Home
last modified time | relevance | path

Searched refs:nbonds (Results 1 – 25 of 212) sorted by relevance

123456789

/dports/science/py-pymol/pymol-open-source-2.4.0/contrib/uiuc/plugins/molfile_plugin/src/
H A Dmol2plugin.cpp66 int match, nbonds, optflags; in open_mol2_read() local
85 nbonds = 0; in open_mol2_read()
105 mol2->nbonds = nbonds; in open_mol2_read()
187 if (mol2->nbonds == 0) { in read_mol2_bonds_aux()
188 *nbonds = 0; in read_mol2_bonds_aux()
255 *nbonds = 0; in read_mol2_bonds_aux()
330 data->nbonds = 0; in open_mol2_write()
484 data->nbonds = nbonds; in write_mol2_bonds()
493 data->nbonds = nbonds; in write_mol2_bonds()
546 if (mol2->nbonds > 0) { in read_mol2_bonds()
[all …]
H A Dbgfplugin.cpp50 int nbonds, optflags; in open_bgf_read() local
52 nbonds=0; in open_bgf_read()
71 nbonds += nbline; in open_bgf_read()
86 bgf->nbonds = nbonds; in open_bgf_read()
289 data->nbonds = 0; in open_bgf_write()
314 if (bgf->nbonds == 0) { in read_bgf_bonds_aux()
315 *nbonds = 0; in read_bgf_bonds_aux()
428 *nbonds = i; in read_bgf_bonds_aux()
442 *nbonds=bgf->nbonds; in read_bgf_bonds()
443 if (bgf->nbonds > 0) { in read_bgf_bonds()
[all …]
H A Dxbgfplugin.cpp53 int nbonds, optflags; in open_xbgf_read() local
55 nbonds=0; in open_xbgf_read()
84 nbonds += nbline; in open_xbgf_read()
110 bgf->nbonds = nbonds; in open_xbgf_read()
335 data->nbonds = 0; in open_xbgf_write()
354 if (bgf->nbonds == 0) { in read_xbgf_bonds_aux()
355 *nbonds = 0; in read_xbgf_bonds_aux()
464 *nbonds = i; in read_xbgf_bonds_aux()
479 *nbonds=bgf->nbonds; in read_xbgf_bonds()
480 if (bgf->nbonds > 0) { in read_xbgf_bonds()
[all …]
H A Dparm7plugin.cpp31 int nbonds; member
105 if (!parse_parm7_bonds(buf, prm->Nbona, p->from+p->nbonds, in read_parm7_structure()
106 p->to+p->nbonds, file)) break; in read_parm7_structure()
107 p->nbonds += prm->Nbona; in read_parm7_structure()
109 if (!parse_parm7_bonds(buf, prm->Nbonh, p->from+p->nbonds, in read_parm7_structure()
110 p->to+p->nbonds, file)) break; in read_parm7_structure()
111 p->nbonds += prm->Nbonh; in read_parm7_structure()
125 static int read_parm7_bonds(void *v, int *nbonds, int **fromptr, int **toptr, in read_parm7_bonds() argument
129 *nbonds = p->nbonds; in read_parm7_bonds()
H A Djsplugin.c197 int nbonds; member
554 swap4_aligned(&js->nbonds, 1); in read_js_structure()
561 offset += 2L * js->nbonds * sizeof(int); in read_js_structure()
563 offset += js->nbonds * sizeof(float); in read_js_structure()
901 swap4_aligned(&js->nbonds, 1); in read_js_structure()
912 swap4_aligned(js->bondfrom, js->nbonds); in read_js_structure()
913 swap4_aligned(js->bondto, js->nbonds); in read_js_structure()
924 swap4_aligned(js->bondorders, js->nbonds); in read_js_structure()
1010 *nbonds = 0; in read_js_bonds()
1019 *nbonds = js->nbonds; in read_js_bonds()
[all …]
H A Dpsfplugin.c43 int nbonds; member
476 if (*nbonds > 0) { in read_bonds()
477 psf->from = (int *) malloc(*nbonds*sizeof(int)); in read_bonds()
478 psf->to = (int *) malloc(*nbonds*sizeof(int)); in read_bonds()
760 psf->nbonds = 0; in open_psf_write()
874 for (i=0; i<psf->nbonds; i++) { in write_psf_structure()
979 psf->nbonds = nbonds; in write_bonds()
980 psf->from = (int *) malloc(nbonds * sizeof(int)); in write_bonds()
981 memcpy(psf->from, fromptr, nbonds * sizeof(int)); in write_bonds()
982 psf->to = (int *) malloc(nbonds * sizeof(int)); in write_bonds()
[all …]
/dports/science/lammps/lammps-stable_29Sep2021/tools/
H A Dmicelle2d.f9080 nbonds = nsurf*ntails
81 IF (nonflag.EQ.1) nbonds = nbonds + nsurf*(ntails-1)
82 ALLOCATE(bondatom(2,nbonds), bondtype(nbonds))
