| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/ |
| H A D | coord_set.hpp | 62 AtomSet *atomSet; member in CoordSet
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| H A D | alignment_set.hpp | 72 bool Draw(const AtomSet *atomSet = NULL) const { return false; } // not drawable in Draw()
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| H A D | sequence_set.hpp | 66 bool Draw(const AtomSet *atomSet = NULL) const { return false; } // not drawable in Draw()
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| H A D | structure_base.hpp | 68 virtual bool Draw(const AtomSet *atomSet = NULL) const { return true; } in Draw()
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| H A D | cn3d_threader.cpp | 489 static void GetVirtualResidue(const AtomSet *atomSet, const Molecule *mol, in GetVirtualResidue()
546 static void GetVirtualPeptide(const AtomSet *atomSet, const Molecule *mol, in GetVirtualPeptide()
563 static void GetVirtualCoordinates(const Molecule *mol, const AtomSet *atomSet, in GetVirtualCoordinates()
678 static void GetMinimumLoopLengths(const Molecule *mol, const AtomSet *atomSet, Fld_Mtf *fldMtf) in GetMinimumLoopLengths()
732 const AtomSet *atomSet = object->coordSets.front()->atomSet; in CreateFldMtf() local
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| H A D | chemical_graph.cpp | 133 AtomSet *atomSet = object->coordSets.front()->atomSet; in ChemicalGraph() local
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| H A D | style_manager.cpp | 1106 const AtomSet *atomSet; in GetBondStyle() local
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| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | SSSRFinder.java | 27 List<Atom> atomSet = frag.getAtomList(); in getSetOfSmallestRings() local
48 private static List<Ring> getRings(List<Atom> atomSet ){ in getRings()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/domdec/ |
| H A D | localatomsetmanager.cpp | 91 for (const auto& atomSet : impl_->atomSetData_) in setIndicesInDomainDecomposition() local
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| /dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/ |
| H A D | ring.h | 213 int getComplexity(QVector<Atom *> atomSet) { in getComplexity()
223 bool notAllPositioned(QVector<Atom *> atomSet) { in notAllPositioned()
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| H A D | sdg.h | 109 QVector<Atom *> atomSet; variable
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| /dports/www/firefox/firefox-99.0/js/src/vm/ |
| H A D | JSAtom.cpp | 226 Rooted<UniquePtr<AtomSet>> atomSet(cx, in initializeAtoms() local
580 JSContext* cx, AtomSet& atomSet, const CharT* chars, size_t length, in PermanentlyAtomizeAndCopyCharsNonStaticValidLength()
863 AtomSet& atomSet, in PermanentlyAtomizeCharsValidLength()
876 AtomSet& atomSet, in PermanentlyAtomizeCharsNonStaticValidLength()
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smiles/smarts/ |
| H A D | SMARTSQueryTool.java | 411 BitSet atomSet = new BitSet(); in getUniqueMatchingAtoms() local
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| /dports/science/molsketch/Molsketch-0.7.2/libmolsketch/ |
| H A D | molecule.cpp | 309 auto atomSet = toSet(atomList); in split() local
401 auto atomSet = toSet(atomList); in canSplit() local
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/applied_forces/densityfitting/ |
| H A D | densityfitting.cpp | 384 …LocalAtomSet atomSet = localAtomSetManager->add(densityFittingOptions_.buildParameters().indices_); in constructLocalAtomSet() local
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/jvxl/readers/ |
| H A D | AtomDataReader.java | 203 BS atomSet = BSUtil.copy(bsMySelected); in getAtoms() local
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| /dports/www/firefox/firefox-99.0/js/src/frontend/ |
| H A D | ParserAtom.cpp | 157 JSContext* cx, AtomSet& atomSet, ParserAtomIndex index, in instantiatePermanentAtom()
1151 bool InstantiateMarkedAtomsAsPermanent(JSContext* cx, AtomSet& atomSet, in InstantiateMarkedAtomsAsPermanent()
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| H A D | Stencil.cpp | 2022 JSContext* cx, AtomSet& atomSet, CompilationAtomCache& atomCache) const { in instantiateSelfHostedAtoms()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/pulling/ |
| H A D | pull_internal.h | 104 gmx::LocalAtomSet atomSet; /**< Global to local atom set mapper */ member
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| H A D | pull.cpp | 119 gmx::LocalAtomSet atomSet, in pull_group_work_t()
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| H A D | pull_rotation.cpp | 148 std::unique_ptr<gmx::LocalAtomSet> atomSet; member
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/ |
| H A D | ASNFormat.cpp | 605 const AtomCoordSet &atomSet = atomSetCache.value(index); in loadIntraResidueBonds() local
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/ |
| H A D | SmilesParser.java | 871 private SmilesAtom parseAtom(SmilesSearch search, SmilesAtom atomSet, in parseAtom()
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| /dports/biology/protomol/protomol/framework/topology/ |
| H A D | topologyutilities.cpp | 663 void getAtomsBondedtoDihedral(const GenericTopology* topology, in getAtomsBondedtoDihedral()
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