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Searched refs:residueName (Results 1 – 25 of 62) sorted by relevance

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/dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/
H A Dresiduetypes.cpp63 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()
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H A Datomprop.cpp76 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()
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H A Dresiduetypes.h65 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);
H A Dmtop_lookup.h206 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()
/dports/science/gromacs/gromacs-2021.4/api/nblib/
H A Dmolecules.cpp63 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()
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H A Dparticlesequencer.cpp56 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()
H A Dmolecules.h95 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;
/dports/science/gabedit/GabeditSrc251_300720/src/MolecularMechanics/
H A DPDBTemplate.c42 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()
H A DPDBTemplate.h19 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);
H A DSavePDBTemplate.c42 fprintf(file,"%s\n",pdbTemplate->residueTemplates[i].residueName); in saveResiduesList()
53 fprintf(file,"Begin %s Residue\n",pdbTemplate->residueTemplates[residueNumber].residueName); in saveOneResidue()
H A DSetPDBTemplate.c202 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()
H A DLoadPDBTemplate.c90 pdbTemplate->residueTemplates[i].residueName = g_strdup(t[i]); in setResiduesList()
111 sprintf(title,"Begin %s Residue",pdbTemplate->residueTemplates[residueNumber].residueName); in setOneResidue()
/dports/biology/protomol/protomol/framework/base/
H A DPDB.cpp11 residueName(""), in PDBAtom()
43 residueName(rname), in PDBAtom()
90 …OS <<p.elementType<<","<<p.elementNum<<","<<p.elementName<<","<<p.altLoc<<","<<p.residueName<<","<… in operator <<()
H A DPDB.h33 std::string residueName,
49 std::string residueName; ///< residue_name member
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/gamer/src/biom/
H A DReadPDB.C43 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()
H A DPDB2Volume.h42 char residueName[4]; member
/dports/science/gabedit/GabeditSrc251_300720/utils/MolecularMechanics/
H A DcreateTPLfile.c129 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()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/io/
H A Dmmtftest.cpp124 EXPECT_EQ(res.residueName(), "VAL"); in TEST()
130 EXPECT_EQ(res2.residueName(), "HEM"); in TEST()
136 EXPECT_EQ(res3.residueName(), "HOH"); in TEST()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/io/
H A Dmmtftest.cpp124 EXPECT_EQ(res.residueName(), "VAL"); in TEST()
130 EXPECT_EQ(res2.residueName(), "HEM"); in TEST()
136 EXPECT_EQ(res3.residueName(), "HOH"); in TEST()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/
H A DSmilesAtom.java67 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()
/dports/science/gabedit/GabeditSrc251_300720/src/SemiEmpirical/
H A DMoleculeSE.c379 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A DMonomerInfo.h69 const std::string &residueName = "", int residueNumber = 0,
79 d_residueName(residueName), in AtomMonomerInfo()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dpdbformat.cpp68 string residueName = lexicalCast<string>(buffer.substr(17, 3), ok); in read() local
81 r = &mol.addResidue(residueName, currentResidueId, chainId); in read()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dgromacsformat.cpp139 string residueName = lexicalCast<string>(buffer.substr(5, 5), ok); in read() local
147 r = &molecule.addResidue(residueName, currentResidueId, dummyChainId); in read()
H A Dpdbformat.cpp68 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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