/dports/science/openbabel/openbabel-3.1.1/src/ |
H A D | bondtyper.cpp | 145 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()
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H A D | builder.cpp | 686 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() [all …]
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H A D | phmodel.cpp | 278 _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()
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H A D | kekulize.cpp | 187 m_mol->GetBond(bit)->SetBondOrder(2); in AssignDoubleBonds() 372 OBBond *bond = m_mol->GetBond(m_path[i], m_path[i + 1]); in BackTrack()
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H A D | distgeom.cpp | 329 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()
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H A D | alias.cpp | 156 firstAttachFlags = mol.GetBond(XxAtom, firstAttachAtom)->GetFlags(); in FromNameLookup() 157 firstAttachOrder = mol.GetBond(XxAtom, firstAttachAtom)->GetBondOrder(); in FromNameLookup()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seq/ |
H A D | seq_loc_reverse_complementer.cpp | 144 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seq/ |
H A D | seq_loc_reverse_complementer.cpp | 144 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()
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/dports/math/vtk8/VTK-8.2.0/Filters/Core/ |
H A D | vtkMoleculeAppend.cxx | 160 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()
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/dports/math/vtk9/VTK-9.1.0/Filters/Core/ |
H A D | vtkMoleculeAppend.cxx | 165 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()
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/dports/science/openbabel/openbabel-3.1.1/test/ |
H A D | rotortest.cpp | 35 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()
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/dports/science/openbabel/openbabel-3.1.1/src/forcefields/ |
H A D | forcefieldmmff94.cpp | 1898 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() [all …]
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/dports/math/vtk8/VTK-8.2.0/Domains/Chemistry/ |
H A D | vtkMoleculeToLinesFilter.cxx | 39 vtkBond bond = input->GetBond(bondInd); in RequestData()
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/dports/math/vtk9/VTK-9.1.0/Domains/Chemistry/ |
H A D | vtkMoleculeToLinesFilter.cxx | 44 vtkBond bond = input->GetBond(bondInd); in RequestData()
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/ |
H A D | FragmentMatcher.py | 90 def GetBond(self, idx): member in FragmentMatcher
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/dports/science/openbabel/openbabel-3.1.1/src/ops/ |
H A D | conformer.cpp | 273 OBBond* b = pmol->GetBond(it); in Do() 292 OBBond* b = pmol->GetBond(p1,p2); in Do()
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/dports/science/gchemutils/gnome-chemistry-utils-0.14.16/plugins/paint/cycles/ |
H A D | cycletool.cc | 307 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()
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/dports/science/openbabel/openbabel-3.1.1/src/formats/ |
H A D | smilesformat.cpp | 1033 _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() [all …]
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H A D | xedformat.cpp | 93 bond = mol.GetBond(i); in WriteMolecule()
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H A D | fastsearchformat.cpp | 692 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()
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/dports/science/openbabel/openbabel-3.1.1/include/openbabel/ |
H A D | mol.h | 281 OBBond *GetBond(int idx) const; 286 OBBond *GetBond(int a, int b) const; 289 OBBond *GetBond(OBAtom* bgn, OBAtom* end) const;
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/dports/math/vtk6/VTK-6.2.0/Common/DataModel/ |
H A D | vtkMolecule.cxx | 102 this->GetBond(i).PrintSelf(os, subIndent); in PrintSelf() 233 vtkBond vtkMolecule::GetBond(vtkIdType bondId) in GetBond() function in vtkMolecule
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/dports/science/openbabel/openbabel-3.1.1/src/stereo/ |
H A D | gen3dstereohelper.cpp | 63 OBBond *bond = mol->GetBond(begin, end); in Setup()
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/dports/science/gchemutils/gnome-chemistry-utils-0.14.16/plugins/paint/bonds/ |
H A D | chaintool.cc | 296 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()
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/dports/math/vtk9/VTK-9.1.0/Common/DataModel/ |
H A D | vtkMolecule.cxx | 117 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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