/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/geometry/ |
H A D | GeometryToolsTest.java | 80 atom2 = new Atom("C"); in testHas2DCoordinates_IAtomContainer() 253 ac.addAtom(atom2); in testRotate_IAtomContainer_Point2d_double() 273 ac.addAtom(atom2); in testGetMinMax_IAtomContainer() 290 ac.addAtom(atom2); in testGetMinMax2() 339 ac.addAtom(atom2); in testGet2DCenter_IAtomContainer() 355 ac.addAtom(atom2); in testGet2DCenterOfMass_IAtomContainer() 384 ac.addAtom(atom2); in testGet2DCenter_IRingSet() 400 ac.addAtom(atom2); in testGet2DCenter_Iterator() 570 ac.addAtom(atom2); in testTranslateAllPositive_IAtomContainer_HashMap() 587 ac.addAtom(atom2); 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 | 82 atom2 = new Atom("C"); in testHas2DCoordinates_IAtomContainer() 255 ac.addAtom(atom2); in testRotate_IAtomContainer_Point2d_double() 275 ac.addAtom(atom2); in testGetMinMax_IAtomContainer() 292 ac.addAtom(atom2); in testGetMinMax2() 325 ac.addAtom(atom2); in testGet2DCenter_IAtomContainer() 341 ac.addAtom(atom2); in testGet2DCenterOfMass_IAtomContainer() 370 ac.addAtom(atom2); in testGet2DCenter_IRingSet() 386 ac.addAtom(atom2); in testGet2DCenter_Iterator() 556 ac.addAtom(atom2); in testTranslateAllPositive_IAtomContainer_HashMap() 573 ac.addAtom(atom2); 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 | 47 IAtom atom2 = mock(IAtom.class); in anyMatch() local 52 assertTrue(matcher.matches(atom1, atom2)); in anyMatch() 53 assertTrue(matcher.matches(atom2, atom1)); in anyMatch() 56 assertTrue(matcher.matches(atom2, atom3)); in anyMatch() 65 IAtom atom2 = mock(IAtom.class); in elementMatch() local 68 assertTrue(matcher.matches(atom1, atom2)); in elementMatch() 76 IAtom atom2 = mock(IAtom.class); in elementMismatch() local 87 IAtom atom2 = mock(IPseudoAtom.class); in elementPseudo() local 96 IAtom atom2 = mock(IAtom.class); in elementError() local 99 matcher.matches(atom1, atom2); in elementError() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
H A D | Bond.java | 39 public Atom atom2; field in Bond 56 this.atom2 = atom2; in Bond() 82 + atom2.getInfo() + " " + atom1.distance(atom2); in getIdentity() 121 if (atom2 != null) in deleteAtomReferences() 122 atom2.deleteBond(this); in deleteAtomReferences() 123 atom1 = atom2 = null; in deleteAtomReferences() 147 return atom2.i; in getAtomIndex2() 156 return (atom1 == thisAtom ? atom2 : atom2 == thisAtom ? atom1 : null); in getOtherAtom() 165 return (atom1 == thisAtom ? atom2 : atom2 == thisAtom || thisAtom == null ? atom1 : null); in getOtherNode() 176 if (a != atom2) in setAtropisomerOptions() [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() 54 int atom2; ///< bonded atom 2 number member 65 Angle():number(0),atom1(0),atom2(0),atom3(0){} in Angle() 70 int atom2; ///< angle atom 2 number member 87 int atom2; ///< dihedral atom 2 number member 104 int atom2; ///< improper atom 2 number member 116 Donor():number(0),atom1(0),atom2(0){} in Donor() 121 int atom2; ///< donor atom 2 number member 131 Acceptor():number(0),atom1(0),atom2(0){} in Acceptor() 136 int atom2; ///< acceptor atom 2 number member [all …]
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/dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/ |
H A D | bond.cpp | 349 QString atom1, atom2, swp; in Enthalpy() local 352 atom2 = end->element; in Enthalpy() 353 if (QString::compare(atom1, atom2) > 0) { in Enthalpy() 355 atom1 = atom2; in Enthalpy() 356 atom2 = swp; in Enthalpy() 363 if (atom2 == "OH") { in Enthalpy() 365 atom2 = "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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/dports/science/lammps/lammps-stable_29Sep2021/src/ |
