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Searched refs:AtomCoord (Results 1 – 23 of 23) sorted by relevance

/dports/science/gabedit/GabeditSrc251_300720/src/Display/
H A DGeomOrbXYZ.c324 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in gl_read_molden_gabedit_geom_conv_file()
422 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in gl_read_xyz_file_geomi()
523 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in gl_read_xyz_file()
1189 AtomCoord[1],AtomCoord[2],AtomCoord[3]); in gl_read_molden_or_gabedit_file_geom()
1812 sscanf(t,"%s %s %s %s %s",AtomCoord[0],dum, AtomCoord[1], AtomCoord[2],AtomCoord[3]); in gl_read_gamess_file_geomi()
2025 sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in gl_read_mpqc_file_geomi()
2158 sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1], AtomCoord[2],AtomCoord[3]); in gl_read_molcas_file_geomi()
2801 sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in gl_read_mopac_output_file_geomi()
3714 …sscanf(t,"%d %s %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[4],AtomCoord[1],AtomCoord[2],AtomCoord… in gl_read_nwchem_file_geomi()
3902 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in gl_read_psicode_file_geomi()
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H A DAnimationGeomConv.c1264 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_molden_gabedit_file_geomi()
1379 kk = sscanf(t,"%s %s %s %s %s",AtomCoord[0],AtomCoord[1], AtomCoord[2],AtomCoord[3], dum); in read_dalton_file_geomi()
1380 if(kk==5) sscanf(t,"%s %s %s %s %s",AtomCoord[0],dum, AtomCoord[1], AtomCoord[2],AtomCoord[3]); in read_dalton_file_geomi()
1483 sscanf(t,"%s %s %s %s %s",AtomCoord[0],dum, AtomCoord[1], AtomCoord[2],AtomCoord[3]); in read_gamess_file_geomi()
1738 sscanf(t,"%s %s %s %s %s",AtomCoord[0],dum, AtomCoord[1], AtomCoord[2],AtomCoord[3]); in read_gamess_irc_file_geomi()
1938 …if(itype==0) sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]… in read_gaussian_file_geomi_str()
2082 …sscanf(t,"%d %s %s %s %s %s",&idummy, AtomCoord[0],AtomCoord[1],AtomCoord[1], AtomCoord[2],AtomCoo… in read_molpro_file_geomi()
2221 sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_mpqc_file_geomi()
2360 sscanf(t,"%s %s %s",AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_mopac_aux_file_geomi()
2472 sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_qchem_file_geomi()
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H A DOrbitalsQChem.c98 gchar *AtomCoord[5]; in read_geomorb_qchem_file_geom() local
113 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_geomorb_qchem_file_geom()
123 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_geomorb_qchem_file_geom()
155 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_geomorb_qchem_file_geom()
177 sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_geomorb_qchem_file_geom()
179 AtomCoord[0][0]=toupper(AtomCoord[0][0]); in read_geomorb_qchem_file_geom()
180 l=strlen(AtomCoord[0]); in read_geomorb_qchem_file_geom()
181 if (l==2) AtomCoord[0][1]=tolower(AtomCoord[0][1]); in read_geomorb_qchem_file_geom()
182 if(isdigit(AtomCoord[0][1]))l=1; in read_geomorb_qchem_file_geom()
184 else sprintf(t,"%c%c",AtomCoord[0][0],AtomCoord[0][1]); in read_geomorb_qchem_file_geom()
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H A DOrbitalsGamess.c130 gchar *AtomCoord[5]; in read_geomorb_gamess_file_geom() local
