/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/geometry/ |
H A D | GeometryToolsTest.java | 78 atom1 = new Atom("C"); in testHas2DCoordinates_IAtomContainer() 252 ac.addAtom(atom1); in testRotate_IAtomContainer_Point2d_double() 272 ac.addAtom(atom1); in testGetMinMax_IAtomContainer() 289 ac.addAtom(atom1); in testGetMinMax2() 338 ac.addAtom(atom1); in testGet2DCenter_IAtomContainer() 354 ac.addAtom(atom1); in testGet2DCenterOfMass_IAtomContainer() 383 ac.addAtom(atom1); in testGet2DCenter_IRingSet() 399 ac.addAtom(atom1); in testGet2DCenter_Iterator() 569 ac.addAtom(atom1); in testTranslateAllPositive_IAtomContainer_HashMap() 586 ac.addAtom(atom1); in testGetLength2D_IBond_HashMap() [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/geometry/ |
H A D | GeometryUtilTest.java | 80 atom1 = new Atom("C"); in testHas2DCoordinates_IAtomContainer() 254 ac.addAtom(atom1); in testRotate_IAtomContainer_Point2d_double() 274 ac.addAtom(atom1); in testGetMinMax_IAtomContainer() 291 ac.addAtom(atom1); in testGetMinMax2() 324 ac.addAtom(atom1); in testGet2DCenter_IAtomContainer() 340 ac.addAtom(atom1); in testGet2DCenterOfMass_IAtomContainer() 369 ac.addAtom(atom1); in testGet2DCenter_IRingSet() 385 ac.addAtom(atom1); in testGet2DCenter_Iterator() 555 ac.addAtom(atom1); in testTranslateAllPositive_IAtomContainer_HashMap() 572 ac.addAtom(atom1); in testGetLength2D_IBond_HashMap() [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ |
H A D | AtomMatcherTest.java | 46 IAtom atom1 = mock(IAtom.class); in anyMatch() local 52 assertTrue(matcher.matches(atom1, atom2)); in anyMatch() 53 assertTrue(matcher.matches(atom2, atom1)); in anyMatch() 54 assertTrue(matcher.matches(atom1, atom3)); in anyMatch() 55 assertTrue(matcher.matches(atom3, atom1)); in anyMatch() 57 assertTrue(matcher.matches(atom1, null)); in anyMatch() 64 IAtom atom1 = mock(IAtom.class); in elementMatch() local 75 IAtom atom1 = mock(IAtom.class); in elementMismatch() local 86 IAtom atom1 = mock(IPseudoAtom.class); in elementPseudo() local 95 IAtom atom1 = mock(IAtom.class); in elementError() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ |
H A D | AtomTetrahedralLigandPlacer3DTest.java | 42 IAtom atom1 = new Atom("C"); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() local 48 IBond bond1 = new Bond(atom1, atom2); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 49 IBond bond2 = new Bond(atom1, atom3); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 50 IBond bond3 = new Bond(atom1, atom4); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 53 atom1.setFormalNeighbourCount(4); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 58 ac.addAtom(atom1); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 73 IAtom atom1 = new Atom("C"); in rescaleBondLength_IAtom_IAtom_Point3d() local 75 atom1.setCovalentRadius(0.2); in rescaleBondLength_IAtom_IAtom_Point3d() 86 IAtom atom1 = new Atom("C"); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double() local 97 ac.addAtom(atom1); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double() [all …]
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/dports/biology/protomol/protomol/framework/base/ |
H A D | PSF.h | 49 Bond():number(0),atom1(0),atom2(0){} in Bond() 53 int atom1; ///< bonded atom 1 number member 69 int atom1; ///< angle atom 1 number member 86 int atom1; ///< dihedral atom 1 number member 103 int atom1; ///< improper atom 1 number member 116 Donor():number(0),atom1(0),atom2(0){} in Donor() 120 int atom1; ///< donor atom 1 number member 131 Acceptor():number(0),atom1(0),atom2(0){} in Acceptor() 147 Nonbonded():number(0),atom1(0){} in Nonbonded() 151 int atom1; ///< nonbonded atom number member [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
