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Searched refs:atom3 (Results 1 – 25 of 223) sorted by relevance

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/dports/science/py-moltemplate/moltemplate-2.19.14/moltemplate/nbody_alt_symmetry/
H A Dgaff_imp.py71 atom3 = match[0][3]
76 if atom0 <= atom3:
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:
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/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
227 atom3 = domain->closest_image(i,atom3); in angle_all()
247 int i,m,atom1,atom2,atom3; in angle_partial() local
276 atom3 = domain->closest_image(i,atom3); in angle_partial()
335 int i,m,atom1,atom2,atom3,atom4; in dihedral_all() local
366 atom3 = domain->closest_image(i,atom3); in dihedral_all()
389 int i,m,atom1,atom2,atom3,atom4; in dihedral_partial() local
421 atom3 = domain->closest_image(i,atom3); in dihedral_partial()
500 int i,m,atom1,atom2,atom3,atom4; in improper_all() local
531 atom3 = domain->closest_image(i,atom3); in improper_all()
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H A Ddelete_bonds.cpp160 int atom1,atom2,atom3,atom4; in command() local
202 atom3 = atom->map(atom->angle_atom3[i][m]); in command()
203 if (atom1 == -1 || atom2 == -1 || atom3 == -1) in command()
207 mask[atom3] & groupbit) consider = 1; in command()
215 type[atom3] == which)) flag = 1; in command()
237 atom3 = atom->map(atom->dihedral_atom3[i][m]); in command()
274 atom3 = atom->map(atom->improper_atom3[i][m]); in command()
348 atom3 = atom->map(atom->angle_atom3[i][m]); in command()
351 mask[atom3] & groupbit) flag = 1; in command()
374 atom3 = atom->map(atom->dihedral_atom3[i][m]); in command()
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/dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/
H A DDeduceBondOrderTestFromExplicitHydrogens.java101 keto.addAtom(atom3); in testKeto()
126 addHydrogens(enol, atom3, 1); in testEnol()
134 enol.addAtom(atom3); in testEnol()
159 addHydrogens(enol, atom3, 1); in xtestButadiene()
170 enol.addAtom(atom3); in xtestButadiene()
197 addHydrogens(enol, atom3, 1); in testQuinone()
218 enol.addAtom(atom3); in testQuinone()
260 addHydrogens(enol, atom3, 1); in testBenzene()
278 enol.addAtom(atom3); in testBenzene()
335 enol.addAtom(atom3); in testPyrrole()
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/dports/biology/protomol/protomol/framework/base/
H A DPSF.h65 Angle():number(0),atom1(0),atom2(0),atom3(0){} in Angle()
66 Angle(int a, int b, int c, int d):number(a),atom1(b),atom2(c),atom3(d){} in Angle()
71 int atom3; ///< angle atom 3 number member
82 Dihedral():number(0),atom1(0),atom2(0),atom3(0),atom4(0){} in Dihedral()
83 Dihedral(int a, int b, int c, int d, int e):number(a),atom1(b),atom2(c),atom3(d),atom4(e){} in Dihedral()
88 int atom3; ///< dihedral atom 3 number member
99 Improper():number(0),atom1(0),atom2(0),atom3(0),atom4(0){} in Improper()
105 int atom3; ///< improper atom 3 number member
161 Ngrp():number(0),atom1(0),atom2(0),atom3(0){} in Ngrp()
162 Ngrp(int a, int b, int c, int d):number(a),atom1(b),atom2(c),atom3(d){} in Ngrp()
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/dports/science/gromacs/gromacs-2021.4/api/nblib/tests/
H A Dinteractions.cpp63 ParticleType atom3(ParticleTypeName("a3"), Mass(1)); in TEST() local
79 interactions.add(atom3.name(), c6_3, c12_3); in TEST()
80 interactions.add(atom2.name(), atom3.name(), c6comb, c12comb); 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()
115 interactions.add(atom3.name(), atom4.name(), C6(1), C12(2)); in TEST()
124 ParticleType atom3(ParticleTypeName("a3"), Mass(1)); in TEST() local
140 interactions.add(atom3.name(), c6_3, c12_3); in TEST()
141 interactions.add(atom2.name(), atom3.name(), c6comb, c12comb); in TEST()
163 EXPECT_REAL_EQ_TOL(std::sqrt(c6_3 * c6_4), nbfp.getC6(atom3.name(), atom4.name()), in TEST()
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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/lib/include/
H A Dcalc_distances.h581 vb[0] = atom3[i][0] - atom2[i][0]; in _calc_dihedral()
582 vb[1] = atom3[i][1] - atom2[i][1]; in _calc_dihedral()
583 vb[2] = atom3[i][2] - atom2[i][2]; in _calc_dihedral()
585 vc[0] = atom4[i][0] - atom3[i][0]; in _calc_dihedral()
