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Source code changes of the file "layer2/CifMoleculeReader.cpp" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

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CifMoleculeReader.cpp  (pymol-v1.8.6.0.tar.bz2):CifMoleculeReader.cpp  (pymol-v2.1.0.tar.bz2)
skipping to change at line 34 skipping to change at line 34
#include "P.h" #include "P.h"
#include "Util.h" #include "Util.h"
#include "Scene.h" #include "Scene.h"
#include "Rep.h" #include "Rep.h"
#include "ObjectMolecule.h" #include "ObjectMolecule.h"
#include "CifFile.h" #include "CifFile.h"
#include "CifBondDict.h" #include "CifBondDict.h"
#include "Util2.h" #include "Util2.h"
#include "Vector.h" #include "Vector.h"
#include "Lex.h" #include "Lex.h"
#include "strcasecmp.h"
// canonical amino acid three letter codes // canonical amino acid three letter codes
const char * aa_three_letter[] = { const char * aa_three_letter[] = {
"ALA", // A "ALA", // A
"ASX", // B for ambiguous asparagine/aspartic-acid "ASX", // B for ambiguous asparagine/aspartic-acid
"CYS", // C "CYS", // C
"ASP", // D "ASP", // D
"GLU", // E "GLU", // E
"PHE", // F "PHE", // F
"GLY", // G "GLY", // G
skipping to change at line 863 skipping to change at line 864
} }
/* /*
* Read CHEM_COMP_ATOM * Read CHEM_COMP_ATOM
*/ */
static CoordSet ** read_chem_comp_atom_model(PyMOLGlobals * G, cif_data * data, static CoordSet ** read_chem_comp_atom_model(PyMOLGlobals * G, cif_data * data,
AtomInfoType ** atInfoPtr) { AtomInfoType ** atInfoPtr) {
const cif_array *arr_x, *arr_y = NULL, *arr_z = NULL; const cif_array *arr_x, *arr_y = NULL, *arr_z = NULL;
if ((arr_x = data->get_arr("_chem_comp_atom.pdbx_model_cartn_x_ideal"))) { // setting to exclude one or more coordinate columns
unsigned mask = SettingGetGlobal_i(G, cSetting_chem_comp_cartn_use);
const char * feedback = "";
if (!mask) {
mask = 0xFF;
}
if ((mask & 0x01)
&& (arr_x = data->get_arr("_chem_comp_atom.pdbx_model_cartn_x_ideal"))
&& !arr_x->is_missing_all()) {
arr_y = data->get_arr("_chem_comp_atom.pdbx_model_cartn_y_ideal"); arr_y = data->get_arr("_chem_comp_atom.pdbx_model_cartn_y_ideal");
arr_z = data->get_arr("_chem_comp_atom.pdbx_model_cartn_z_ideal"); arr_z = data->get_arr("_chem_comp_atom.pdbx_model_cartn_z_ideal");
} else if ((arr_x = data->get_arr("_chem_comp_atom.x"))) { feedback = ".pdbx_model_Cartn_{x,y,z}_ideal";
arr_y = data->get_arr("_chem_comp_atom.y"); } else if ((mask & 0x02)
arr_z = data->get_arr("_chem_comp_atom.z"); && (arr_x = data->get_arr("_chem_comp_atom.model_cartn_x"))) {
} else if ((arr_x = data->get_arr("_chem_comp_atom.model_cartn_x"))) {
arr_y = data->get_arr("_chem_comp_atom.model_cartn_y"); arr_y = data->get_arr("_chem_comp_atom.model_cartn_y");
arr_z = data->get_arr("_chem_comp_atom.model_cartn_z"); arr_z = data->get_arr("_chem_comp_atom.model_cartn_z");
feedback = ".model_Cartn_{x,y,z}";
} else if ((mask & 0x04)
&& (arr_x = data->get_arr("_chem_comp_atom.x"))
&& !arr_x->is_missing_all()) {
arr_y = data->get_arr("_chem_comp_atom.y");
arr_z = data->get_arr("_chem_comp_atom.z");
feedback = ".{x,y,z}";
} }
if (!arr_x || !arr_y || !arr_z) { if (!arr_x || !arr_y || !arr_z) {
return NULL; return NULL;
} }
PRINTFB(G, FB_Executive, FB_Details) PRINTFB(G, FB_Executive, FB_Details)
