| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/atomtypes/ |
| H A D | OWLAtomTypeHandler.java | 158 String hybridization = attrValue.substring(attrValue.indexOf('#') + 1); in startAtomTypeElement() local
159 if ("sp3".equals(hybridization)) { in startAtomTypeElement()
161 } else if ("sp2".equals(hybridization)) { in startAtomTypeElement()
163 } else if ("sp1".equals(hybridization)) { in startAtomTypeElement()
165 } else if ("s".equals(hybridization)) { in startAtomTypeElement()
167 } else if ("planar".equals(hybridization)) { in startAtomTypeElement()
169 } else if ("sp3d1".equals(hybridization)) { in startAtomTypeElement()
171 } else if ("sp3d2".equals(hybridization)) { in startAtomTypeElement()
173 } else if ("sp3d3".equals(hybridization)) { in startAtomTypeElement()
175 } else if ("sp3d4".equals(hybridization)) { in startAtomTypeElement()
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| /dports/science/lammps/lammps-stable_29Sep2021/tools/msi2lmp/frc_files/ |
| H A D | pcff_templates.dat | 20 hybridization:SP3
71 hybridization:SP3
81 hybridization:SP3
91 hybridization:SP3
101 hybridization:SP3
111 hybridization:SP3
121 hybridization:SP3
406 hybridization:SP2
415 hybridization:SP2
832 hybridization:SP2
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| /dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/ |
| H A D | AtomType.java | 84 protected IAtomType.Hybridization hybridization = (Hybridization) CDKConstants.UNSET; field in AtomType
146 this.hybridization = ((IAtomType) element).getHybridization(); in AtomType()
281 public void setHybridization(IAtomType.Hybridization hybridization) { in setHybridization() argument
282 this.hybridization = hybridization; in setHybridization()
294 return this.hybridization; in getHybridization()
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| /dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/ |
| H A D | hydrogentools.cpp | 241 Core::AtomHybridization hybridization = Core::SP3; // default to sp3 in perceiveHybridization() local
263 hybridization = Core::SP; // sp in perceiveHybridization()
265 hybridization = Core::SP2; // sp2 in perceiveHybridization()
268 return hybridization; in perceiveHybridization()
278 Core::AtomHybridization hybridization = atom.hybridization(); in generateNewHydrogenPositions() local
279 if (hybridization == Core::HybridizationUnknown) { in generateNewHydrogenPositions()
281 hybridization = perceiveHybridization(atom); in generateNewHydrogenPositions()
303 Vector3 newPos = generateNewBondVector(atom, allVectors, hybridization); in generateNewHydrogenPositions()
315 Core::AtomHybridization hybridization) in generateNewBondVector() argument
383 switch (hybridization) { in generateNewBondVector()
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| /dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/ |
| H A D | hydrogentools.cpp | 241 Core::AtomHybridization hybridization = Core::SP3; // default to sp3 in perceiveHybridization() local
263 hybridization = Core::SP; // sp in perceiveHybridization()
265 hybridization = Core::SP2; // sp2 in perceiveHybridization()
268 return hybridization; in perceiveHybridization()
278 Core::AtomHybridization hybridization = atom.hybridization(); in generateNewHydrogenPositions() local
279 if (hybridization == Core::HybridizationUnknown) { in generateNewHydrogenPositions()
281 hybridization = perceiveHybridization(atom); in generateNewHydrogenPositions()
303 Vector3 newPos = generateNewBondVector(atom, allVectors, hybridization); in generateNewHydrogenPositions()
315 Core::AtomHybridization hybridization) in generateNewBondVector() argument
383 switch (hybridization) { in generateNewBondVector()
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/ |
| H A D | AtomType.java | 87 protected IAtomType.Hybridization hybridization = (Hybridization) CDKConstants.UNSET; field in AtomType
149 this.hybridization = ((IAtomType) element).getHybridization(); in AtomType()
289 public void setHybridization(IAtomType.Hybridization hybridization) { in setHybridization() argument
290 this.hybridization = hybridization; in setHybridization()
303 return this.hybridization; in getHybridization()
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| /dports/math/mfem/mfem-4.3/fem/ |
| H A D | bilinearform.cpp | 75 hybridization = NULL; in BilinearForm()
93 hybridization = NULL; in BilinearForm()
170 delete hybridization; in EnableHybridization()
174 hybridization = NULL; in EnableHybridization()
231 if (hybridization) { hybridization->Finalize(); } in Finalize()
350 if (hybridization) in AssembleElementMatrix()
378 if (hybridization) in AssembleBdrElementMatrix()
716 if (hybridization) in FormLinearSystem()
735 if (hybridization) in FormLinearSystem()
794 if (hybridization) in FormSystemMatrix()
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| H A D | pbilinearform.cpp | 368 else if (hybridization) in FormLinearSystem()
376 hybridization->ReduceRHS(true_B, B); in FormLinearSystem()
435 if (hybridization) in FormSystemMatrix()
437 hybridization->GetParallelMatrix(A); in FormSystemMatrix()
462 else if (hybridization) in RecoverFEMSolution()
469 hybridization->ComputeSolution(true_B, X, true_X); in RecoverFEMSolution()
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| H A D | pbilinearform.hpp | 86 if (hybridization) { hybridization->SetOperatorType(tid); } in SetOperatorType()
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| /dports/science/cdk/cdk-cdk-2.3/tool/hash/src/main/java/org/openscience/cdk/hash/ |
