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Searched refs:GetBond (Results 1 – 25 of 127) sorted by relevance

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/dports/science/openbabel/openbabel-3.1.1/src/
H A Dbondtyper.cpp145 b1 = a1->GetBond(a2); in AssignFunctionalGroupBonds()
174 b1 = a1->GetBond(a2); in AssignFunctionalGroupBonds()
201 b1 = a1->GetBond(a2); in AssignFunctionalGroupBonds()
234 b1 = a1->GetBond(a2); in AssignFunctionalGroupBonds()
235 b2 = a2->GetBond(a3); in AssignFunctionalGroupBonds()
263 b1 = a1->GetBond(a2); in AssignFunctionalGroupBonds()
H A Dbuilder.cpp686 OBBond *bond = atom->GetBond(nbr); in GetNewBondVector()
963 OBBond *bond1 = mol.GetBond(idxA, idxB); in SwapWithVector()
1005 OBBond *bond1 = mol.GetBond(idxA, idxB); in Swap()
1006 OBBond *bond2 = mol.GetBond(idxC, idxD); in Swap()
1102 workMol.DeleteBond(workMol.GetBond(0)); in Build()
1177 OBBond *bond = atom1->GetBond(atom2); in Build()
1277 if (a->GetBond(prev)->IsAromatic()) in Build()
1302 OBBond *bond = a->GetBond(prev); // from mol in Build()
1312 workMol.DeleteBond(workMol.GetBond(0)); in Build()
1596 workMol.DeleteBond(workMol.GetBond(idx, nbrs[0])); in FlipSpiro()
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H A Dphmodel.cpp278 _bgn.GetBond(bsrc,bdst,bord,i); in Init()
286 _end.GetBond(esrc,edst,eord,j); in Init()
342 bond = mol.GetBond((*i)[j->first.first],(*i)[j->first.second]); in Apply()
H A Dkekulize.cpp187 m_mol->GetBond(bit)->SetBondOrder(2); in AssignDoubleBonds()
372 OBBond *bond = m_mol->GetBond(m_path[i], m_path[i + 1]); in BackTrack()
H A Ddistgeom.cpp329 if (b->GetBond(c) != nullptr) in Set13Bounds()
487 if (a->GetBond(d) != nullptr) in Set14Bounds()
565 bc = _mol.GetBond(path[b], path[c]); in Set14Bounds()
687 bc = _mol.GetBond(b, c); in GetCisTransStereo()
731 cd = _mol.GetBond(c, d); in Set15Bounds()
736 if (_mol.GetBond(a, &*e) != nullptr) in Set15Bounds()
768 ab = _mol.GetBond(a, b); in Set15Bounds()
773 if (_mol.GetBond(d, &*z) != nullptr) in Set15Bounds()
919 if (!_mol.GetBond(a, b) in SetLowerBounds()
1229 if (_mol.GetBond(a, b)) in CheckBounds()
H A Dalias.cpp156 firstAttachFlags = mol.GetBond(XxAtom, firstAttachAtom)->GetFlags(); in FromNameLookup()
157 firstAttachOrder = mol.GetBond(XxAtom, firstAttachAtom)->GetBondOrder(); in FromNameLookup()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seq/
H A Dseq_loc_reverse_complementer.cpp144 bond.SetA(*s_SeqPntRevCmp(loc.GetBond().GetA())); in GetReverseComplement()
145 if ( loc.GetBond().CanGetB() ) { in GetReverseComplement()
146 bond.SetA(*s_SeqPntRevCmp(loc.GetBond().GetB())); in GetReverseComplement()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seq/
H A Dseq_loc_reverse_complementer.cpp144 bond.SetA(*s_SeqPntRevCmp(loc.GetBond().GetA())); in GetReverseComplement()
145 if ( loc.GetBond().CanGetB() ) { in GetReverseComplement()
146 bond.SetA(*s_SeqPntRevCmp(loc.GetBond().GetB())); in GetReverseComplement()
/dports/math/vtk8/VTK-8.2.0/Filters/Core/
H A DvtkMoleculeAppend.cxx160 vtkBond bond = input->GetBond(i); in RequestData()
212 vtkBond bond = input->GetBond(i); in RequestData()
236 vtkIdType atom1 = output->GetBond(bondId).GetBeginAtomId(); in RequestData()
237 vtkIdType atom2 = output->GetBond(bondId).GetEndAtomId(); in RequestData()
/dports/math/vtk9/VTK-9.1.0/Filters/Core/
H A DvtkMoleculeAppend.cxx165 vtkBond bond = input->GetBond(i); in RequestData()
217 vtkBond bond = input->GetBond(i); in RequestData()
241 vtkIdType atom1 = output->GetBond(bondId).GetBeginAtomId(); in RequestData()
242 vtkIdType atom2 = output->GetBond(bondId).GetEndAtomId(); in RequestData()
/dports/science/openbabel/openbabel-3.1.1/test/
H A Drotortest.cpp35 OB_ASSERT(rotor.GetBond()->GetIdx() == bond.GetIdx()); in testOBRotorGetSet()
74 OBBond *bond = mol->GetBond(3); in testOBRotorSetToAngle()
106 OBBond *bond = mol->GetBond(3); in testOBRotorSetRotor()
/dports/science/openbabel/openbabel-3.1.1/src/forcefields/
H A Dforcefieldmmff94.cpp1898 bond = _mol.GetBond(&*nbr, atom); in GetType()
2248 bond = _mol.GetBond(&*nbr, atom); in GetType()
