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Searched refs:removeBond (Results 1 – 25 of 87) sorted by relevance

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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/
H A Dmolecule.cpp119 removeBond(atomBonds.back()); in removeAtom()
215 bool Molecule::removeBond(Index index) in removeBond() function in Avogadro::QtGui::Molecule
243 bool Molecule::removeBond(const BondType& bond_) in removeBond() function in Avogadro::QtGui::Molecule
245 return removeBond(bond_.index()); in removeBond()
248 bool Molecule::removeBond(const AtomType& a, const AtomType& b) in removeBond() function in Avogadro::QtGui::Molecule
250 return removeBond(bond(a, b).index()); in removeBond()
253 bool Molecule::removeBond(Index a, Index b) in removeBond() function in Avogadro::QtGui::Molecule
255 return removeBond(bond(a, b).index()); in removeBond()
H A Drwmolecule.h377 bool removeBond(Index bondId);
378 bool removeBond(const BondType& bond);
379 bool removeBond(Index atom1, Index atom2);
380 bool removeBond(const AtomType& atom1, const AtomType& atom2);
802 inline bool RWMolecule::removeBond(const RWMolecule::BondType& b) in removeBond() function
804 return b.molecule() == this ? removeBond(b.index()) : false; in removeBond()
807 inline bool RWMolecule::removeBond(Index atom1, Index atom2) in removeBond() function
809 return removeBond(bond(atom1, atom2).index()); in removeBond()
812 inline bool RWMolecule::removeBond(const RWMolecule::AtomType& atom1, in removeBond() function
817 return removeBond(bond(atom1.index(), atom2.index()).index()); in removeBond()
H A Dmolecule.h180 bool removeBond(Index index) override;
188 bool removeBond(const BondType& bond) override;
198 bool removeBond(const AtomType& atom1, const AtomType& atom2) override;
199 bool removeBond(Index atom1, Index atom2) override;
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/
H A Dmolecule.cpp119 removeBond(atomBonds.back()); in removeAtom()
215 bool Molecule::removeBond(Index index) in removeBond() function in Avogadro::QtGui::Molecule
243 bool Molecule::removeBond(const BondType& bond_) in removeBond() function in Avogadro::QtGui::Molecule
245 return removeBond(bond_.index()); in removeBond()
248 bool Molecule::removeBond(const AtomType& a, const AtomType& b) in removeBond() function in Avogadro::QtGui::Molecule
250 return removeBond(bond(a, b).index()); in removeBond()
253 bool Molecule::removeBond(Index a, Index b) in removeBond() function in Avogadro::QtGui::Molecule
255 return removeBond(bond(a, b).index()); in removeBond()
H A Drwmolecule.h377 bool removeBond(Index bondId);
378 bool removeBond(const BondType& bond);
379 bool removeBond(Index atom1, Index atom2);
380 bool removeBond(const AtomType& atom1, const AtomType& atom2);
802 inline bool RWMolecule::removeBond(const RWMolecule::BondType& b) in removeBond() function
804 return b.molecule() == this ? removeBond(b.index()) : false; in removeBond()
807 inline bool RWMolecule::removeBond(Index atom1, Index atom2) in removeBond() function
809 return removeBond(bond(atom1, atom2).index()); in removeBond()
812 inline bool RWMolecule::removeBond(const RWMolecule::AtomType& atom1, in removeBond() function
817 return removeBond(bond(atom1.index(), atom2.index()).index()); in removeBond()
H A Dmolecule.h180 bool removeBond(Index index) override;
188 bool removeBond(const BondType& bond) override;
198 bool removeBond(const AtomType& atom1, const AtomType& atom2) override;
199 bool removeBond(Index atom1, Index atom2) override;
/dports/science/cdk/cdk-cdk-2.3/tool/structgen/src/main/java/org/openscience/cdk/structgen/
H A DRandomGenerator.java215 ac.removeBond(b1); in mutate()
226 ac.removeBond(b2); in mutate()
237 ac.removeBond(b3); in mutate()
248 ac.removeBond(b4); in mutate()
