/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/ |
H A D | Table.cpp | 22 PeriodicTable *GetTable() { return PeriodicTable::getTable(); } in GetTable() 64 python::class_<PeriodicTable>( in wrap() 70 PeriodicTable::getAtomicWeight) in wrap() 73 PeriodicTable::getAtomicNumber) in wrap() 77 (double (PeriodicTable::*)(UINT) const) & PeriodicTable::getRvdw) in wrap() 84 PeriodicTable::getRcovalent) in wrap() 89 PeriodicTable::getDefaultValence) in wrap() 92 PeriodicTable::getValenceList, in wrap() 96 PeriodicTable::getValenceList, in wrap() 102 PeriodicTable::getNouterElecs) in wrap() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/ |
H A D | PeriodicTable_doc.i | 34 %typemap(javaimports) RDKit::PeriodicTable " 46 %javamethodmodifiers RDKit::PeriodicTable::getAtomicWeight ( char * elementSymbol ) const " 60 %javamethodmodifiers RDKit::PeriodicTable::getDefaultValence ( char * elementSymbol ) const… 74 %javamethodmodifiers RDKit::PeriodicTable::getNouterElecs ( char * elementSymbol ) const " 88 %javamethodmodifiers RDKit::PeriodicTable::getRb0 ( char * elementSymbol ) const " 95 %javamethodmodifiers RDKit::PeriodicTable::getRb0 ( const std::string & elementSymbol ) con… 102 %javamethodmodifiers RDKit::PeriodicTable::getRcovalent ( char * elementSymbol ) const " 116 %javamethodmodifiers RDKit::PeriodicTable::getRvdw ( char * elementSymbol ) const " 123 %javamethodmodifiers RDKit::PeriodicTable::getRvdw ( const std::string & elementSymbol ) co… 130 %javamethodmodifiers RDKit::PeriodicTable::getValenceList ( char * elementSymbol ) const " [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/tools/periodictable/ |
H A D | PeriodicTableTest.java | 37 Assert.assertEquals(CDKConstants.UNSET, PeriodicTable.getVdwRadius("Co")); in testTable() 38 Assert.assertEquals(1.7, PeriodicTable.getVdwRadius("C"), 0.001); in testTable() 39 Assert.assertEquals(39, PeriodicTable.getAtomicNumber("Y"), 0.001); in testTable() 40 Assert.assertEquals(2.55, PeriodicTable.getPaulingElectronegativity("C"), 0.001); in testTable() 41 Assert.assertEquals(CDKConstants.UNSET, PeriodicTable.getPaulingElectronegativity("He")); in testTable() 43 org.openscience.cdk.tools.periodictable.PeriodicTable.getCovalentRadius("Pu")); in testTable() 44 Assert.assertEquals(0.32, PeriodicTable.getCovalentRadius("He"), 0.001); in testTable() 45 Assert.assertEquals(14, PeriodicTable.getGroup("C"), 0.01); in testTable() 47 Assert.assertEquals("H", PeriodicTable.getSymbol(1)); in testTable() 48 Assert.assertEquals("C", PeriodicTable.getSymbol(6)); in testTable()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | PeriodicTable.cpp | 24 class std::unique_ptr<PeriodicTable> PeriodicTable::ds_instance = nullptr; 26 PeriodicTable::PeriodicTable() { in PeriodicTable() function in RDKit::PeriodicTable 102 void PeriodicTable::initInstance() { in initInstance() 103 ds_instance = std::unique_ptr<PeriodicTable>(new PeriodicTable()); in initInstance() 106 PeriodicTable *PeriodicTable::getTable() { in getTable()
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H A D | Atom.cpp | 31 switch (PeriodicTable::getTable()->getNouterElecs(atomicNum)) { in isEarlyAtom() 64 d_atomicNum = PeriodicTable::getTable()->getAtomicNumber(what); in Atom() 142 res = PeriodicTable::getTable()->getElementSymbol(d_atomicNum); in getSymbol() 224 unsigned int dv = PeriodicTable::getTable()->getDefaultValence(d_atomicNum); in calcExplicitValence() 246 PeriodicTable::getTable()->getValenceList(d_atomicNum); in calcExplicitValence() 283 if (PeriodicTable::getTable()->getNouterElecs(d_atomicNum) >= 4) { in calcExplicitValence() 291 PeriodicTable::getTable()->getValenceList(d_atomicNum); in calcExplicitValence() 375 int dv = PeriodicTable::getTable()->getDefaultValence(d_atomicNum); in calcImplicitValence() 393 PeriodicTable::getTable()->getValenceList(d_atomicNum); in calcImplicitValence() 482 << PeriodicTable::getTable()->getElementSymbol(d_atomicNum) in calcImplicitValence() [all …]
