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Searched refs:PeriodicTable (Results 1 – 25 of 139) sorted by relevance

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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/
H A DTable.cpp22 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/
H A DPeriodicTable_doc.i34 %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 "
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/dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/tools/periodictable/
H A DPeriodicTableTest.java37 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A DPeriodicTable.cpp24 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()
H A DAtom.cpp31 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()
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H A DPeriodicTable.h32 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;
/dports/science/vipster/vipster-1.19.1b-14-g7168a1b/vipster/
H A Dperiodictable.cpp17 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()
H A Dperiodictable.h25 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;
H A Dmolecule.h19 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>();
H A Dperiodictable.py.cpp5 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()
/dports/science/qbox/qbox-public-rel1_73_3/util/upf2qso/src/
H A DPeriodicTable.cpp23 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
H A DPeriodicTable.h37 class PeriodicTable
46 PeriodicTable(void);
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/
H A DMolDescriptors.cpp34 const PeriodicTable *table = PeriodicTable::getTable(); in calcAMW()
45 const PeriodicTable *table = PeriodicTable::getTable(); in calcExactMW()
121 const PeriodicTable *table = PeriodicTable::getTable(); in calcMolFormula()
H A DConnectivityDescriptors.cpp27 const PeriodicTable *tbl = PeriodicTable::getTable(); in hkDeltas()
56 const PeriodicTable *tbl = PeriodicTable::getTable(); in nVals()
270 const PeriodicTable *tbl = PeriodicTable::getTable(); in calcHallKierAlpha()
/dports/math/vtk6/VTK-6.2.0/Domains/ChemistryOpenGL2/
H A DvtkOpenGLMoleculeMapper.cxx35 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()
/dports/math/vtk9/VTK-9.1.0/IO/Chemistry/
H A DvtkMoleculeReaderBase.cxx253 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/source/
H A Drdkit.Chem.PeriodicTable.rst1 rdkit.Chem.PeriodicTable module
4 .. automodule:: rdkit.Chem.PeriodicTable
/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/
H A DNumericalSurface.java29 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()
/dports/science/vipster/vipster-1.19.1b-14-g7168a1b/gui/qt/mainwidgets/molwidget_aux/
H A Dnewelement.h16 explicit newelement(Vipster::PeriodicTable& table, QWidget *parent = nullptr);
24 Vipster::PeriodicTable &table;
/dports/devel/py-cclib/cclib-1.7.1/cclib/bridge/
H A Dcclib2biopython.py9 from cclib.parser.utils import PeriodicTable
25 pt = PeriodicTable()
/dports/science/cdk/cdk-cdk-2.3/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/
H A DAtomicNumberRule.java26 import org.openscience.cdk.tools.periodictable.PeriodicTable;
45 return PeriodicTable.getAtomicNumber(ligand.getLigandAtom().getSymbol()); in getAtomicNumber()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/
H A DPeriodicGroupNumberAtom.java28 import org.openscience.cdk.tools.periodictable.PeriodicTable;
62 int group = PeriodicTable.getGroup(symbol); in matches()
/dports/science/vipster/vipster-1.19.1b-14-g7168a1b/gui/qt/mainwidgets/
H A Dperiodictablewidget.h21 void setTable(Vipster::PeriodicTable* table);
36 Vipster::PeriodicTable* table{nullptr};
/dports/devel/py-cclib/cclib-1.7.1/test/data/
H A DtestCore.py15 from cclib.parser.utils import PeriodicTable
32 pt = PeriodicTable()
/dports/math/py-yt/yt-4.0.1/yt/utilities/
H A Dperiodic_table.py140 class PeriodicTable: class
166 periodic_table = PeriodicTable()

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