154 nbonds = nsurf*ntails
158 nbonds = nbonds + 1
159 bondatom(1,nbonds) = bondatom(1,k)
161 bondtype(nbonds) = 2
170 nbonds = nsurf*ntails
171 IF (nonflag == 1) nbonds = nbonds + nsurf*(ntails-1)
185 WRITE (6,*) nbonds,' bonds'
[all …]
/dports/science/wxmacmolplt/wxmacmolplt-7.7-43-g9a46f7a/src/
H A Dbondsdlg.cpp236 long nbonds = lFrame->GetNumBonds(); in ResetList() local
237 if (nbonds > 0) { in ResetList()
246 for (long i=0; i<nbonds; i++) { in ResetList()
287 long nbonds = lFrame->GetNumBonds(); in UpdateControls() local
290 for (long i=0; i<nbonds; i++) { in UpdateControls()
386 bondGrid->SelectRow(nbonds, true); in OnAddClick()
405 for (int i=(nbonds-1); i>=0; i--) { in OnDeleteClick()
429 for (int i=0; i<nbonds; i++) { in OnChoiceSelected()
475 for (int i=0; i<nbonds; i++) { in OnSelectCell()
479 if ((row>=0)&&(row<nbonds)) { in OnSelectCell()
[all …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/argos/
H A Dargos_cafe_lsb.F3 + idb,nsb,nbonds,mbonds,nconst,lbonds,itemp)
15 integer isb,nbi,nbj,nbonds,nconst,ibloc,jbloc,isbloc,iq,jq
29 nbonds=0
56 nbonds=nbonds+1
58 if(nbonds.gt.mbonds)
60 lbonds(nbonds)=isb
H A Dargos_cafe_shakes.F13 integer lptr,nbonds
16 nbonds=int_mb(lptr)
17 if(nbonds.gt.0) then
18 call argos_cafe_shks(nbonds,int_mb(lptr+1),mbt(2),mbp(2),
/dports/science/nwchem-data/nwchem-7.0.2-release/src/argos/
H A Dargos_cafe_lsb.F3 + idb,nsb,nbonds,mbonds,nconst,lbonds,itemp)
15 integer isb,nbi,nbj,nbonds,nconst,ibloc,jbloc,isbloc,iq,jq
29 nbonds=0
56 nbonds=nbonds+1
58 if(nbonds.gt.mbonds)
60 lbonds(nbonds)=isb
H A Dargos_cafe_shakes.F13 integer lptr,nbonds
16 nbonds=int_mb(lptr)
17 if(nbonds.gt.0) then
18 call argos_cafe_shks(nbonds,int_mb(lptr+1),mbt(2),mbp(2),
/dports/science/lammps/lammps-stable_29Sep2021/unittest/c-library/
H A Dtest_library_scatter_gather.cpp64 bigint nbonds = *(bigint *)lammps_extract_global(lmp, "nbonds"); in TEST_F() local
65 EXPECT_EQ(nbonds, 24); in TEST_F()
67 tagint *bonds = new tagint[3 * nbonds]; in TEST_F()
79 for (bigint i = 0; i < nbonds; ++i) { in TEST_F()
104 bigint nbonds = *(bigint *)lammps_extract_global(lmp, "nbonds"); in TEST_F() local
105 EXPECT_EQ(nbonds, 24); in TEST_F()
107 tagint *bonds = new tagint[3 * nbonds]; in TEST_F()
119 for (bigint i = 0; i < nbonds; ++i) { in TEST_F()
/dports/science/xcrysden/xcrysden-1.6.2/C/
H A Dremakestr.c79 printf("ReMakeStr:: nbonds_BEFORE = %d\n",nbonds); in ReMakeStr()
83 tmp_nobjects = tmp_nobjects - nbonds; in ReMakeStr()
87 tmp_nobjects = tmp_nobjects + nbonds; in ReMakeStr()
89 nobjects = natoms + nbonds + nframes; in ReMakeStr()
91 printf("ReMakeStr:: nbonds_AFTER = %d\n",nbonds); in ReMakeStr()
/dports/science/lammps/lammps-stable_29Sep2021/unittest/python/
H A Dpython-scatter-gather.py48 nbonds, bonds = self.lmp.gather_bonds()
49 self.assertEqual(nbonds, 24)
52 for i in range(0,nbonds):
71 nbonds, bonds = self.lmp.gather_bonds()
72 self.assertEqual(nbonds, 24)
75 for i in range(0,nbonds):
/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxpreprocess/
H A Dnm2type.cpp122 nm2t[nnnm].nbonds = nb; in rd_nm2type_file()
155 nm2t[i].nbonds); in dump_nm2type()
156 for (j = 0; (j < nm2t[i].nbonds); j++) in dump_nm2type()
202 int* nbonds, in nm2type() argument
214 maxbond = std::max(maxbond, nbonds[i]); in nm2type()
247 if (nb != nbonds[i]) in nm2type()
249 gmx_fatal(FARGS, "Counting number of bonds nb = %d, nbonds[%d] = %d", nb, i, nbonds[i]); in nm2type()
269 if (nm2t[k].nbonds == nb) in nm2type()
H A Dx2top.cpp84 for (j = 0; (j < nmt[i].nbonds); j++) in is_bond()
175 int* nbonds, in set_atom_type() argument
183 nresolved = nm2type(nnm, nm2t, tab, atoms, atypes, nbonds, bonds); in set_atom_type()
