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/dports/science/xcrysden/xcrysden-1.6.2/C/
H A Dhbonds.c30 H_Bond hbonds = { variable
66 hbonds.start_coor = (VEC3d*) xcCalloc(hbonds.max_n, sizeof(VEC3d)); in make_H_Bonds()
67 hbonds.end_coor = (VEC3d*) xcCalloc(hbonds.max_n, sizeof(VEC3d)); in make_H_Bonds()
121 if ( dis < hbonds.length_max && dis > hbonds.length_min ) { in make_H_Bonds()
146 if (n >= hbonds.max_n) in make_H_Bonds()
149 hbonds.max_n *= 2; in make_H_Bonds()
150 hbonds.start_coor = (VEC3d*) in make_H_Bonds()
151 xcRealloc(hbonds.start_coor, hbonds.max_n * sizeof(VEC3d)); in make_H_Bonds()
153 xcRealloc(hbonds.end_coor, hbonds.max_n * sizeof(VEC3d)); in make_H_Bonds()
168 hbonds.n = n; in make_H_Bonds()
[all …]
H A DxcHBonds.c29 extern H_Bond hbonds;
100 _Hbond_PrintList(interp, hbonds.H_like_list); in XC_HBondsCmd()
105 _Hbond_PrintList(interp, hbonds.O_like_list); in XC_HBondsCmd()
119 sprintf(string,"%15.10f ", hbonds.angle_min); in XC_HBondsCmd()
140 hbonds.color[0], hbonds.color[1], hbonds.color[2]); in XC_HBondsCmd()
182 hbonds.length_min = num; in XC_HBondsCmd()
193 hbonds.length_max = num; in XC_HBondsCmd()
204 hbonds.angle_min = num; in XC_HBondsCmd()
215 hbonds.line_width = (float) num; in XC_HBondsCmd()
237 hbonds.line_patternsize = inum; in XC_HBondsCmd()
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H A DloadValues.c34 extern H_Bond hbonds;
211 if ( !hbonds.H_like_list ) {
214 if ( !hbonds.O_like_list ) {
217 hbonds.H_like_list[0] = 1; /* Hydrogen */
218 hbonds.H_like_list[1] = 0; /* end-of-list */
220 hbonds.O_like_list[0] = 7; /* Nitrogen */
221 hbonds.O_like_list[1] = 8; /* Oxygen */
222 hbonds.O_like_list[2] = 9; /* Fluorine */
223 hbonds.O_like_list[3] = 16; /* Sulfur */
224 hbonds.O_like_list[4] = 17; /* Chlorine */
[all …]
/dports/science/lammps/lammps-stable_29Sep2021/src/REAXFF/
H A Dreaxff_forces.cpp81 reax_list *bonds, *hbonds; in Validate_Lists() local
106 hbonds = *lists + HBONDS; in Validate_Lists()
115 comp = Start_Index(Hindex+1, hbonds); in Validate_Lists()
116 else comp = hbonds->num_intrs; in Validate_Lists()
118 if (End_Index(Hindex, hbonds) > comp) in Validate_Lists()
137 reax_list *far_nbrs, *bonds, *hbonds; in Init_Forces_noQEq() local
145 hbonds = *lists + HBONDS; in Init_Forces_noQEq()
179 ihb_top = End_Index(atom_i->Hindex, hbonds); in Init_Forces_noQEq()
206 hbonds->select.hbond_list[ihb_top].nbr = j; in Init_Forces_noQEq()
207 hbonds->select.hbond_list[ihb_top].scl = 1; in Init_Forces_noQEq()
[all …]
H A Dreaxff_reset_tools.cpp70 reax_list *bonds, *hbonds; in Reset_Neighbor_Lists() local
95 hbonds = (*lists) + HBONDS; in Reset_Neighbor_Lists()
102 Set_Start_Index(Hindex, total_hbonds, hbonds); in Reset_Neighbor_Lists()
103 Set_End_Index(Hindex, total_hbonds, hbonds); in Reset_Neighbor_Lists()
109 if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) { in Reset_Neighbor_Lists()
110 workspace->realloc.hbonds = 1; in Reset_Neighbor_Lists()
111 if (total_hbonds >= hbonds->num_intrs) in Reset_Neighbor_Lists()
114 total_hbonds, hbonds->num_intrs)); in Reset_Neighbor_Lists()
H A Dreaxff_hydrogen_bonds.cpp51 reax_list *bonds, *hbonds; in Hydrogen_Bonds() local
60 hbonds = (*lists) + HBONDS; in Hydrogen_Bonds()
61 hbond_list = hbonds->select.hbond_list; in Hydrogen_Bonds()
68 hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds); in Hydrogen_Bonds()
69 hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds); in Hydrogen_Bonds()
H A Dreaxff_allocate.cpp171 static int Reallocate_HBonds_List(reax_system *system, reax_list *hbonds) in Reallocate_HBonds_List() argument
185 Delete_List(hbonds); in Reallocate_HBonds_List()
186 Make_List(system->Hcap, total_hbonds, TYP_HBOND, hbonds); in Reallocate_HBonds_List()
280 if (Hflag || wsr->hbonds) { in ReAllocate()
282 wsr->hbonds = 0; in ReAllocate()
/dports/science/lammps/lammps-stable_29Sep2021/src/OPENMP/
H A Dreaxff_forces_omp.cpp162 reax_list *bonds, *hbonds; in Validate_ListsOMP() local
194 hbonds = *lists + HBONDS; in Validate_ListsOMP()
206 comp = Start_Index(Hindex+1, hbonds); in Validate_ListsOMP()
207 else comp = hbonds->num_intrs; in Validate_ListsOMP()
209 if (End_Index(Hindex, hbonds) > comp) in Validate_ListsOMP()
235 reax_list *hbonds = *lists + HBONDS; in Init_Forces_noQEq_OMP() local
410 ihb_top = End_Index(atom_i->Hindex, hbonds); in Init_Forces_noQEq_OMP()
413 jhb_top = End_Index(atom_j->Hindex, hbonds); in Init_Forces_noQEq_OMP()
418 hbonds->select.hbond_list[ihb_top].nbr = j; in Init_Forces_noQEq_OMP()