" ExecutiveLoad-Detail: Detected chem_comp CIF\n" ENDFB(G); " ExecutiveLoad-Detail: Detected chem_comp CIF (%s)\n", feedback
ENDFB(G);
const cif_array * arr_name = data->get_opt("_chem_comp_atom.atom_id "); const cif_array * arr_name = data->get_opt("_chem_comp_atom.atom_id ");
const cif_array * arr_symbol = data->get_opt("_chem_comp_atom.type_sy mbol"); const cif_array * arr_symbol = data->get_opt("_chem_comp_atom.type_sy mbol");
const cif_array * arr_resn = data->get_opt("_chem_comp_atom.comp_id "); const cif_array * arr_resn = data->get_opt("_chem_comp_atom.comp_id ");
const cif_array * arr_partial_charge = data->get_opt("_chem_comp_atom.partial _charge"); const cif_array * arr_partial_charge = data->get_opt("_chem_comp_atom.partial _charge");
const cif_array * arr_formal_charge = data->get_opt("_chem_comp_atom.charge" ); const cif_array * arr_formal_charge = data->get_opt("_chem_comp_atom.charge" );
const cif_array * arr_stereo = data->get_opt("_chem_comp_atom.pdbx_st ereo_config"); const cif_array * arr_stereo = data->get_opt("_chem_comp_atom.pdbx_st ereo_config");
int nrows = arr_x->get_nrows(); int nrows = arr_x->get_nrows();
AtomInfoType *ai; AtomInfoType *ai;
skipping to change at line 915 skipping to change at line 933
LexAssign(G, ai->name, arr_name->as_s(i)); LexAssign(G, ai->name, arr_name->as_s(i));
LexAssign(G, ai->resn, arr_resn->as_s(i)); LexAssign(G, ai->resn, arr_resn->as_s(i));
strncpy(ai->elem, arr_symbol->as_s(i), cElemNameLen); strncpy(ai->elem, arr_symbol->as_s(i), cElemNameLen);
ai->partialCharge = arr_partial_charge->as_d(i); ai->partialCharge = arr_partial_charge->as_d(i);
ai->formalCharge = arr_formal_charge->as_i(i); ai->formalCharge = arr_formal_charge->as_i(i);
ai->hetatm = 1; ai->hetatm = 1;
ai->visRep = auto_show; ai->visRep = auto_show;
ai->stereo = convertCharToStereo(arr_stereo->as_s(i)[0]); AtomInfoSetStereo(ai, arr_stereo->as_s(i));
AtomInfoAssignParameters(G, ai); AtomInfoAssignParameters(G, ai);
AtomInfoAssignColors(G, ai); AtomInfoAssignColors(G, ai);
coord[atomCount * 3 + 0] = arr_x->as_d(i); coord[atomCount * 3 + 0] = arr_x->as_d(i);
coord[atomCount * 3 + 1] = arr_y->as_d(i); coord[atomCount * 3 + 1] = arr_y->as_d(i);
coord[atomCount * 3 + 2] = arr_z->as_d(i); coord[atomCount * 3 + 2] = arr_z->as_d(i);
atomCount++; atomCount++;
} }
skipping to change at line 1034 skipping to change at line 1052
arr_u = data->get_arr("_atom_site?u_iso_or_equiv"); // NULL arr_u = data->get_arr("_atom_site?u_iso_or_equiv"); // NULL
arr_q = data->get_opt("_atom_site?occupancy"); arr_q = data->get_opt("_atom_site?occupancy");
arr_ID = data->get_opt("_atom_site.id", arr_ID = data->get_opt("_atom_site.id",
"_atom_site_label"); "_atom_site_label");
arr_mod_num = data->get_opt("_atom_site.pdbx_pdb_model_num"); arr_mod_num = data->get_opt("_atom_site.pdbx_pdb_model_num");
arr_entity_id = data->get_arr("_atom_site.label_entity_id"); // NULL arr_entity_id = data->get_arr("_atom_site.label_entity_id"); // NULL
const cif_array * arr_color = data->get_arr("_atom_site.pymol_color"); const cif_array * arr_color = data->get_arr("_atom_site.pymol_color");
const cif_array * arr_reps = data->get_arr("_atom_site.pymol_reps"); const cif_array * arr_reps = data->get_arr("_atom_site.pymol_reps");