290 static void dump_hybridization(FILE* fp, t_atoms* atoms, int nbonds[]) in dump_hybridization() argument
294 fprintf(fp, "Atom %5s has %1d bonds\n", *atoms->atomname[i], nbonds[i]); in dump_hybridization()
397 int * nbonds, *cgnr; in gmx_x2top() local
525 snew(nbonds, atoms->nr); in gmx_x2top()
526 mk_bonds(nnm, nm2t, atoms, x, &(plist[F_BONDS]), nbonds, bPBC, box); in gmx_x2top()
530 set_atom_type(&atypes, &symtab, atoms, &(plist[F_BONDS]), nbonds, nnm, nm2t, logger); in gmx_x2top()
581 dump_hybridization(debug, atoms, nbonds); in gmx_x2top()
/dports/science/smoldyn/smoldyn-2.67/source/BioNetGen/Perl2/
H A DComponent.pm294 my $nbonds = 0;
304 ++$nbonds;
309 $nbonds = ($nbonds>0) ? $nbonds.$wildcard : $wildcard;
311 $string .= " numberOfBonds=\"" . $nbonds . "\"";
/dports/science/mpqc/mpqc-2.3.1/src/lib/chemistry/molecule/
H A Dmolrender.cc160 int nbonds; in init() local
166 nbonds = 0; in init()
169 if (bonding(mol_, atominfo_, i, j)) nbonds++; in init()
174 if (use_color_) nvertex += 2*nbonds; in init()
177 o->initialize(nvertex, nbonds, RenderedPolylines::Vertex); in init()
198 nbonds = 0; in init()
219 o->set_polyline(nbonds, i, ibonds2, ibonds2+1, j); in init()
223 o->set_polyline(nbonds, i, j); in init()
225 nbonds++; in init()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/listed_forces/
H A Dbonded.cpp267 for (i = 0; (i < nbonds);) in morse_bonds()
335 for (i = 0; (i < nbonds);) in cubic_bonds()
390 for (i = 0; (i < nbonds);) in FENE_bonds()
454 bonds(int nbonds, in bonds() argument
472 for (i = 0; (i < nbonds);) in bonds()
509 bonds(int nbonds, in bonds() argument
622 for (i = 0; (i < nbonds);) in restraint_bonds()
808 if (nbonds > 0) in water_pol()
999 for (i = 0; i < nbonds;) in angles()
2299 for (i = 0; i < nbonds;) in low_angres()
[all …]
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/core/
H A Dtopologyobjects.py540 nbonds = len(bondidx)
543 type = np.repeat(None, nbonds).reshape(nbonds, 1)
545 guessed = np.repeat(True, nbonds).reshape(nbonds, 1)
547 guessed = np.repeat(guessed, nbonds).reshape(nbonds, 1)
549 guessed = np.asarray(guessed, dtype=np.bool).reshape(nbonds, 1)
551 order = np.repeat(None, nbonds).reshape(nbonds, 1)
553 if nbonds > 0:
/dports/science/py-rmf/rmf-1.3.1/plugins/vmd/
H A DData_read.cpp71 int Data::read_bonds(int *nbonds, int **fromptr, int **toptr, in read_bonds() argument
79 *nbonds = bond_type_.size(); in read_bonds()
80 RMF_TRACE("Found " << *nbonds << " bonds."); in read_bonds()
97 boost::make_iterator_range(*bondtype, *bondtype + *nbonds)) { in read_bonds()
/dports/science/openbabel/openbabel-3.1.1/src/formats/
H A Dchemdrawct.cpp120 unsigned int natoms, nbonds; in ReadMolecule() local
136 sscanf(buffer," %d %d", &natoms, &nbonds); in ReadMolecule()
153 if (nbonds != 0) in ReadMolecule()
154 for (unsigned int i = 0; i < nbonds; i++) in ReadMolecule()
/dports/science/rmf/rmf-1.3.1/plugins/vmd/
H A DData_read.cpp71 int Data::read_bonds(int *nbonds, int **fromptr, int **toptr, in read_bonds() argument
79 *nbonds = bond_type_.size(); in read_bonds()
80 RMF_TRACE("Found " << *nbonds << " bonds."); in read_bonds()
97 boost::make_iterator_range(*bondtype, *bondtype + *nbonds)) { in read_bonds()
/dports/science/py-ase/ase-3.22.0/ase/io/
H A Dxsd.py313 nbonds = len(bonds)
319 NumChildren=str(natoms + nbonds),
339 for x in range(nbonds):
350 Children=','.join(map(str, range(4, natoms + nbonds + 5))),
361 ID=str(natoms + nbonds + 5),
370 Props = dict(ID=str(natoms + nbonds + 6), NumImageMappings='0')
378 DefectObjects='%i,%i' % (natoms + nbonds + 4, natoms + nbonds + 8),

123456789