141 for(i=0;i<5;i++) AtomCoord[i]=g_malloc(taille*sizeof(char)); in read_geomorb_gamess_file_geom()
146 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_geomorb_gamess_file_geom()
156 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_geomorb_gamess_file_geom()
197 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_geomorb_gamess_file_geom()
220 sscanf(t,"%s %s %s %s %s",AtomCoord[0],dum, AtomCoord[1], AtomCoord[2],AtomCoord[3]); in read_geomorb_gamess_file_geom()
222 GeomOrb[j].Symb=g_strdup(AtomCoord[0]); in read_geomorb_gamess_file_geom()
226 GeomOrb[j].C[i]=atof((AtomCoord[i+1])); in read_geomorb_gamess_file_geom()
246 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_geomorb_gamess_file_geom()
H A DVibration.c3803 gchar *AtomCoord[5]; in read_dalton_geom() local
3864 kk = sscanf(t,"%s %s %s %s %s",AtomCoord[0],AtomCoord[1], AtomCoord[2],AtomCoord[3], dum); in read_dalton_geom()
3865 if(kk==5) sscanf(t,"%s %s %s %s %s",AtomCoord[0],dum, AtomCoord[1], AtomCoord[2],AtomCoord[3]); in read_dalton_geom()
3867 for(i=0;i<(gint)strlen(AtomCoord[0]);i++) if(isdigit(AtomCoord[0][i])) AtomCoord[0][i] = ' '; in read_dalton_geom()
3869 AtomCoord[0][0]=toupper(AtomCoord[0][0]); in read_dalton_geom()
3871 if (l==2) AtomCoord[0][1]=tolower(AtomCoord[0][1]); in read_dalton_geom()
4239 gchar *AtomCoord[5]; in read_gamess_geom() local
4300 sscanf(t,"%s %s %s %s %s",AtomCoord[0],dum, AtomCoord[1], AtomCoord[2],AtomCoord[3]); in read_gamess_geom()
4302 for(i=0;i<(gint)strlen(AtomCoord[0]);i++) if(isdigit(AtomCoord[0][i])) AtomCoord[0][i] = ' '; in read_gamess_geom()
4304 AtomCoord[0][0]=toupper(AtomCoord[0][0]); in read_gamess_geom()
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H A DAtomicOrbitals.c256 gchar *AtomCoord[5]; in read_atomic_orbitals_in_gabedit() local
293 AtomCoord[i]=g_malloc(taille*sizeof(char)); in read_atomic_orbitals_in_gabedit()
428 g_free(AtomCoord[i]); in read_atomic_orbitals_in_gabedit()
H A DAnimationMD.c1790 gchar *AtomCoord[5]; in read_gaussian_file_geomi_str() local
1806 for(i=0;i<5;i++) AtomCoord[i]=g_malloc(BSIZE*sizeof(char)); in read_gaussian_file_geomi_str()
1832 for(i=0;i<5;i++) g_free(AtomCoord[i]); in read_gaussian_file_geomi_str()
1849 …if(itype==0) sscanf(t,"%d %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]… in read_gaussian_file_geomi_str()
1850 …else sscanf(t,"%d %s %d %s %s %s",&idummy,AtomCoord[0],&idummy,AtomCoord[1],AtomCoord[2],AtomCoord… in read_gaussian_file_geomi_str()
1852 AtomCoord[0][0]=toupper(AtomCoord[0][0]); in read_gaussian_file_geomi_str()
1853 l=strlen(AtomCoord[0]); in read_gaussian_file_geomi_str()
1854 if (l==2) AtomCoord[0][1]=tolower(AtomCoord[0][1]); in read_gaussian_file_geomi_str()
1856 sprintf(listOfAtoms[j].symbol,"%s",symb_atom_get((guint)atoi(AtomCoord[0]))); in read_gaussian_file_geomi_str()
1857 for(i=0;i<3;i++) listOfAtoms[j].C[i]=atof(ang_to_bohr(AtomCoord[i+1])); in read_gaussian_file_geomi_str()
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H A DOrbitalsOrca.c453 gchar *AtomCoord[NCOLS]; in read_one_block_orbitals_in_orca_output_file() local
468 for(i=0;i<NCOLS;i++) AtomCoord[i]=g_malloc(BSIZE*sizeof(gchar)); in read_one_block_orbitals_in_orca_output_file()
