/gromacs-2021.4/api/nblib/ |
H A D | molecules.cpp | 63 const ResidueName& residueName, in addParticle() argument 92 const ResidueName& residueName, in addParticle() argument 95 addParticle(particleName, residueName, Charge(0), particleType); in addParticle() 116 ResidueName Molecule::residueName(const ParticleIdentifier& particleIdentifier) in residueName() function in nblib::Molecule 118 return (particleIdentifier.residueName() == ResidueName{}) ? ResidueName(name_) in residueName() 149 particleJ.particleName(), residueName(particleJ)); in addInteraction() 166 residueName(particleK)); in addInteraction() 184 residueName(particleK), particleL.particleName(), residueName(particleL)); in addInteraction() 203 residueName(particleK), particleL.particleName(), residueName(particleL), in addInteraction() 204 particleM.particleName(), residueName(particleM)); in addInteraction() [all …]
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H A D | particlesequencer.cpp | 56 const ResidueName& residueName, in operator ()() argument 61 return data_.at(moleculeName).at(moleculeNr).at(residueName).at(particleName); in operator ()() 66 if (moleculeName.value() == residueName.value()) in operator ()() 69 residueName.value().c_str(), moleculeName.value().c_str()); in operator ()() 96 moleculeNrMap[molecule.residueName(j)][molecule.particleName(j)] = currentID++; in build()
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H A D | molecules.h | 95 ParticleIdentifier(ParticleName particleName, ResidueName residueName) : in ParticleIdentifier() argument 97 residueName_(std::move(residueName)) in ParticleIdentifier() 102 [[nodiscard]] const ResidueName& residueName() const { return residueName_; } in residueName() function 132 ResidueName residueName(const ParticleIdentifier& particleIdentifier); 143 const ResidueName& residueName, 149 const ResidueName& residueName, 216 ResidueName residueName(int i) const;
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/dports/science/gabedit/GabeditSrc251_300720/src/MolecularMechanics/ |
H A D | PDBTemplate.c | 42 if(pdbTemplate->residueTemplates[i].residueName) in freePDBTpl() 43 g_free(pdbTemplate->residueTemplates[i].residueName); in freePDBTpl() 112 static gint getResiduePDBTplNumber(gchar* residueName) in getResiduePDBTplNumber() argument 120 if(!strcmp(staticPDBTemplate->residueTemplates[i].residueName,residueName)) in getResiduePDBTplNumber() 146 gchar* getMMTypeFromPDBTpl(gchar* residueName,gchar* pdbType,gdouble* charge) in getMMTypeFromPDBTpl() argument 154 residueNumber = getResiduePDBTplNumber(residueName); in getMMTypeFromPDBTpl() 205 gint getHydrogensFromPDBTpl(gchar* residueName,gchar* pdbType, gchar** hAtoms) in getHydrogensFromPDBTpl() argument 213 residueNumber = getResiduePDBTplNumber(residueName); in getHydrogensFromPDBTpl() 267 gchar** getListPDBTypes(gchar* residueName, gint* nlist) in getListPDBTypes() argument 271 gint residueNumber = getResiduePDBTplNumber(residueName); in getListPDBTypes()
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H A D | PDBTemplate.h | 19 gchar* residueName; member 32 gchar* getMMTypeFromPDBTpl(gchar* residueName,gchar* pdbType,gdouble* charge); 33 gint getHydrogensFromPDBTpl(gchar* residueName,gchar* pdbType, gchar** hAtoms); 37 gchar** getListPDBTypes(gchar* residueName, gint* nlist);
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H A D | SavePDBTemplate.c | 42 fprintf(file,"%s\n",pdbTemplate->residueTemplates[i].residueName); in saveResiduesList() 53 fprintf(file,"Begin %s Residue\n",pdbTemplate->residueTemplates[residueNumber].residueName); in saveOneResidue()
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H A D | SetPDBTemplate.c | 202 gchar *residueName; in newResidue() local 224 residueName = g_strdup(gtk_entry_get_text(GTK_ENTRY(Entrys[E_RESIDUE]))); in newResidue() 225 delete_all_spaces(residueName); in newResidue() 236 residueTemplates[numberOfResidues-1].residueName = g_strdup(residueName); in newResidue() 248 g_free(residueName); in newResidue() 447 pdbTemplate->residueTemplates[residueNumber].residueName); in editnewDlg() 611 t =g_strdup_printf(format,pdbTemplate->residueTemplates[residueNumber].residueName); in deleteResidueDlg() 954 node = addNode(pdbTemplate->residueTemplates[i].residueName,i); in addResidueList()