586 vc[1] = atom4[i][1] - atom3[i][1]; in _calc_dihedral()
587 vc[2] = atom4[i][2] - atom3[i][2]; in _calc_dihedral()
615 vb[0] = atom3[i][0] - atom2[i][0]; in _calc_dihedral_ortho()
616 vb[1] = atom3[i][1] - atom2[i][1]; in _calc_dihedral_ortho()
617 vb[2] = atom3[i][2] - atom2[i][2]; in _calc_dihedral_ortho()
620 vc[0] = atom4[i][0] - atom3[i][0]; in _calc_dihedral_ortho()
[all …]
/dports/science/lammps/lammps-stable_29Sep2021/src/
H A Dntopo_angle_all.cpp42 int i,m,atom1,atom2,atom3; in build() local
60 atom3 = atom->map(angle_atom3[i][m]); in build()
61 if (atom1 == -1 || atom2 == -1 || atom3 == -1) { in build()
72 atom3 = domain->closest_image(i,atom3); in build()
73 if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) { in build()
80 anglelist[nanglelist][2] = atom3; in build()
H A Dntopo_angle_partial.cpp42 int i,m,atom1,atom2,atom3; in build() local
61 atom3 = atom->map(angle_atom3[i][m]); in build()
62 if (atom1 == -1 || atom2 == -1 || atom3 == -1) { in build()
73 atom3 = domain->closest_image(i,atom3); in build()
74 if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) { in build()
81 anglelist[nanglelist][2] = atom3; in build()
H A Dntopo_dihedral_partial.cpp43 int i,m,atom1,atom2,atom3,atom4; in build() local
63 atom3 = atom->map(dihedral_atom3[i][m]); in build()
65 if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { in build()
77 atom3 = domain->closest_image(i,atom3); in build()
80 (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) { in build()
87 dihedrallist[ndihedrallist][2] = atom3; in build()
H A Dntopo_dihedral_all.cpp42 int i,m,atom1,atom2,atom3,atom4; in build() local
61 atom3 = atom->map(dihedral_atom3[i][m]); in build()
63 if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { in build()
75 atom3 = domain->closest_image(i,atom3); in build()
78 (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) { in build()
85 dihedrallist[ndihedrallist][2] = atom3; in build()
H A Dntopo_improper_all.cpp42 int i,m,atom1,atom2,atom3,atom4; in build() local
61 atom3 = atom->map(improper_atom3[i][m]); in build()
63 if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { in build()
75 atom3 = domain->closest_image(i,atom3); in build()
78 (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) { in build()
85 improperlist[nimproperlist][2] = atom3; in build()
H A Dntopo_improper_partial.cpp43 int i,m,atom1,atom2,atom3,atom4; in build() local
63 atom3 = atom->map(improper_atom3[i][m]); in build()
65 if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { in build()
79 atom3 = domain->closest_image(i,atom3); in build()
82 (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) { in build()
89 improperlist[nimproperlist][2] = atom3; in build()
H A Dntopo_angle_template.cpp44 int i,m,atom1,atom2,atom3; in build() local
78 atom3 = atom->map(angle_atom3[iatom][m]+tagprev); in build()
79 if (atom1 == -1 || atom2 == -1 || atom3 == -1) { in build()
92 atom3 = domain->closest_image(i,atom3); in build()
93 if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) { in build()
100 anglelist[nanglelist][2] = atom3; in build()
H A Dcompute_improper_local.cpp111 int i,m,n,ni,atom1,atom2,atom3,atom4,imol,iatom; in compute_impropers() local
159 atom3 = atom->map(improper_atom3[atom2][i]); in compute_impropers()
165 atom3 = atom->map(onemols[imol]->improper_atom3[atom2][i]+tagprev); in compute_impropers()
170 if (atom3 < 0 || !(mask[atom3] & groupbit)) continue; in compute_impropers()
183 vb2x = x[atom3][0] - x[atom2][0]; in compute_impropers()
184 vb2y = x[atom3][1] - x[atom2][1]; in compute_impropers()
185 vb2z = x[atom3][2] - x[atom2][2]; in compute_impropers()
188 vb3x = x[atom4][0] - x[atom3][0]; in compute_impropers()
189 vb3y = x[atom4][1] - x[atom3][1]; in compute_impropers()
190 vb3z = x[atom4][2] - x[atom3][2]; in compute_impropers()
H A Ddelete_bonds.cpp146 int atom1,atom2,atom3,atom4; in command() local
191 atom3 = atom->map(atom->angle_atom3[i][m]); in command()
192 if (atom1 == -1 || atom2 == -1 || atom3 == -1) in command()
196 mask[atom3] & groupbit) consider = 1; in command()
204 tlist[type[atom3]]) flag = 1; in command()
229 atom3 = atom->map(atom->dihedral_atom3[i][m]); in command()
269 atom3 = atom->map(atom->improper_atom3[i][m]); in command()
348 atom3 = atom->map(atom->angle_atom3[i][m]); in command()
