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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/geometry/
H A DGeometryToolsTest.java78 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()
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/geometry/
H A DGeometryUtilTest.java80 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()
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/
H A DAtomMatcherTest.java46 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
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/dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/
H A DAtomTetrahedralLigandPlacer3DTest.java42 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()
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/dports/biology/protomol/protomol/framework/base/
H A DPSF.h49 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
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/
H A DBond.java38 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()
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/dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/
H A Dbond.cpp349 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()
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H A Ddpoint.h344 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()
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/
H A Dbonds.py174 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:
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/
H A Dneigh_bond.cpp74 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()
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H A Dcompute_bond_local.cpp155 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()
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/dports/science/py-moltemplate/moltemplate-2.19.14/moltemplate/nbody_alt_symmetry/
H A Dgaff_imp.py69 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))
/dports/biology/protomol/protomol/framework/topology/
H A DExclusionTable.h78 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()
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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()
37 lowDeltas[atom1*Constant::FASTDELTAMAX+delta]=type; in add()
39 highDeltas[PairInt(atom1,delta)]=type; in add()
/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)
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)
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/dports/science/tinker/tinker/utility/
H A Dnoesetup.f45 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)
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/dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/
H A DDeduceBondOrderTestFromExplicitHydrogens.java63 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/
H A DSmilesBond.java99 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()
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/dports/science/lammps/lammps-stable_29Sep2021/src/
H A Dcompute_bond_local.cpp265 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()
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/dports/science/cdk/cdk-cdk-2.3/misc/diff/src/test/java/org/openscience/cdk/tools/diff/
H A DChemObjectDiffTest.java37 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()
H A DAtomDiffTest.java41 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()
/dports/science/py-ase/ase-3.22.0/ase/test/constraints/
H A Dtest_external_force.py20 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)
/dports/science/py-molmod/molmod-1.4.8/molmod/
H A Drandomize.py145 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):
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/dports/science/cdk/cdk-cdk-2.3/base/reaction/src/main/java/org/openscience/cdk/reaction/type/
H A DElectronImpactSDBReaction.java128 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()
H A DHeterolyticCleavagePBReaction.java137 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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