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H A D | LoadPDBTemplate.c | 90 pdbTemplate->residueTemplates[i].residueName = g_strdup(t[i]); in setResiduesList() 111 sprintf(title,"Begin %s Residue",pdbTemplate->residueTemplates[residueNumber].residueName); in setOneResidue()
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/dports/biology/protomol/protomol/framework/base/ |
H A D | PDB.cpp | 11 residueName(""), in PDBAtom() 43 residueName(rname), in PDBAtom() 90 …OS <<p.elementType<<","<<p.elementNum<<","<<p.elementName<<","<<p.altLoc<<","<<p.residueName<<","<… in operator <<()
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H A D | PDB.h | 33 std::string residueName, 49 std::string residueName; ///< residue_name member
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/gamer/src/biom/ |
H A D | ReadPDB.C | 43 char residueName[4]; member 353 (eInfo.residueName[0] == line[17]) && in ReadPDB() 354 (eInfo.residueName[1] == line[18]) && in ReadPDB() 355 (eInfo.residueName[2] == line[19]) ) { in ReadPDB()
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H A D | PDB2Volume.h | 42 char residueName[4]; member
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/dports/science/gabedit/GabeditSrc251_300720/utils/MolecularMechanics/ |
H A D | createTPLfile.c | 129 void printTPLResidue(FILE* file,char* residueName) in printTPLResidue() argument 147 sprintf(title,"%s",residueName); in printTPLResidue() 165 printf("\tfprintf(fout,\"Begin %s Residue\\n\");\n",residueName); in printTPLResidue()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/io/ |
H A D | mmtftest.cpp | 124 EXPECT_EQ(res.residueName(), "VAL"); in TEST() 130 EXPECT_EQ(res2.residueName(), "HEM"); in TEST() 136 EXPECT_EQ(res3.residueName(), "HOH"); in TEST()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/io/ |
H A D | mmtftest.cpp | 124 EXPECT_EQ(res.residueName(), "VAL"); in TEST() 130 EXPECT_EQ(res2.residueName(), "HEM"); in TEST() 136 EXPECT_EQ(res3.residueName(), "HOH"); in TEST()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/ |
H A D | SmilesAtom.java | 67 String residueName, residueChar; field in SmilesAtom 514 return residueName == null ? "" : residueName; in getGroup3() 835 String s = (residueChar != null || residueName != null ? (residueChar == null ? residueName in toString()
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/dports/science/gabedit/GabeditSrc251_300720/src/SemiEmpirical/ |
H A D | MoleculeSE.c | 379 molecule.atoms[i].residueName = g_strdup(geom[i].Residue); in createMoleculeSE() 440 molecule.atoms[i].residueName = g_strdup(GeomXYZ[i].Residue); in createFromGeomXYZMoleculeSE() 501 geometry0[i].Residue = g_strdup(molecule->atoms[i].residueName); in redrawMoleculeSE() 515 geometry[i].Residue = g_strdup(molecule->atoms[i].residueName); in redrawMoleculeSE() 585 molecule.atoms[i].residueName = g_strdup(m->atoms[i].residueName); in copyMoleculeSE() 858 gchar residueName[SZ]; in readGeometryFromGenericOutputFile() local 927 symbol,mmType,pdbType,residueName, in readGeometryFromGenericOutputFile() 937 mol->atoms[i].residueName=strdup(residueName); in readGeometryFromGenericOutputFile() 991 molecule->atoms[j].residueName, in addGeometryMoleculeSEToGabedit()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | MonomerInfo.h | 69 const std::string &residueName = "", int residueNumber = 0, 79 d_residueName(residueName), in AtomMonomerInfo()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | pdbformat.cpp | 68 string residueName = lexicalCast<string>(buffer.substr(17, 3), ok); in read() local 81 r = &mol.addResidue(residueName, currentResidueId, chainId); in read()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | gromacsformat.cpp | 139 string residueName = lexicalCast<string>(buffer.substr(5, 5), ok); in read() local 147 r = &molecule.addResidue(residueName, currentResidueId, dummyChainId); in read()
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H A D | pdbformat.cpp | 68 string residueName = lexicalCast<string>(buffer.substr(17, 3), ok); in read() local 81 r = &mol.addResidue(residueName, currentResidueId, chainId); in read()
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