const cif_array * arr_ss = data->get_opt("_atom_site.pymol_ss"); const cif_array * arr_ss = data->get_opt("_atom_site.pymol_ss");
const cif_array * arr_formal_charge = data->get_opt("_atom_site.pdbx_formal_ch arge");
if (!arr_chain) if (!arr_chain)
arr_chain = arr_segi; arr_chain = arr_segi;
ModelStateMapper model_to_state(!SettingGetGlobal_i(G, cSetting_pdb_honor_mode l_number)); ModelStateMapper model_to_state(!SettingGetGlobal_i(G, cSetting_pdb_honor_mode l_number));
int nrows = arr_x->get_nrows(); int nrows = arr_x->get_nrows();
AtomInfoType *ai; AtomInfoType *ai;
int atomCount = 0; int atomCount = 0;
int auto_show = RepGetAutoShowMask(G); int auto_show = RepGetAutoShowMask(G);
int first_model_num = model_to_state(arr_mod_num->as_i(0, 1)); int first_model_num = model_to_state(arr_mod_num->as_i(0, 1));
skipping to change at line 1156 skipping to change at line 1175
} }
if (arr_reps) { if (arr_reps) {
ai->visRep = arr_reps->as_i(i, auto_show); ai->visRep = arr_reps->as_i(i, auto_show);
ai->flags |= cAtomFlag_inorganic; // suppress auto_show_classified ai->flags |= cAtomFlag_inorganic; // suppress auto_show_classified
} else { } else {
ai->visRep = auto_show; ai->visRep = auto_show;
} }
ai->ssType[0] = arr_ss->as_s(i)[0]; ai->ssType[0] = arr_ss->as_s(i)[0];
ai->formalCharge = arr_formal_charge->as_i(i);
AtomInfoAssignParameters(G, ai); AtomInfoAssignParameters(G, ai);
if (arr_color) { if (arr_color) {
ai->color = arr_color->as_i(i); ai->color = arr_color->as_i(i);
} else { } else {
AtomInfoAssignColors(G, ai); AtomInfoAssignColors(G, ai);
} }
if (arr_entity_id != NULL) { if (arr_entity_id != NULL) {
skipping to change at line 1979 skipping to change at line 1999
if (nBond) { if (nBond) {
VLASize(bondvla, BondType, nBond); VLASize(bondvla, BondType, nBond);
} else { } else {
VLAFreeP(bondvla); VLAFreeP(bondvla);
} }
return bondvla; return bondvla;
} }
/* /*
* Read bonds from _pymol_bond (non-standard extension)
*
* return: BondType VLA
*/
static BondType * read_pymol_bond(PyMOLGlobals * G, cif_data * data,
AtomInfoType * atInfo) {
const cif_array *col_ID_1, *col_ID_2, *col_order;
if ((col_ID_1 = data->get_arr("_pymol_bond.atom_site_id_1")) == NULL ||
(col_ID_2 = data->get_arr("_pymol_bond.atom_site_id_2")) == NULL ||
(col_order = data->get_arr("_pymol_bond.order")) == NULL)
return NULL;
int nrows = col_ID_1->get_nrows();
int nAtom = VLAGetSize(atInfo);
BondType *bondvla, *bond;
bondvla = bond = VLACalloc(BondType, nrows);
// ID -> atom index
std::map<int, int> id_dict;
for (int atm = 0; atm < nAtom; ++atm) {
id_dict[atInfo[atm].id] = atm;
}
for (int i = 0; i < nrows; i++) {
auto key1 = col_ID_1->as_i(i);
auto key2 = col_ID_2->as_i(i);
auto order_value = col_order->as_i(i);
int i1, i2;
if (find2(id_dict, i1, key1, i2, key2)) {
BondTypeInit2(bond++, i1, i2, order_value);
} else {
PRINTFB(G, FB_Executive, FB_Details)
" Executive-Detail: _pymol_bond name lookup failed: %d %d\n",
key1, key2 ENDFB(G);
}
}
return bondvla;
}
/*
* Create a new (multi-state) object-molecule from datablock * Create a new (multi-state) object-molecule from datablock
*/ */
static ObjectMolecule *ObjectMoleculeReadCifData(PyMOLGlobals * G, cif_data * da static ObjectMolecule *ObjectMoleculeReadCifData(PyMOLGlobals * G,