419 hbonds->select.hbond_list[ihb_top].scl = 1; in Init_Forces_noQEq_OMP()
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H A Dreaxff_hydrogen_bonds_omp.cpp69 reax_list *bonds, *hbonds; in Hydrogen_BondsOMP() local
78 hbonds = (*lists) + HBONDS; in Hydrogen_BondsOMP()
79 hbond_list = hbonds->select.hbond_list; in Hydrogen_BondsOMP()
108 hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds); in Hydrogen_BondsOMP()
109 hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds); in Hydrogen_BondsOMP()
/dports/science/plumed/plumed2-2.7.2/src/adjmat/
H A DAdjacencyMatrixVessel.cpp40 parseFlag("SYMMETRIC",symmetric); parseFlag("HBONDS",hbonds); in AdjacencyMatrixVessel()
41 if( symmetric && hbonds ) error("matrix should be either symmetric or hbonds"); in AdjacencyMatrixVessel()
43 …if( hbonds && function->ablocks[0].size()!=function->ablocks[1].size() ) error("matrix is suppose… in AdjacencyMatrixVessel()
51 return ( symmetric || hbonds ); in undirectedGraph()
67 if( !symmetric && !hbonds ) return (function->ablocks[1].size())*ielem + jelem; in getStoreIndexFromMatrixIndices()
H A DAdjacencyMatrixVessel.h46 bool symmetric, hbonds; variable
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/analysis/
H A Dtest_hbonds.py26 import MDAnalysis.analysis.hbonds
79 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(universe, **kw)
107 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u, 'resname SOL', 'protein')
120 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u)
127 …h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u,'protein','resname ASP', distance=3.0, angle…
240 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(self.universe, **kw)
324 h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(universe, **self.kwargs)
H A Dtest_wbridge.py7 from MDAnalysis.analysis.hbonds.wbridge_analysis import WaterBridgeAnalysis
11 from MDAnalysis.analysis.hbonds import WaterBridgeAnalysis
/dports/biology/protomol/protomol/framework/io/
H A DPARWriter.cpp206 count = par.hbonds.size(); in write()
211 << par.hbonds[i].atom1 in write()
213 << par.hbonds[i].atom2 in write()
215 << par.hbonds[i].emin in write()
217 << par.hbonds[i].rmin in write()
355 count = par.hbonds.size(); in write()
360 << par.hbonds[i].atom1 in write()
362 << par.hbonds[i].atom2 in write()
364 << par.hbonds[i].emin in write()
366 << par.hbonds[i].rmin in write()
/dports/science/py-oddt/oddt-0.7/asv_bench/benchmarks/
H A Dinteractions.py3 from oddt.interactions import close_contacts, hbonds
28 hbonds(mol, self.protein)
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/analysis/hbonds/
H A Dhbond_analysis.py1240 hbonds = defaultdict(int)
1255 hbonds[hb_key] += 1
1264 out = np.empty((len(hbonds),), dtype=dtype)
1268 for cursor, (key, count) in enumerate(six.iteritems(hbonds)):
1309 hbonds = defaultdict(list)
1322 hbonds[hb_key].append(t)
1326 for ts_list in six.itervalues(hbonds):
1338 for (key, times) in six.iteritems(hbonds):
/dports/science/py-oddt/oddt-0.7/tests/
H A Dtest_interactions.py8 hbonds,
43 hbonds_count = [hbonds(rec, mol)[2].sum() for mol in mols]
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/doc/sphinx/source/documentation_pages/analysis/
H A Dhbond_analysis.rst1 .. automodule:: MDAnalysis.analysis.hbonds.hbond_analysis
H A Dhbond_autocorrel.rst1 .. automodule:: MDAnalysis.analysis.hbonds.hbond_autocorrel
H A Dwbridge_analysis.rst1 .. automodule:: MDAnalysis.analysis.hbonds.wbridge_analysis
/dports/biology/protomol/protomol/framework/base/
H A DPAR.cpp20 hbonds.clear(); in clear()
/dports/science/multiwfn/gMultiwfn-3.4.1-0-14-ge873677/examples/aRDG/
H A Dpr.mdp50 constraints = hbonds
H A Dmd.mdp52 constraints = hbonds
/dports/science/mmdb2/mmdb2-2.0.20/mmdb2/
H A Dmmdb_model.cpp4999 imatrix hbonds; in CalcSecStructure() local
5111 hbonds [ir2][k] = irdif; in CalcSecStructure()
5124 if (hbonds[i][k]==-5) { in CalcSecStructure()
5130 if (hbonds[i][k]==-3) { in CalcSecStructure()
5140 if (hbonds[i][k]==-4) { in CalcSecStructure()
5165 irdif = hbonds[i][k]; in CalcSecStructure()
5171 if (hbonds[j][l]==-irdif) { in CalcSecStructure()
5176 if (hbonds[j][l]==-irdif-2) { in CalcSecStructure()
5195 j = i + hbonds[i][k] + 2; in CalcSecStructure()
5214 j = i + hbonds[i][k] - 1; in CalcSecStructure()
[all …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/QA/tests/libxc_waterdimer_bmk/
H A Dlibxc_waterdimer_bmk.nw3 #https://theochem.weizmann.ac.il/web/papers/BMK/hbonds.txt

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