532 for(i=0;i<NCOLS;i++) g_free(AtomCoord[i]); in read_one_block_orbitals_in_orca_output_file()
H A DGridCube.c1067 gchar *AtomCoord[3]; in read_geometry_from_gauss_cube_file() local
1078 AtomCoord[i]=g_malloc(len*sizeof(gchar)); in read_geometry_from_gauss_cube_file()
1101 if(5 != sscanf(t,"%d %lf %s %s %s",&N,&dum,AtomCoord[0],AtomCoord[1],AtomCoord[2])) in read_geometry_from_gauss_cube_file()
1113 GeomOrb[j].C[i] = atof(AtomCoord[i]); in read_geometry_from_gauss_cube_file()
1124 g_free(AtomCoord[i]); in read_geometry_from_gauss_cube_file()
H A DOrbitals.c1324 gchar *AtomCoord[5]; in read_last_orbitals_in_gaussian_file() local
1362 AtomCoord[i]=g_malloc(taille*sizeof(char)); in read_last_orbitals_in_gaussian_file()
1416 g_free(AtomCoord[i]); in read_last_orbitals_in_gaussian_file()
1722 g_free(AtomCoord[i]); in read_last_orbitals_in_gaussian_file()
1733 gchar *AtomCoord[5]; in read_orbitals_in_gabedit_or_molden_file() local
1765 AtomCoord[i]=g_malloc(taille*sizeof(char)); in read_orbitals_in_gabedit_or_molden_file()
1866 g_free(AtomCoord[i]); in read_orbitals_in_gabedit_or_molden_file()
/dports/science/gabedit/GabeditSrc251_300720/src/Geometry/
H A DGeomZmatrix.c4186 AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3], in read_Zmat_from_molcas_input_file()
4396 AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3], in read_Zmat_from_molpro_input_file()
4657 AtomCoord[3],AtomCoord[4],AtomCoord[5],AtomCoord[6] in read_Zmat_from_demon_input_file()
4888 AtomCoord[3],AtomCoord[4],AtomCoord[5],AtomCoord[6] in read_Zmat_from_gauss_input_file()
5132 AtomCoord[3],AtomCoord[4],AtomCoord[5],AtomCoord[6] in read_Zmat_from_nwchem_input_file()
5388 AtomCoord[3],AtomCoord[4],AtomCoord[5],AtomCoord[6] in read_Zmat_from_psicode_input_file()
5637 AtomCoord[3],AtomCoord[4],AtomCoord[5],AtomCoord[6] in read_Zmat_from_orca_input_file()
5891 AtomCoord[3],AtomCoord[4],AtomCoord[5],AtomCoord[6] in read_Zmat_from_qchem_input_file()
6504 AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3],AtomCoord[4] in read_ZMatrix_file_no_add_list()
6534 AtomCoord[3],AtomCoord[4],AtomCoord[5],AtomCoord[6] in read_ZMatrix_file_no_add_list()
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H A DGeomXYZ.c7267 sscanf(t,"%s %s %s %s",AtomCoord[1], AtomCoord[2],AtomCoord[3], AtomCoord[0]); in read_geom_from_turbomole_output_file()
7753 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_geom_from_xyz_file()
8030 …sscanf(t,"%d %s %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[1], AtomCoord[2],AtomCoor… in read_geom_from_molpro_file()
9064 …sscanf(t,"%d %s %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[4],AtomCoord[1],AtomCoord[2],AtomCoord… in read_geom_from_nwchem_file()
9246 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_geom_from_psicode_file()
9607 AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_XYZ_from_mopac_irc_output_file()
10226 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_geom_from_orca_file()
10959 …sscanf(t,"%d %s %s %s %s %s",&idummy,AtomCoord[0],AtomCoord[1],AtomCoord[1],AtomCoord[2],AtomCoord… in read_first_molpro_file()
13370 sscanf(t,"%s %s %s %s",AtomCoord[1],AtomCoord[2],AtomCoord[3],AtomCoord[0]); in read_mol_file_no_add_list()
13492 sscanf(t,"%s %s %s %s",AtomCoord[0],AtomCoord[1],AtomCoord[2],AtomCoord[3]); in read_XYZ_file_no_add_list()