H A D | compute_improper_local.cpp | 144 for (atom2 = 0; atom2 < nlocal; atom2++) { in compute_impropers() 149 if (molindex[atom2] < 0) continue; in compute_impropers() 150 imol = molindex[atom2]; in compute_impropers() 151 iatom = molatom[atom2]; in compute_impropers() 157 if (tag[atom2] != improper_atom2[atom2][i]) continue; in compute_impropers() 162 if (tag[atom2] != onemols[imol]->improper_atom2[atom2][i]) continue; in compute_impropers() 163 tagprev = tag[atom2] - iatom - 1; in compute_impropers() 178 vb1x = x[atom1][0] - x[atom2][0]; in compute_impropers() 179 vb1y = x[atom1][1] - x[atom2][1]; in compute_impropers() 180 vb1z = x[atom1][2] - x[atom2][2]; in compute_impropers() [all …]
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H A D | compute_angle_local.cpp | 224 for (atom2 = 0; atom2 < nlocal; atom2++) { in compute_angles() 229 if (molindex[atom2] < 0) continue; in compute_angles() 230 imol = molindex[atom2]; in compute_angles() 231 iatom = molatom[atom2]; in compute_angles() 237 if (tag[atom2] != angle_atom2[atom2][i]) continue; in compute_angles() 238 atype = angle_type[atom2][i]; in compute_angles() 242 if (tag[atom2] != onemols[imol]->angle_atom2[atom2][i]) continue; in compute_angles() 244 tagprev = tag[atom2] - iatom - 1; in compute_angles() 261 delx1 = x[atom1][0] - x[atom2][0]; in compute_angles() 262 dely1 = x[atom1][1] - x[atom2][1]; in compute_angles() [all …]
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H A D | compute_dihedral_local.cpp | 221 for (atom2 = 0; atom2 < nlocal; atom2++) { in compute_dihedrals() 227 imol = molindex[atom2]; in compute_dihedrals() 228 iatom = molatom[atom2]; in compute_dihedrals() 234 if (tag[atom2] != dihedral_atom2[atom2][i]) continue; in compute_dihedrals() 239 if (tag[atom2] != onemols[imol]->dihedral_atom2[atom2][i]) continue; in compute_dihedrals() 257 vb1x = x[atom1][0] - x[atom2][0]; in compute_dihedrals() 258 vb1y = x[atom1][1] - x[atom2][1]; in compute_dihedrals() 259 vb1z = x[atom1][2] - x[atom2][2]; in compute_dihedrals() 262 vb2x = x[atom3][0] - x[atom2][0]; in compute_dihedrals() 263 vb2y = x[atom3][1] - x[atom2][1]; in compute_dihedrals() [all …]
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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/lib/include/ |
H A D | calc_distances.h | 346 dx[0] = atom1[i][0] - atom2[i][0]; in _calc_bond_distance() 347 dx[1] = atom1[i][1] - atom2[i][1]; in _calc_bond_distance() 348 dx[2] = atom1[i][2] - atom2[i][2]; in _calc_bond_distance() 370 dx[0] = atom1[i][0] - atom2[i][0]; in _calc_bond_distance_ortho() 371 dx[1] = atom1[i][1] - atom2[i][1]; in _calc_bond_distance_ortho() 372 dx[2] = atom1[i][2] - atom2[i][2]; in _calc_bond_distance_ortho() 399 dx[0] = atom1[i][0] - atom2[i][0]; in _calc_bond_distance_triclinic() 400 dx[1] = atom1[i][1] - atom2[i][1]; in _calc_bond_distance_triclinic() 401 dx[2] = atom1[i][2] - atom2[i][2]; in _calc_bond_distance_triclinic() 577 va[0] = atom2[i][0] - atom1[i][0]; in _calc_dihedral() [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 | 65 addHydrogens(keto, atom2, 1); in testAcetylene() 71 keto.addAtom(atom2); in testAcetylene() 92 addHydrogens(keto, atom2, 1); in testKeto() 100 keto.addAtom(atom2); in testKeto() 124 addHydrogens(enol, atom2, 1); in testEnol() 133 enol.addAtom(atom2); in testEnol() 169 enol.addAtom(atom2); in xtestButadiene() 217 enol.addAtom(atom2); in testQuinone() 277 enol.addAtom(atom2); in testBenzene() 334 enol.addAtom(atom2); in testPyrrole() [all …]
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/dports/science/tinker/tinker/utility/ |
H A D | noesetup.f | 45 character*4 atom1,atom2 165 atom2 = ' ' 171 atom2(i:i) = ' ' 173 atom2(1:1) = letter 175 atom2(i:i) = letter 181 if (atom2(i:i) .ne. ' ') then 182 if ((atom2(i:i).eq.'+' .or. atom2(i:i).eq.'*') 186 atom2(1:1) = atom2(i:i) 187 atom2(i:i) = ' ' 206 call fixpdb (amino(res2),atom2) [all …]
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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) 250 self.assertEqual(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) [all …]
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/core/ |