| H A D | BasicAtomEncoder.java | 140 IAtomType.Hybridization hybridization = atom.getHybridization(); in encode() local
141 return hybridization != null ? hybridization.ordinal() : 32451301; in encode()
|
| /dports/science/cdk/cdk-cdk-2.3/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/ |
| H A D | AbstractAtomTypeTest.java | 131 Hybridization hybridization = Hybridization.SP1; in testSetHybridization_IAtomType_Hybridization() local
134 atom.setHybridization(hybridization); in testSetHybridization_IAtomType_Hybridization()
135 Assert.assertEquals(hybridization, atom.getHybridization()); in testSetHybridization_IAtomType_Hybridization()
145 Hybridization hybridization = Hybridization.SP1; in testSetHybridization_Null() local
148 atom.setHybridization(hybridization); in testSetHybridization_Null()
149 Assert.assertEquals(hybridization, atom.getHybridization()); in testSetHybridization_Null()
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| /dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/ |
| H A D | QueryAtom.java | 106 protected IAtomType.Hybridization hybridization = (Hybridization) CDKConstants.UNSET; field in QueryAtom
490 public void setHybridization(IAtomType.Hybridization hybridization) { in setHybridization() argument
491 this.hybridization = hybridization; in setHybridization()
504 return this.hybridization; in getHybridization()
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| /dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/ |
| H A D | stssearch.isee | 7 <td>Pick PCR primers and hybridization oligos</td>
12 <td>Pick PCR primers and hybridization oligos</td>
|
| H A D | primersearch.isee | 7 <td>Pick PCR primers and hybridization oligos</td>
12 <td>Pick PCR primers and hybridization oligos</td>
|
| H A D | eprimer32.ione | 1 Pick PCR primers and hybridization oligos
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| H A D | eprimer3.ione | 1 Pick PCR primers and hybridization oligos
|
| /dports/math/mfem/mfem-4.3/examples/ |
| H A D | ex4p.cpp | 70 bool hybridization = false; in main() local
86 args.AddOption(&hybridization, "-hb", "--hybridization", "-no-hb", in main()
213 else if (hybridization) in main()
242 if (hybridization) { prec = new HypreBoomerAMG(*A.As<HypreParMatrix>()); } in main()
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| H A D | ex4.cpp | 64 bool hybridization = false; in main() local
80 args.AddOption(&hybridization, "-hb", "--hybridization", "-no-hb", in main()
180 else if (hybridization) in main()
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| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/ |
| H A D | ImmutableAtomType.java | 50 private final IAtomType.Hybridization hybridization; field in ImmutableAtomType
67 this.hybridization = type.getHybridization(); in ImmutableAtomType()
322 public void setHybridization(Hybridization hybridization) { in setHybridization() argument
328 return this.hybridization; in getHybridization()
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| /dports/math/mfem/mfem-4.3/examples/petsc/ |
| H A D | ex4p.cpp | 54 bool hybridization = false; in main() local
71 args.AddOption(&hybridization, "-hb", "--hybridization", "-no-hb", in main()
199 else if (hybridization) in main()
230 if (hybridization) { prec = new HypreBoomerAMG(A); } in main()
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| /dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
| H A D | atom.h | 147 AtomHybridization hybridization() const;
305 AtomHybridization AtomTemplate<Molecule_T>::hybridization() const in hybridization() function
307 return m_molecule->hybridization(m_index); in hybridization()
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| /dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
| H A D | atom.h | 147 AtomHybridization hybridization() const;
305 AtomHybridization AtomTemplate<Molecule_T>::hybridization() const in hybridization() function
307 return m_molecule->hybridization(m_index); in hybridization()
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| /dports/science/cdk/cdk-cdk-2.3/base/datadebug/src/main/java/org/openscience/cdk/debug/ |
| H A D | DebugAtomType.java | 337 public void setHybridization(IAtomType.Hybridization hybridization) { in setHybridization() argument
338 logger.debug("Setting hybridization: ", hybridization); in setHybridization()
339 super.setHybridization(hybridization); in setHybridization()
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| H A D | DebugFragmentAtom.java | 260 public void setHybridization(IAtomType.Hybridization hybridization) { in setHybridization() argument
261 logger.debug("Setting hybridization: ", hybridization); in setHybridization()
262 super.setHybridization(hybridization); in setHybridization()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
| H A D | AtomCollection.java | 1611 String hybridization = null; in getHybridizationAndAxes() local
1630 hybridization = "sp3"; in getHybridizationAndAxes()
1637 hybridization = "sp"; in getHybridizationAndAxes()
1649 hybridization = "sp2"; in getHybridizationAndAxes()
1658 hybridization = "sp"; in getHybridizationAndAxes()
1670 hybridization = lcaoType; in getHybridizationAndAxes()
1675 hybridization = "sp2"; in getHybridizationAndAxes()
1683 hybridization = "sp3"; in getHybridizationAndAxes()
1686 if (hybridization == null) in getHybridizationAndAxes()
1700 return hybridization; in getHybridizationAndAxes()
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