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/dports/science/lammps/lammps-stable_29Sep2021/src/REAXFF/
H A Dfix_reaxff_species.h33 } AtomCoord; typedef
52 AtomCoord *x0;
64 AtomCoord chAnchor(AtomCoord, AtomCoord);
H A Dfix_reaxff_species.cpp390 AtomCoord FixReaxFFSpecies::chAnchor(AtomCoord in1, AtomCoord in2) in chAnchor()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/
H A Datom_set.hpp56 class AtomCoord : public StructureBase class
59 AtomCoord(StructureBase *parent);
97 const AtomCoord* GetAtom(const AtomPntr& atom,
107 typedef std::list < const AtomCoord * > AtomAltList;
H A Datom_set.cpp152 AtomCoord *atom = new AtomCoord(this); in BEGIN_SCOPE()
231 const double AtomCoord::NO_TEMPERATURE = -1.0;
232 const double AtomCoord::NO_OCCUPANCY = -1.0;
233 const char AtomCoord::NO_ALTCONFID = '-';
252 const AtomCoord* AtomSet::GetAtom(const AtomPntr& ap, in GetAtom()
280 AtomCoord::AtomCoord(StructureBase *parent) : in AtomCoord() function in AtomCoord
H A Dbond.cpp113 const AtomCoord *a1 = atomSet->GetAtom(atom1, overlayEnsembles, true); in Draw()
115 const AtomCoord *a2 = atomSet->GetAtom(atom2, overlayEnsembles, true); in Draw()
137 const AtomCoord *a0 = atomSet->GetAtom(previousVirtual->atom1, overlayEnsembles, true); in Draw()
143 const AtomCoord *a3 = atomSet->GetAtom(nextVirtual->atom2, overlayEnsembles, true); in Draw()
H A Dmolecule.cpp151 … const AtomCoord* atom1 = object->coordSets.front()->atomSet->GetAtom(ap1, true, true); in Molecule()
153 … const AtomCoord* atom2 = object->coordSets.front()->atomSet->GetAtom(ap2, true, true); in Molecule()
237 const AtomCoord *atomCoord = object->coordSets.front()->atomSet-> in GetResidueColor()
295 const AtomCoord* atomCoord = object->coordSets.front()->atomSet->GetAtom(atom); in GetAlphaCoords()
341 const AtomCoord *atom = in DrawAllWithTerminiLabels()
H A Dstyle_manager.hpp233 class AtomCoord;
269 const AtomCoord *coord, AtomStyle *atomStyle,
273 const AtomPntr& atom1, const AtomCoord *coord1,
274 const AtomPntr& atom2, const AtomCoord *coord2,
H A Dresidue.cpp309 const AtomCoord *atom, *l1 = NULL, *l2 = NULL, *l3 = NULL; in Draw()
360 const AtomCoord *prevAlpha = NULL, *nextAlpha = NULL; in Draw()
H A Dstructure_set.cpp868 … const AtomCoord* atom = objects.front()->coordSets.front()->atomSet->GetAtom(ap, true, true); in CenterViewOnStructure()
910 const AtomCoord* atom = masterObject->coordSets.front()->atomSet->GetAtom(ap, true, true); in CenterViewOnAlignedResidues()
991 const AtomCoord *pickedAtom = object->coordSets.front()->atomSet-> in SelectedAtom()
1478 typedef vector < const AtomCoord * > CoordList; in SelectByDistance()
1492 const AtomCoord *atomCoord = coordSets.front()->atomSet-> in SelectByDistance()
1536 const AtomCoord *uAtomCoord = coordSets.front()->atomSet-> in SelectByDistance()
H A Dstyle_manager.cpp581 const AtomPntr& atom, const AtomCoord *coord, in GetAtomStyle()
799 (coord && coord->averageTemperature != AtomCoord::NO_TEMPERATURE && in GetAtomStyle()
924 const AtomPntr& atom1, const AtomCoord *coord1, in GetBondStyle()
925 const AtomPntr& atom2, const AtomCoord *coord2, in GetBondStyle()
H A Dcn3d_threader.cpp493 const AtomCoord *C = NULL, *CA = NULL, *CB = NULL, *N = NULL; in GetVirtualResidue()
553 const AtomCoord in GetVirtualPeptide()
681 const AtomCoord *a1, *a2; in GetMinimumLoopLengths()