H A D | atomtest.cpp | 53 Atom atom2 = molecule.addAtom(6); in TEST() local 54 atom2.setPosition2d(Vector2(0.42, 3.14)); in TEST() 57 EXPECT_EQ(atom2.position2d().x(), 0.42); in TEST() 58 EXPECT_EQ(atom2.position2d().y(), 3.14); in TEST() 78 Atom atom2 = molecule.addAtom(6); in TEST() local 79 atom2.setPosition3d(Vector3(0.42, 3.14, 6.66)); in TEST() 83 EXPECT_EQ(atom2.position3d().x(), 0.42); in TEST() 84 EXPECT_EQ(atom2.position3d().y(), 3.14); in TEST() 85 EXPECT_EQ(atom2.position3d().z(), 6.66); in TEST() 92 Atom atom2 = molecule.addAtom(2); in TEST() local [all …]
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/core/ |
H A D | atomtest.cpp | 53 Atom atom2 = molecule.addAtom(6); in TEST() local 54 atom2.setPosition2d(Vector2(0.42, 3.14)); in TEST() 57 EXPECT_EQ(atom2.position2d().x(), 0.42); in TEST() 58 EXPECT_EQ(atom2.position2d().y(), 3.14); in TEST() 78 Atom atom2 = molecule.addAtom(6); in TEST() local 79 atom2.setPosition3d(Vector3(0.42, 3.14, 6.66)); in TEST() 83 EXPECT_EQ(atom2.position3d().x(), 0.42); in TEST() 84 EXPECT_EQ(atom2.position3d().y(), 3.14); in TEST() 85 EXPECT_EQ(atom2.position3d().z(), 6.66); in TEST() 92 Atom atom2 = molecule.addAtom(2); in TEST() local [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/ |
H A D | SmilesBond.java | 100 SmilesAtom atom2; field in SmilesBond 184 set2a(atom1, atom2); in SmilesBond() 198 atom2 = a2; in set2a() 212 atom2 = atom; in setAtom2() 213 if (atom2 != null) { in setAtom2() 254 return (atom1 == a ? atom2 : atom1); in getOtherAtom() 264 return atom2.index; in getAtomIndex2() 274 return (atom == atom1 ? atom2 : atom == atom2 || atom == null ? atom1 : null); in getOtherNode() 295 atom1 = atom2; in switchAtoms() 296 atom2 = a; in switchAtoms() [all …]
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/ |
H A D | neigh_bond.cpp | 199 int i,m,atom1,atom2,atom3; in angle_all() local 226 atom2 = domain->closest_image(i,atom2); in angle_all() 247 int i,m,atom1,atom2,atom3; in angle_partial() local 275 atom2 = domain->closest_image(i,atom2); in angle_partial() 335 int i,m,atom1,atom2,atom3,atom4; in dihedral_all() local 365 atom2 = domain->closest_image(i,atom2); in dihedral_all() 389 int i,m,atom1,atom2,atom3,atom4; in dihedral_partial() local 420 atom2 = domain->closest_image(i,atom2); in dihedral_partial() 500 int i,m,atom1,atom2,atom3,atom4; in improper_all() local 530 atom2 = domain->closest_image(i,atom2); in improper_all() [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 | 44 IAtom atom2 = new Atom("H"); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() local 48 IBond bond1 = new Bond(atom1, atom2); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 54 atom2.setFormalNeighbourCount(1); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 59 ac.addAtom(atom2); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() 76 IAtom atom2 = new Atom("C"); in rescaleBondLength_IAtom_IAtom_Point3d() local 78 atom2.setCovalentRadius(0.2); in rescaleBondLength_IAtom_IAtom_Point3d() 79 …newpoint = new AtomTetrahedralLigandPlacer3D().rescaleBondLength(atom1, atom2, atom2.getPoint3d()); in rescaleBondLength_IAtom_IAtom_Point3d() 88 IAtom atom2 = new Atom("H"); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double() local 92 IBond bond1 = new Bond(atom1, atom2); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double() 98 ac.addAtom(atom2); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double() [all …]
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/dports/science/gromacs/gromacs-2021.4/api/nblib/tests/ |
H A D | interactions.cpp | 62 ParticleType atom2(ParticleTypeName("a2"), Mass(1)); in TEST() local 78 interactions.add(atom2.name(), c6_2, c12_2); in TEST() 80 interactions.add(atom2.name(), atom3.name(), c6comb, c12comb); in TEST() 90 EXPECT_REAL_EQ_TOL(std::sqrt(c6_1 * c6_2), nbfp.getC6(atom1.name(), atom2.name()), in TEST() 93 EXPECT_REAL_EQ_TOL(std::sqrt(c6_1 * c6_2), nbfp.getC6(atom2.name(), atom1.name()), in TEST() 97 EXPECT_REAL_EQ_TOL(std::sqrt(c12_1 * c12_2), nbfp.getC12(atom1.name(), atom2.name()), in TEST() 109 EXPECT_REAL_EQ_TOL(c12comb, nbfp.getC12(atom2.name(), atom3.name()), in TEST() 111 EXPECT_REAL_EQ_TOL(c12comb, nbfp.getC12(atom3.name(), atom2.name()), in TEST() 123 ParticleType atom2(ParticleTypeName("a2"), Mass(1)); in TEST() local 139 interactions.add(atom2.name(), c6_2, c12_2); in TEST() [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/ |