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H A D | PeriodicTable.h | 32 class RDKIT_GRAPHMOL_EXPORT PeriodicTable { 45 static PeriodicTable *getTable(); 47 ~PeriodicTable() { in ~PeriodicTable() 312 PeriodicTable(); 313 PeriodicTable &operator=(const PeriodicTable &); 316 static class std::unique_ptr<PeriodicTable> ds_instance;
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/dports/science/vipster/vipster-1.19.1b-14-g7168a1b/vipster/ |
H A D | periodictable.cpp | 17 const Vipster::PeriodicTable Vipster::pte = { 143 PeriodicTable::PeriodicTable(std::initializer_list<PeriodicTable::value_type> il, in PeriodicTable() function in PeriodicTable 144 const PeriodicTable *r) in PeriodicTable() 148 PeriodicTable::iterator PeriodicTable::find_or_fallback(const std::string &k) in find_or_fallback() 151 const PeriodicTable& root = this->root? *this->root : Vipster::pte; in find_or_fallback() 205 Element& PeriodicTable::operator [](const std::string& k) in operator []() 237 void to_json(nlohmann::json& j, const PeriodicTable& m) in to_json() 244 void from_json(const nlohmann::json& j, PeriodicTable& m) in from_json()
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H A D | periodictable.h | 25 class PeriodicTable: public StaticMap<std::string, Element> 30 PeriodicTable(std::initializer_list<PeriodicTable::value_type> il={}, 31 const PeriodicTable *r=nullptr); 34 const PeriodicTable *root; 37 extern const PeriodicTable pte;
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H A D | molecule.h | 19 pte = std::make_shared<PeriodicTable>(step.getPTE()); 29 PeriodicTable& getPTE(); 30 const PeriodicTable& getPTE() const; 43 std::shared_ptr<PeriodicTable> pte = std::make_shared<PeriodicTable>();
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H A D | periodictable.py.cpp | 5 py::class_<PeriodicTable, std::shared_ptr<PeriodicTable>>(m, "__PeriodicTable") in Table() 6 … .def("__getitem__", &PeriodicTable::operator [], py::return_value_policy::reference_internal) in Table() 7 .def("__setitem__", [](PeriodicTable &pte, std::string n, Element& e){pte[n] = e;}) in Table()
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/dports/science/qbox/qbox-public-rel1_73_3/util/upf2qso/src/ |
H A D | PeriodicTable.cpp | 23 int PeriodicTable::z(string symbol) const in z() 31 string PeriodicTable::symbol(int z) const in symbol() 38 string PeriodicTable::configuration(int z) const in configuration() 45 string PeriodicTable::configuration(string symbol) const in configuration() 51 double PeriodicTable::mass(int z) const in mass() 58 double PeriodicTable::mass(string symbol) const in mass() 64 int PeriodicTable::size(void) const in size() 70 PeriodicTable::PeriodicTable(void) in PeriodicTable() function in PeriodicTable
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H A D | PeriodicTable.h | 37 class PeriodicTable 46 PeriodicTable(void);
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/ |
H A D | MolDescriptors.cpp | 34 const PeriodicTable *table = PeriodicTable::getTable(); in calcAMW() 45 const PeriodicTable *table = PeriodicTable::getTable(); in calcExactMW() 121 const PeriodicTable *table = PeriodicTable::getTable(); in calcMolFormula()
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H A D | ConnectivityDescriptors.cpp | 27 const PeriodicTable *tbl = PeriodicTable::getTable(); in hkDeltas() 56 const PeriodicTable *tbl = PeriodicTable::getTable(); in nVals() 270 const PeriodicTable *tbl = PeriodicTable::getTable(); in calcHallKierAlpha()
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/dports/math/vtk6/VTK-6.2.0/Domains/ChemistryOpenGL2/ |