H A D | Bond.java | 38 public Atom atom1; field in Bond 55 this.atom1 = atom1; in Bond() 119 if (atom1 != null) in deleteAtomReferences() 120 atom1.deleteBond(this); in deleteAtomReferences() 123 atom1 = atom2 = null; in deleteAtomReferences() 141 return atom1.i; in getAtomIndex1() 156 return (atom1 == thisAtom ? atom2 : atom2 == thisAtom ? atom1 : null); in getOtherAtom() 165 return (atom1 == thisAtom ? atom2 : atom2 == thisAtom || thisAtom == null ? atom1 : null); in getOtherNode() 173 Bond[] bonds = atom1.bonds; in setAtropisomerOptions() 183 if (a != atom1) in setAtropisomerOptions() [all …]
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/dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/ |
H A D | bond.cpp | 349 QString atom1, atom2, swp; in Enthalpy() local 351 atom1 = start->element; in Enthalpy() 353 if (QString::compare(atom1, atom2) > 0) { in Enthalpy() 354 swp = atom1; in Enthalpy() 355 atom1 = atom2; in Enthalpy() 359 if (atom1 == "OH") { in Enthalpy() 361 atom1 = "O"; in Enthalpy() 373 if ((atom1 == "C") && (atom2 == "C")) in Enthalpy() 377 if ((atom1 == "C") && (atom2 == "F")) in Enthalpy() 379 if ((atom1 == "C") && (atom2 == "H")) in Enthalpy() [all …]
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H A D | dpoint.h | 344 atom1 = 1; in getAtomicNumber() 346 atom1 = 6; in getAtomicNumber() 348 atom1 = 6; in getAtomicNumber() 350 atom1 = 6; in getAtomicNumber() 352 atom1 = 6; in getAtomicNumber() 354 atom1 = 6; in getAtomicNumber() 356 atom1 = 6; in getAtomicNumber() 358 atom1 = 6; in getAtomicNumber() 360 atom1 = 6; in getAtomicNumber() 362 atom1 = 6; in getAtomicNumber() [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/ |
H A D | bonds.py | 174 for atom1 in cys1.atoms: 175 if atom1.name == 'SG': 185 for atom1 in residue.atoms: 203 for atom1 in residue1.atoms: 204 if atom1.name == 'C': 213 for atom1 in residue.atoms: 229 for atom1 in atoms: 231 key = '%s-%s'%(atom1.resName,atom1.name) 240 if atom2.name in self.protein_bonds[atom1.resName][atom1.name]: 396 if atom1 in atom2.bonded_atoms or atom2 in atom1.bonded_atoms: [all …]
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/ |
H A D | neigh_bond.cpp | 74 int i,m,atom1; in bond_all() local 90 if (atom1 == -1) { in bond_all() 97 atom1 = domain->closest_image(i,atom1); in bond_all() 126 int i,m,atom1; in bond_partial() local 150 atom1 = domain->closest_image(i,atom1); in bond_partial() 225 atom1 = domain->closest_image(i,atom1); in angle_all() 274 atom1 = domain->closest_image(i,atom1); in angle_partial() 364 atom1 = domain->closest_image(i,atom1); in dihedral_all() 419 atom1 = domain->closest_image(i,atom1); in dihedral_partial() 529 atom1 = domain->closest_image(i,atom1); in improper_all() [all …]
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H A D | compute_bond_local.cpp | 155 int i,m,n,atom1,atom2; in compute_bonds() local 172 for (atom1 = 0; atom1 < nlocal; atom1++) { in compute_bonds() 173 if (!(mask[atom1] & groupbit)) continue; in compute_bonds() 174 for (i = 0; i < num_bond[atom1]; i++) { in compute_bonds() 175 atom2 = atom->map(bond_atom[atom1][i]); in compute_bonds() 178 if (bond_type[atom1][i] == 0) continue; in compute_bonds() 181 delx = x[atom1][0] - x[atom2][0]; in compute_bonds() 182 dely = x[atom1][1] - x[atom2][1]; in compute_bonds() 183 delz = x[atom1][2] - x[atom2][2]; in compute_bonds() 188 if (bond_type[atom1][i] > 0) in compute_bonds() [all …]
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/dports/science/py-moltemplate/moltemplate-2.19.14/moltemplate/nbody_alt_symmetry/ |
H A D | gaff_imp.py | 69 atom1 = match[0][1] 79 if atom0 <= atom1: 80 if atom1 <= atom3: 83 return ((atom0,atom3,atom2,atom1), (bond0,bond2,bond1)) 85 return ((atom1,atom0,atom2,atom3), (bond1,bond0,bond2)) 86 elif atom3 <= atom1: 87 if atom0 <= atom1: 88 return ((atom3,atom0,atom2,atom1), (bond2,bond0,bond1)) 90 return ((atom3,atom1,atom2,atom0), (bond2,bond1,bond0)) 92 return ((atom1,atom3,atom2,atom0), (bond1,bond2,bond0))
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/dports/biology/protomol/protomol/framework/topology/ |