H A D | bonds.py | 176 for atom2 in cys2.atoms: 177 if atom2.name == 'SG': 187 for atom2 in residue.atoms: 188 if atom2.name == 'C': 206 if atom2.name == 'N': 220 for atom2 in residue.atoms: 239 for atom2 in atoms: 395 def has_bond(self, atom1, atom2): argument 396 if atom1 in atom2.bonded_atoms or atom2 in atom1.bonded_atoms: 401 def make_bond(self, atom1, atom2): argument [all …]
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/dports/biology/protomol/protomol/framework/topology/ |
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()
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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 | 129 IAtom atom2 = bondi.getEnd(); in initiate() local 131 … && atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER) in initiate() 133 … && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0 in initiate() 135 && reactant.getConnectedSingleElectronsCount(atom2) == 0) { in initiate() 143 atomList.add(atom2); in initiate() 145 atomList.add(atom2); in initiate() 177 IAtom atom2 = bondi.getEnd(); in setActiveCenters() local 180 … && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0 in setActiveCenters() 182 && reactant.getConnectedSingleElectronsCount(atom2) == 0) { in setActiveCenters() 185 atom2.setFlag(CDKConstants.REACTIVE_CENTER, true); in setActiveCenters()
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H A D | HeterolyticCleavagePBReaction.java | 138 IAtom atom2 = bondi.getEnd(); in initiate() local 140 … && atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER) in initiate() 142 … && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0 in initiate() 144 && reactant.getConnectedSingleElectronsCount(atom2) == 0) { in initiate() 152 atomList.add(atom2); in initiate() 154 atomList.add(atom2); in initiate() 191 IAtom atom2 = bond.getEnd(); in setActiveCenters() local 194 … && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0 in setActiveCenters() 196 && reactant.getConnectedSingleElectronsCount(atom2) == 0) { in setActiveCenters() 198 atom2.setFlag(CDKConstants.REACTIVE_CENTER, true); in setActiveCenters()
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H A D | HeterolyticCleavageSBReaction.java | 138 IAtom atom2 = bondi.getEnd(); in initiate() local 140 … && atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER) in initiate() 142 … && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0 in initiate() 144 && reactant.getConnectedSingleElectronsCount(atom2) == 0) { in initiate() 152 atomList.add(atom2); in initiate() 154 atomList.add(atom2); in initiate() 191 IAtom atom2 = bond.getEnd(); in setActiveCenters() local 194 … && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0 in setActiveCenters() 196 && reactant.getConnectedSingleElectronsCount(atom2) == 0) { in setActiveCenters() 198 atom2.setFlag(CDKConstants.REACTIVE_CENTER, true); in setActiveCenters()
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/ |
H A D | IDCreatorTest.java | 48 Atom atom2 = new Atom("C"); in testCreateIDs_IChemObject() local 50 mol.addAtom(atom2); in testCreateIDs_IChemObject() 51 Bond bond = new Bond(atom1, atom2); in testCreateIDs_IChemObject() 80 Atom atom2 = new Atom("C"); in testNoDuplicateCreation() local 82 mol.addAtom(atom2); in testNoDuplicateCreation() 99 Atom atom2 = new Atom("C"); in testCallingTwice() local 101 mol.addAtom(atom2); in testCallingTwice() 111 atom2 = new Atom("C"); in testCallingTwice() 113 mol.addAtom(atom2); in testCallingTwice() 123 atom2 = new Atom("C"); in testCallingTwice() [all …]
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