H A D | vtkOpenGLMoleculeMapper.cxx | 35 this->PeriodicTable->GetDefaultLUT(lut.GetPointer()); in vtkStandardNewMacro() 38 (0, this->PeriodicTable->GetNumberOfElements()); in vtkStandardNewMacro() 117 this->PeriodicTable->GetDefaultLUT(lut.GetPointer()); in UpdateBondGlyphPolyData() 120 (0, this->PeriodicTable->GetNumberOfElements()); in UpdateBondGlyphPolyData()
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/dports/math/vtk9/VTK-9.1.0/IO/Chemistry/ |
H A D | vtkMoleculeReaderBase.cxx | 253 this->PeriodicTable->GetDefaultRGBTuple(AtomType->GetValue(i), rgb); in ReadMolecule() 279 double radius = this->PeriodicTable->GetVDWRadius(AtomType->GetValue(i)); in ReadMolecule() 326 (this->PeriodicTable->GetCovalentRadius(atom1Type) + 2.0 + 0.56) * std::max(BScale, HBScale); in MakeBonds() 357 dist = this->PeriodicTable->GetCovalentRadius(atom1Type) + in MakeBonds() 358 this->PeriodicTable->GetCovalentRadius(atom2Type) + 0.56; in MakeBonds() 406 unsigned int atomNumber = this->PeriodicTable->GetAtomicNumber(atomTypeName); in MakeAtomType() 415 return this->PeriodicTable->GetAtomicNumber(std::string(1, atomTypeName[0])); in MakeAtomType()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/source/ |
H A D | rdkit.Chem.PeriodicTable.rst | 1 rdkit.Chem.PeriodicTable module 4 .. automodule:: rdkit.Chem.PeriodicTable
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/ |
H A D | NumericalSurface.java | 29 import org.openscience.cdk.tools.periodictable.PeriodicTable; 131 double vdwr = PeriodicTable.getVdwRadius(atom.getSymbol()); in init() 133 maxRadius = PeriodicTable.getVdwRadius(atom.getSymbol()) + solventRadius; in init() 260 double totalRadius = PeriodicTable.getVdwRadius(atom.getSymbol()) + solventRadius; in translatePoints() 290 double totalRadius = PeriodicTable.getVdwRadius(atom.getSymbol()) + solventRadius; in atomicSurfacePoints() 302 double tmp = PeriodicTable.getVdwRadius(atoms[nlist[i]].getSymbol()) + solventRadius; in atomicSurfacePoints()
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/dports/science/vipster/vipster-1.19.1b-14-g7168a1b/gui/qt/mainwidgets/molwidget_aux/ |
H A D | newelement.h | 16 explicit newelement(Vipster::PeriodicTable& table, QWidget *parent = nullptr); 24 Vipster::PeriodicTable &table;
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/dports/devel/py-cclib/cclib-1.7.1/cclib/bridge/ |
H A D | cclib2biopython.py | 9 from cclib.parser.utils import PeriodicTable 25 pt = PeriodicTable()
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/dports/science/cdk/cdk-cdk-2.3/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/ |
H A D | AtomicNumberRule.java | 26 import org.openscience.cdk.tools.periodictable.PeriodicTable; 45 return PeriodicTable.getAtomicNumber(ligand.getLigandAtom().getSymbol()); in getAtomicNumber()
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ |
H A D | PeriodicGroupNumberAtom.java | 28 import org.openscience.cdk.tools.periodictable.PeriodicTable; 62 int group = PeriodicTable.getGroup(symbol); in matches()
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/dports/science/vipster/vipster-1.19.1b-14-g7168a1b/gui/qt/mainwidgets/ |
H A D | periodictablewidget.h | 21 void setTable(Vipster::PeriodicTable* table); 36 Vipster::PeriodicTable* table{nullptr};
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/dports/devel/py-cclib/cclib-1.7.1/test/data/ |
H A D | testCore.py | 15 from cclib.parser.utils import PeriodicTable 32 pt = PeriodicTable()
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/dports/math/py-yt/yt-4.0.1/yt/utilities/ |
H A D | periodic_table.py | 140 class PeriodicTable: class 166 periodic_table = PeriodicTable()
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