351 mask[atom3] & groupbit) flag = 1; in command()
374 atom3 = atom->map(atom->dihedral_atom3[i][m]); in command()
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H A Dntopo_dihedral_template.cpp45 int i,m,atom1,atom2,atom3,atom4; in build() local
79 atom3 = atom->map(dihedral_atom3[iatom][m]+tagprev); in build()
81 if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { in build()
95 atom3 = domain->closest_image(i,atom3); in build()
98 (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) { in build()
105 dihedrallist[ndihedrallist][2] = atom3; in build()
H A Dntopo_improper_template.cpp45 int i,m,atom1,atom2,atom3,atom4; in build() local
79 atom3 = atom->map(improper_atom3[iatom][m]+tagprev); in build()
81 if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) { in build()
95 atom3 = domain->closest_image(i,atom3); in build()
98 (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) { in build()
105 improperlist[nimproperlist][2] = atom3; in build()
/dports/science/openbabel/openbabel-3.1.1/external/coordgen-master/coordgen/
H A DsketcherMinimizerEZConstrainInteraction.h26 atom3 = at3; in sketcherMinimizerEZConstrainInteraction()
50 atom1->coordinates, atom2->coordinates, atom3->coordinates);
53 atom4->coordinates, atom2->coordinates, atom3->coordinates);
62 doubleBondAtom = atom3;
84 atom3->coordinates) != m_isZ; in inversion()
86 sketcherMinimizerAtom* atom3; variable
H A DsketcherMinimizerBendInteraction.h27 atom3 = at3; in sketcherMinimizerBendInteraction()
86 float x3 = atom3->coordinates.x();
87 float y3 = atom3->coordinates.y();
124 atom3->force += n2;
135 float x3 = atom3->coordinates.x(); in angle()
136 float y3 = atom3->coordinates.y(); in angle()
155 sketcherMinimizerAtom* atom3; variable
H A DsketcherMinimizerClashInteraction.h25 atom3 = at3; in sketcherMinimizerClashInteraction()
36 atom2->coordinates, atom1->coordinates, atom3->coordinates); in energy()
60 sketcherMinimizerPointF bondP2 = atom3->coordinates;
69 atom3->force -= f * 0.5;
74 sketcherMinimizerAtom* atom3; variable
/dports/science/coordgenlibs/coordgenlibs-3.0.0/
H A DsketcherMinimizerEZConstrainInteraction.h26 atom3 = at3; in sketcherMinimizerEZConstrainInteraction()
50 atom1->coordinates, atom2->coordinates, atom3->coordinates);
53 atom4->coordinates, atom2->coordinates, atom3->coordinates);
62 doubleBondAtom = atom3;
84 atom3->coordinates) != m_isZ; in inversion()
86 sketcherMinimizerAtom* atom3; variable
H A DsketcherMinimizerBendInteraction.h27 atom3 = at3; in sketcherMinimizerBendInteraction()
86 float x3 = atom3->coordinates.x();
87 float y3 = atom3->coordinates.y();
124 atom3->force += n2;
135 float x3 = atom3->coordinates.x(); in angle()
136 float y3 = atom3->coordinates.y(); in angle()
155 sketcherMinimizerAtom* atom3; variable
/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/
H A DAtomMatcherTest.java48 IAtom atom3 = mock(IAtom.class); in anyMatch() local
51 when(atom3.getAtomicNumber()).thenReturn(8); in anyMatch()
54 assertTrue(matcher.matches(atom1, atom3)); in anyMatch()
55 assertTrue(matcher.matches(atom3, atom1)); in anyMatch()
56 assertTrue(matcher.matches(atom2, atom3)); in anyMatch()
107 IAtom atom3 = mock(IAtom.class); in queryMatch() local
109 when(atom1.matches(atom3)).thenReturn(false); in queryMatch()
111 assertFalse(matcher.matches(atom1, atom3)); in queryMatch()
/dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/
H A DAtomTetrahedralLigandPlacer3DTest.java45 IAtom atom3 = new Atom("H"); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer() local
49 IBond bond2 = new Bond(atom1, atom3); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer()
55 atom3.setFormalNeighbourCount(1); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer()
60 ac.addAtom(atom3); in testAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer()
89 IAtom atom3 = new Atom("H"); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double() local
93 IBond bond2 = new Bond(atom1, atom3); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double()
99 ac.addAtom(atom3); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double()
104 atom3.setFormalNeighbourCount(1); in testGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double()

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