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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/geometry/
H A DGeometryToolsTest.java80 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()
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/geometry/
H A DGeometryUtilTest.java82 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()
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/
H A DAtomMatcherTest.java47 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/
H A DBond.java39 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()
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/dports/biology/protomol/protomol/framework/base/
H A DPSF.h49 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
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/dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/
H A Dbond.cpp349 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()
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/dports/science/lammps/lammps-stable_29Sep2021/src/
H A Dcompute_improper_local.cpp144 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()
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H A Dcompute_angle_local.cpp224 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()
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H A Dcompute_dihedral_local.cpp221 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()
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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/lib/include/
H A Dcalc_distances.h346 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()
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/dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/
H A DDeduceBondOrderTestFromExplicitHydrogens.java65 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()
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/dports/science/tinker/tinker/utility/
H A Dnoesetup.f45 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)
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/dports/devel/py-tables/tables-3.6.1/tables/tests/
H A Dtest_types.py242 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)
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/core/
H A Datomtest.cpp53 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
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/core/
H A Datomtest.cpp53 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
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/
H A DSmilesBond.java100 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()
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/
H A Dneigh_bond.cpp199 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()
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/dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/
H A DAtomTetrahedralLigandPlacer3DTest.java44 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()
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/dports/science/gromacs/gromacs-2021.4/api/nblib/tests/
H A Dinteractions.cpp62 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()
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/
H A Dbonds.py176 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
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/dports/biology/protomol/protomol/framework/topology/
H A DExclusionTable.cpp26 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()
/dports/science/cdk/cdk-cdk-2.3/base/reaction/src/main/java/org/openscience/cdk/reaction/type/
H A DElectronImpactSDBReaction.java129 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()
H A DHeterolyticCleavagePBReaction.java138 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()
H A DHeterolyticCleavageSBReaction.java138 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()
/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/
H A DIDCreatorTest.java48 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()
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