2307 bond = _mol.GetBond(&*nbr, atom); in GetType()
2487 bond = _mol.GetBond(&*nbr, atom); in GetType()
3171 if (b->GetBond(c)->IsAromatic()) { in SetupCalculations()
3196 OBBond *bond = a->GetBond(b); in SetupCalculations()
3252 OBBond *bond = b->GetBond(c); in SetupCalculations()
4485 OBBond *bond = _mol.GetBond(a, b); in GetBondType()
4635 OBBond *bond = _mol.GetBond(b, c); in GetTorsionType()
5041 BOab = a->GetBond(b)->GetBondOrder(); in GetRuleBondLength()
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/dports/math/vtk8/VTK-8.2.0/Domains/Chemistry/
H A DvtkMoleculeToLinesFilter.cxx39 vtkBond bond = input->GetBond(bondInd); in RequestData()
/dports/math/vtk9/VTK-9.1.0/Domains/Chemistry/
H A DvtkMoleculeToLinesFilter.cxx44 vtkBond bond = input->GetBond(bondInd); in RequestData()
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/
H A DFragmentMatcher.py90 def GetBond(self, idx): member in FragmentMatcher
/dports/science/openbabel/openbabel-3.1.1/src/ops/
H A Dconformer.cpp273 OBBond* b = pmol->GetBond(it); in Do()
292 OBBond* b = pmol->GetBond(p1,p2); in Do()
/dports/science/gchemutils/gnome-chemistry-utils-0.14.16/plugins/paint/cycles/
H A Dcycletool.cc307 pBond = (gcp::Bond*) m_Start->GetBond ((gcp::Atom*) pObject); in OnDrag()
312 pBond = (gcp::Bond*) m_End->GetBond ((gcp::Atom*) pObject); in OnDrag()
543 pBond = (gcp::Bond*) pAtom[i]->GetBond (pAtom[i - 1]); in OnRelease()
550 pBond = (gcp::Bond*) pAtom[m_size - 1]->GetBond (pAtom[0]); in OnRelease()
676 if (!pAtom[i]->GetBond (pAtom[(i)? i - 1: m_size -1])) in CheckIfAllowed()
678 if (!pAtom[i]->GetBond (pAtom[(i < m_size - 1)? i + 1: 0])) in CheckIfAllowed()
/dports/science/openbabel/openbabel-3.1.1/src/formats/
H A Dsmilesformat.cpp1033 _upDownMap[mol.GetBond(_prev, mol.NumAtoms())] = _updown; in ParseSimple()
1875 _upDownMap[mol.GetBond(_prev, mol.NumAtoms())] = _updown; in ParseComplex()
1933 _upDownMap[mol.GetBond(bond->prev, atom->GetIdx())] = bond->updown; in CapExternalBonds()
1935 OBBond *refbond = atom->GetBond(mol.GetAtom(bond->prev)); in CapExternalBonds()
2023 _upDownMap[mol.GetBond(bond->prev, _prev)] = upDown; in ParseExternalBond()
2118 _upDownMap[mol.GetBond(bond->prev, _prev)] = upDown; in ParseRingBond()
2127 _stereorbond[mol.GetBond(bond->prev, _prev)] = sb; // Store for later in ParseRingBond()
2608 refbonds[0] = mol->GetBond(mol->GetAtomById(cfg.refs[0]), mol->GetAtomById(cfg.begin)); in GetCisTransBondSymbol()
3133 OBBond *nbr_bond = atom->GetBond(nbr); in BuildCanonTree()
3138 bond = atom->GetBond(*ai); in BuildCanonTree()
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H A Dxedformat.cpp93 bond = mol.GetBond(i); in WriteMolecule()
H A Dfastsearchformat.cpp692 if(patternMol.GetBond(idx)->GetBondOrder()==4) in AddPattern()
694 patternMol.GetBond(idx)->SetBondOrder(1); in AddPattern()
699 patternMols.back().GetBond(idx)->SetBondOrder(5); in AddPattern()
/dports/science/openbabel/openbabel-3.1.1/include/openbabel/
H A Dmol.h281 OBBond *GetBond(int idx) const;
286 OBBond *GetBond(int a, int b) const;
289 OBBond *GetBond(OBAtom* bgn, OBAtom* end) const;
/dports/math/vtk6/VTK-6.2.0/Common/DataModel/
H A DvtkMolecule.cxx102 this->GetBond(i).PrintSelf(os, subIndent); in PrintSelf()
233 vtkBond vtkMolecule::GetBond(vtkIdType bondId) in GetBond() function in vtkMolecule
/dports/science/openbabel/openbabel-3.1.1/src/stereo/
H A Dgen3dstereohelper.cpp63 OBBond *bond = mol->GetBond(begin, end); in Setup()
/dports/science/gchemutils/gnome-chemistry-utils-0.14.16/plugins/paint/bonds/
H A Dchaintool.cc296 pBond = reinterpret_cast<gcp::Bond*> (m_Atoms[nb]->GetBond (m_Atoms[nb - 1])); in OnRelease()
450 n = (!m_Atoms[i]->GetBond(m_Atoms[i - 1]))? 1: 0; in CheckIfAllowed()
451 if ((i < m_CurPoints - 1) && !m_Atoms[i]->GetBond(m_Atoms[i + 1])) in CheckIfAllowed()
/dports/math/vtk9/VTK-9.1.0/Common/DataModel/
H A DvtkMolecule.cxx117 this->GetBond(i).PrintSelf(os, subIndent); in PrintSelf()
266 vtkBond vtkMolecule::GetBond(vtkIdType bondId) in GetBond() function in vtkMolecule
301 vtkBond bond = this->GetBond(bondId); in GetBondLength()

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