/dports/science/py-moltemplate/moltemplate-2.19.14/moltemplate/nbody_alt_symmetry/ |
H A D | gaff_imp.py | 71 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))
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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 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() [all …]
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H A D | delete_bonds.cpp | 160 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() [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 | 101 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() [all …]
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/dports/biology/protomol/protomol/framework/base/ |
H A D | PSF.h | 65 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() [all …]
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/dports/science/gromacs/gromacs-2021.4/api/nblib/tests/ |
H A D | interactions.cpp | 63 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() [all …]
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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/lib/include/ |
H A D | calc_distances.h | 581 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 …]
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/dports/science/lammps/lammps-stable_29Sep2021/src/ |
H A D | ntopo_angle_all.cpp | 42 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()
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H A D | ntopo_angle_partial.cpp | 42 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()
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H A D | ntopo_dihedral_partial.cpp | 43 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()
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H A D | ntopo_dihedral_all.cpp | 42 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()
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H A D | ntopo_improper_all.cpp | 42 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()
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H A D | ntopo_improper_partial.cpp | 43 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()
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H A D | ntopo_angle_template.cpp | 44 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()
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H A D | compute_improper_local.cpp | 111 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()
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H A D | delete_bonds.cpp | 146 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() [all …]
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H A D | ntopo_dihedral_template.cpp | 45 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()
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H A D | ntopo_improper_template.cpp | 45 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()
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/dports/science/openbabel/openbabel-3.1.1/external/coordgen-master/coordgen/ |
H A D | sketcherMinimizerEZConstrainInteraction.h | 26 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
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H A D | sketcherMinimizerBendInteraction.h | 27 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
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H A D | sketcherMinimizerClashInteraction.h | 25 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
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/dports/science/coordgenlibs/coordgenlibs-3.0.0/ |
H A D | sketcherMinimizerEZConstrainInteraction.h | 26 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
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H A D | sketcherMinimizerBendInteraction.h | 27 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
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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 | 48 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()
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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 | 45 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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