H A D | ExclusionTable.h | 78 void add(int atom1, int atom2, ExclusionClass type); 81 ExclusionClass check(int atom1, int atom2) const; 88 bool checkReallyFast(int atom1, int atom2) const; 111 inline bool ExclusionTable::checkReallyFast(int atom1, int atom2) const { in checkReallyFast() argument 112 int delta=atom2-atom1; in checkReallyFast() 118 if(atom2<atom1) in check() 119 std::swap(atom1,atom2); in check() 120 int delta=atom2-atom1; in check() 123 return lowDeltas[atom1*Constant::FASTDELTAMAX+delta]; in check() 126 if(highDeltas.find(PairInt(atom1,delta))==highDeltas.end()) in check() [all …]
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H A D | ExclusionTable.cpp | 26 void ExclusionTable::add(int atom1, int atom2, ExclusionClass type) { in add() argument 27 if(atom1>atom2) in add() 28 std::swap(atom1,atom2); in add() 29 int delta=atom2-atom1; in add() 30 …if(type != EXCLUSION_NONE && atom1 != atom2 && mySet.find(ExclusionPair(atom1,atom2,type)) == mySe… in add() 31 myTable.push_back(ExclusionPair(atom1,atom2,type)); in add() 32 mySet.insert(ExclusionPair(atom1,atom2,type)); in add() 37 lowDeltas[atom1*Constant::FASTDELTAMAX+delta]=type; in add() 39 highDeltas[PairInt(atom1,delta)]=type; in add()
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/dports/devel/py-tables/tables-3.6.1/tables/tests/ |
H A D | test_types.py | 242 atom2 = atom1.copy() 243 self.assertEqual(atom1, atom2) 245 self.assertIsNot(atom1, atom2) 260 self.assertEqual(atom1, atom2) 266 self.assertEqual(atom1, atom2) 273 self.assertEqual(atom1, atom2) 279 self.assertEqual(atom1, atom2) 285 self.assertEqual(atom1, atom2) 291 self.assertEqual(atom1, atom2) 297 self.assertEqual(atom1, atom2) [all …]
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/dports/science/tinker/tinker/utility/ |
H A D | noesetup.f | 45 character*4 atom1,atom2 128 atom1 = ' ' 134 atom1(i:i) = ' ' 136 atom1(1:1) = letter 138 atom1(i:i) = letter 144 if (atom1(i:i) .ne. ' ') then 145 if ((atom1(i:i).eq.'+' .or. atom1(i:i).eq.'*') 149 atom1(1:1) = atom1(i:i) 150 atom1(i:i) = ' ' 205 call fixpdb (amino(res1),atom1) [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ |
H A D | DeduceBondOrderTestFromExplicitHydrogens.java | 63 addHydrogens(keto, atom1, 1); in testAcetylene() 70 keto.addAtom(atom1); in testAcetylene() 90 addHydrogens(keto, atom1, 3); in testKeto() 99 keto.addAtom(atom1); in testKeto() 122 addHydrogens(enol, atom1, 2); in testEnol() 132 enol.addAtom(atom1); in testEnol() 168 enol.addAtom(atom1); in xtestButadiene() 216 enol.addAtom(atom1); in testQuinone() 276 enol.addAtom(atom1); in testBenzene() 333 enol.addAtom(atom1); in testPyrrole() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/ |
H A D | SmilesBond.java | 99 SmilesAtom atom1; field in SmilesBond 103 return atom1; in getAtom1() 184 set2a(atom1, atom2); in SmilesBond() 194 atom1 = a1; in set2a() 199 if (a2.isBioAtomWild && atom1.isBioAtomWild) in set2a() 254 return (atom1 == a ? atom2 : atom1); in getOtherAtom() 259 return atom1.index; in getAtomIndex1() 274 return (atom == atom1 ? atom2 : atom == atom2 || atom == null ? atom1 : null); in getOtherNode() 294 SmilesAtom a = atom1; in switchAtoms() 295 atom1 = atom2; in switchAtoms() [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/src/ |
H A D | compute_bond_local.cpp | 265 for (atom1 = 0; atom1 < nlocal; atom1++) { in compute_bonds() 270 if (molindex[atom1] < 0) continue; in compute_bonds() 271 imol = molindex[atom1]; in compute_bonds() 272 iatom = molatom[atom1]; in compute_bonds() 278 btype = bond_type[atom1][i]; in compute_bonds() 281 tagprev = tag[atom1] - iatom - 1; in compute_bonds() 295 dx = x[atom1][0] - x[atom2][0]; in compute_bonds() 296 dy = x[atom1][1] - x[atom2][1]; in compute_bonds() 297 dz = x[atom1][2] - x[atom2][2]; in compute_bonds() 311 mass1 = rmass[atom1]; in compute_bonds() [all …]
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/dports/science/cdk/cdk-cdk-2.3/misc/diff/src/test/java/org/openscience/cdk/tools/diff/ |