H A DVicinitySampler.java191 ac.removeBond(b1); in change()
205 ac.removeBond(b2); in change()
219 ac.removeBond(b3); in change()
233 ac.removeBond(b4); in change()
/dports/science/cdk/cdk-cdk-2.3/base/interfaces/src/main/java/org/openscience/cdk/interfaces/
H A DIAtomContainer.java553 IBond removeBond(int position); in removeBond() method
562 IBond removeBond(IAtom atom1, IAtom atom2); in removeBond() method
569 void removeBond(IBond bond); in removeBond() method
/dports/science/cdk/cdk-cdk-2.3/base/datadebug/src/main/java/org/openscience/cdk/debug/
H A DDebugAtomContainer.java522 public IBond removeBond(int pos) { in removeBond() method in DebugAtomContainer
524 return super.removeBond(pos); in removeBond()
531 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugAtomContainer
533 return super.removeBond(atom1, atom2); in removeBond()
540 public void removeBond(IBond bond) { in removeBond() method in DebugAtomContainer
542 super.removeBond(bond); in removeBond()
H A DDebugPolymer.java444 public IBond removeBond(int pos) { in removeBond() method in DebugPolymer
446 return super.removeBond(pos); in removeBond()
451 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugPolymer
453 return super.removeBond(atom1, atom2); in removeBond()
458 public void removeBond(IBond bond) { in removeBond() method in DebugPolymer
460 super.removeBond(bond); in removeBond()
H A DDebugMonomer.java442 public IBond removeBond(int pos) { in removeBond() method in DebugMonomer
444 return super.removeBond(pos); in removeBond()
449 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugMonomer
451 return super.removeBond(atom1, atom2); in removeBond()
456 public void removeBond(IBond bond) { in removeBond() method in DebugMonomer
458 super.removeBond(bond); in removeBond()
H A DDebugAminoAcid.java442 public IBond removeBond(int pos) { in removeBond() method in DebugAminoAcid
444 return super.removeBond(pos); in removeBond()
449 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugAminoAcid
451 return super.removeBond(atom1, atom2); in removeBond()
456 public void removeBond(IBond bond) { in removeBond() method in DebugAminoAcid
458 super.removeBond(bond); in removeBond()
H A DDebugStrand.java444 public IBond removeBond(int pos) { in removeBond() method in DebugStrand
446 return super.removeBond(pos); in removeBond()
451 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugStrand
453 return super.removeBond(atom1, atom2); in removeBond()
458 public void removeBond(IBond bond) { in removeBond() method in DebugStrand
460 super.removeBond(bond); in removeBond()
H A DDebugRing.java467 public IBond removeBond(int pos) { in removeBond() method in DebugRing
469 return super.removeBond(pos); in removeBond()
474 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugRing
476 return super.removeBond(atom1, atom2); in removeBond()
481 public void removeBond(IBond bond) { in removeBond() method in DebugRing
483 super.removeBond(bond); in removeBond()
H A DDebugCrystal.java452 public IBond removeBond(int pos) { in removeBond() method in DebugCrystal
454 return super.removeBond(pos); in removeBond()
459 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugCrystal
461 return super.removeBond(atom1, atom2); in removeBond()
466 public void removeBond(IBond bond) { in removeBond() method in DebugCrystal
468 super.removeBond(bond); in removeBond()
H A DDebugBioPolymer.java445 public IBond removeBond(int pos) { in removeBond() method in DebugBioPolymer
447 return super.removeBond(pos); in removeBond()
452 public IBond removeBond(IAtom atom1, IAtom atom2) { in removeBond() method in DebugBioPolymer
454 return super.removeBond(atom1, atom2); in removeBond()
459 public void removeBond(IBond bond) { in removeBond() method in DebugBioPolymer
461 super.removeBond(bond); in removeBond()
/dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/
H A DAtomContainer.java892 removeBond(atomContainer.getBond(f));
929 public IBond removeBond(int position) {
943 public IBond removeBond(IAtom atom1, IAtom atom2) {
948 removeBond(pos);
957 public void removeBond(IBond bond) {
959 if (pos != -1) removeBond(pos);
1013 if (number < this.bondCount) return removeBond(number);
1028 removeBond((IBond) electronContainer);
1053 removeBond(i);
1490 removeBond(--pointer);
[all …]
/dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/
H A DAtomContainer.java916 removeBond(atomContainer.getBond(f));
955 public IBond removeBond(int position) {
971 public IBond removeBond(IAtom atom1, IAtom atom2) {
976 removeBond(pos);
985 public void removeBond(IBond bond) {
987 if (pos != -1) removeBond(pos);
1045 if (number < this.bondCount) return removeBond(number);
1060 removeBond((IBond) electronContainer);
1085 removeBond(i);
1555 removeBond(--pointer);
[all …]
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/
H A Dmolecule.cpp354 removeBond(atomBonds.back()); in removeAtom()
484 bool Molecule::removeBond(Index index) in removeBond() function in Avogadro::Core::Molecule
499 bool Molecule::removeBond(const BondType& bond_) in removeBond() function in Avogadro::Core::Molecule
501 return removeBond(bond_.index()); in removeBond()
504 bool Molecule::removeBond(Index a, Index b) in removeBond() function in Avogadro::Core::Molecule
506 return removeBond(bond(a, b).index()); in removeBond()
509 bool Molecule::removeBond(const AtomType& a, const AtomType& b) in removeBond() function in Avogadro::Core::Molecule
511 return removeBond(bond(a, b).index()); in removeBond()
517 removeBond(0); in clearBonds()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/
H A Dmolecule.cpp354 removeBond(atomBonds.back()); in removeAtom()
484 bool Molecule::removeBond(Index index) in removeBond() function in Avogadro::Core::Molecule
499 bool Molecule::removeBond(const BondType& bond_) in removeBond() function in Avogadro::Core::Molecule
501 return removeBond(bond_.index()); in removeBond()
504 bool Molecule::removeBond(Index a, Index b) in removeBond() function in Avogadro::Core::Molecule
506 return removeBond(bond(a, b).index()); in removeBond()
509 bool Molecule::removeBond(const AtomType& a, const AtomType& b) in removeBond() function in Avogadro::Core::Molecule
511 return removeBond(bond(a, b).index()); in removeBond()
517 removeBond(0); in clearBonds()
/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/
H A DRGroupQuery.java352 boolean removeBond = false; in findConfigurationsRecursively()
355 removeBond = true; in findConfigurationsRecursively()
358 removeBond = true; in findConfigurationsRecursively()
360 if (removeBond) { in findConfigurationsRecursively()
361 rootClone.removeBond(cloneBond); in findConfigurationsRecursively()
H A DQueryAtomContainer.java419 removeBond(--pointer);
549 removeBond(--pointer);
1088 removeBond(atomContainer.getBond(f));
1137 public IBond removeBond(int position) {
1157 public IBond removeBond(IAtom atom1, IAtom atom2) {
1162 removeBond(pos);
1173 public void removeBond(IBond bond) {
1175 if (pos != -1) removeBond(pos);
1244 if (number < this.bondCount) return removeBond(number);
1260 removeBond((IBond) electronContainer);
[all …]
/dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/graph/
H A DAllPairsShortestPaths.java457 … public IBond removeBond(int position) {
463 … public IBond removeBond(IAtom atom1, IAtom atom2) {
469 … public void removeBond(IBond bond) {
/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/
H A DAtomContainerComparatorTest.java116 hexaneNitrogen.removeBond(0); in testCompare_Ring_NonRing()
131 hexaneNitrogen.removeBond(0); in testCompare_Ring_NonRing2()

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