/dports/science/py-pymol/pymol-open-source-2.4.0/contrib/uiuc/plugins/molfile_plugin/src/ |
H A D | mol2plugin.cpp | 66 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 D | bgfplugin.cpp | 50 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 D | xbgfplugin.cpp | 53 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 D | parm7plugin.cpp | 31 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 D | jsplugin.c | 197 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 D | psfplugin.c | 43 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 D | micelle2d.f90 | 80 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 D | bondsdlg.cpp | 236 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 D | argos_cafe_lsb.F | 3 + 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 D | argos_cafe_shakes.F | 13 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 D | argos_cafe_lsb.F | 3 + 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 D | argos_cafe_shakes.F | 13 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 D | test_library_scatter_gather.cpp | 64 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 D | remakestr.c | 79 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 D | python-scatter-gather.py | 48 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 D | nm2type.cpp | 122 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 D | x2top.cpp | 84 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 D | Component.pm | 294 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 D | molrender.cc | 160 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 D | bonded.cpp | 267 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 D | topologyobjects.py | 540 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 D | Data_read.cpp | 71 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 D | chemdrawct.cpp | 120 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 D | Data_read.cpp | 71 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 D | xsd.py | 313 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),
|