H A D | ChemObjectDiffTest.java | 37 IChemObject atom1 = mock(IChemObject.class); in testMatchAgainstItself() local 38 String result = ChemObjectDiff.diff(atom1, atom1); in testMatchAgainstItself() 44 IChemObject atom1 = mock(IChemObject.class); in testDiff() local 46 when(atom1.getFlags()).thenReturn(new boolean[]{false, false, false}); in testDiff() 49 String result = ChemObjectDiff.diff(atom1, atom2); in testDiff() 58 IChemObject atom1 = mock(IChemObject.class); in testDifference() local 60 when(atom1.getFlags()).thenReturn(new boolean[]{false, false, false}); in testDifference() 63 IDifference difference = ChemObjectDiff.difference(atom1, atom2); in testDifference()
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H A D | AtomDiffTest.java | 41 IAtom atom1 = mock(IAtom.class); in testMatchAgainstItself() local 42 String result = AtomDiff.diff(atom1, atom1); in testMatchAgainstItself() 48 IAtom atom1 = mock(IAtom.class); in testDiff() local 50 when(atom1.getSymbol()).thenReturn("H"); in testDiff() 53 String result = AtomDiff.diff(atom1, atom2); in testDiff() 62 IAtom atom1 = mock(IAtom.class); in testDifference() local 64 when(atom1.getSymbol()).thenReturn("H"); in testDifference() 67 IDifference difference = AtomDiff.difference(atom1, atom2); in testDifference()
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/dports/science/py-ase/ase-3.22.0/ase/test/constraints/ |
H A D | test_external_force.py | 20 atom1 = 0 29 dist1 = atoms.get_distance(atom1, atom2) 32 con1 = ExternalForce(atom1, atom2, f_ext) 35 dist2 = atoms.get_distance(atom1, atom2) 42 con2 = FixBondLength(atom1, atom2) 62 con1 = ExternalForce(atom1, atom2, f_ext) 63 d1 = atoms.get_distance(atom1, atom3) 64 con2 = FixBondLength(atom1, atom3) 68 d2 = atoms.get_distance(atom1, atom3)
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/dports/science/py-molmod/molmod-1.4.8/molmod/ |
H A D | randomize.py | 145 atom1, atom2 = self.hinge_atoms 159 atom1, atom2 = self.hinge_atoms 160 center = coordinates[atom1] 173 atom1, atom2, atom3 = self.hinge_atoms 175 a = coordinates[atom1] - coordinates[atom2] 194 atom1, atom2, atom3, atom4 = self.hinge_atoms 195 a = coordinates[atom1] - coordinates[atom2] 207 for atom1, atom2 in graph.edges: 220 for index1, atom1 in enumerate(neighbors): 345 for atom2 in range(atom1): [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/reaction/src/main/java/org/openscience/cdk/reaction/type/ |
H A D | ElectronImpactSDBReaction.java | 128 IAtom atom1 = bondi.getBegin(); in initiate() local 131 … && atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER) in initiate() 132 … && (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0 in initiate() 134 && reactant.getConnectedSingleElectronsCount(atom1) == 0 in initiate() 142 atomList.add(atom1); in initiate() 146 atomList.add(atom1); in initiate() 176 IAtom atom1 = bondi.getBegin(); in setActiveCenters() local 179 … && (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0 in setActiveCenters() 181 && reactant.getConnectedSingleElectronsCount(atom1) == 0 in setActiveCenters() 184 atom1.setFlag(CDKConstants.REACTIVE_CENTER, true); in setActiveCenters()
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H A D | HeterolyticCleavagePBReaction.java | 137 IAtom atom1 = bondi.getBegin(); in initiate() local 140 … && atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER) in initiate() 141 … && (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0 in initiate() 143 && reactant.getConnectedSingleElectronsCount(atom1) == 0 in initiate() 151 atomList.add(atom1); in initiate() 155 atomList.add(atom1); in initiate() 190 IAtom atom1 = bond.getBegin(); in setActiveCenters() local 193 … && (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0 in setActiveCenters() 195 && reactant.getConnectedSingleElectronsCount(atom1) == 0 in setActiveCenters() 197 atom1.setFlag(CDKConstants.REACTIVE_CENTER, true); in setActiveCenters()
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