tablock, int discrete) cif_data * datablock, int discrete, bool quiet)
{ {
CoordSet ** csets = NULL; CoordSet ** csets = NULL;
int ncsets; int ncsets;
CifContentInfo info(G, SettingGetGlobal_b(G, cSetting_cif_use_auth)); CifContentInfo info(G, SettingGetGlobal_b(G, cSetting_cif_use_auth));
const char * assembly_id = SettingGetGlobal_s(G, cSetting_assembly); const char * assembly_id = SettingGetGlobal_s(G, cSetting_assembly);
// title "echo tag"
const char * title = datablock->get_opt("_struct.title")->as_s();
if (!quiet && title[0] &&
strstr(SettingGetGlobal_s(G, cSetting_pdb_echo_tags), "TITLE")) {
PRINTFB(G, FB_ObjectMolecule, FB_Details)
"TITLE %s\n", title ENDFB(G);
}
if (assembly_id && assembly_id[0]) { if (assembly_id && assembly_id[0]) {
if (!get_assembly_chains(G, datablock, info.chains_filter, assembly_id)) if (!get_assembly_chains(G, datablock, info.chains_filter, assembly_id))
PRINTFB(G, FB_Executive, FB_Details) PRINTFB(G, FB_Executive, FB_Details)
" ExecutiveLoad-Detail: No such assembly: '%s'\n", assembly_id ENDFB(G); " ExecutiveLoad-Detail: No such assembly: '%s'\n", assembly_id ENDFB(G);
} }
// allocate ObjectMolecule // allocate ObjectMolecule
ObjectMolecule * I = ObjectMoleculeNew(G, (discrete > 0)); ObjectMolecule * I = ObjectMoleculeNew(G, (discrete > 0));
I->Obj.Color = AtomInfoUpdateAutoColor(G); I->Obj.Color = AtomInfoUpdateAutoColor(G);
skipping to change at line 2088 skipping to change at line 2163
I->Bond = read_chem_comp_bond(G, datablock, I->AtomInfo); I->Bond = read_chem_comp_bond(G, datablock, I->AtomInfo);
break; break;
case CIF_CORE: case CIF_CORE:
I->Bond = read_geom_bond(G, datablock, I->AtomInfo); I->Bond = read_geom_bond(G, datablock, I->AtomInfo);
if (!I->Bond) if (!I->Bond)
I->Bond = read_chemical_conn_bond(G, datablock); I->Bond = read_chemical_conn_bond(G, datablock);
break; break;
case CIF_MMCIF: case CIF_MMCIF:
if (cset) { I->Bond = read_pymol_bond(G, datablock, I->AtomInfo);
if (cset && !I->Bond) {
// sort atoms internally // sort atoms internally
ObjectMoleculeSort(I); ObjectMoleculeSort(I);
// bonds from file, goes to cset->TmpBond // bonds from file, goes to cset->TmpBond
read_struct_conn_(G, datablock, I->AtomInfo, cset, info); read_struct_conn_(G, datablock, I->AtomInfo, cset, info);
// macromolecular bonding // macromolecular bonding
bond_dict_t bond_dict_local; bond_dict_t bond_dict_local;
if (read_chem_comp_bond_dict(datablock, bond_dict_local)) { if (read_chem_comp_bond_dict(datablock, bond_dict_local)) {
ObjectMoleculeConnectComponents(I, &bond_dict_local); ObjectMoleculeConnectComponents(I, &bond_dict_local);
skipping to change at line 2197 skipping to change at line 2274
const char * filename = NULL; const char * filename = NULL;
#ifndef _PYMOL_NO_CXX11 #ifndef _PYMOL_NO_CXX11
auto cif = std::make_shared<cif_file>(filename, st); auto cif = std::make_shared<cif_file>(filename, st);
#else #else
cif_file _cif_stack(filename, st); cif_file _cif_stack(filename, st);
auto cif = &_cif_stack; auto cif = &_cif_stack;
#endif #endif
for (auto it = cif->datablocks.begin(); it != cif->datablocks.end(); ++it) { for (auto it = cif->datablocks.begin(); it != cif->datablocks.end(); ++it) {
ObjectMolecule * obj = ObjectMoleculeReadCifData(G, it->second, discrete); ObjectMolecule * obj = ObjectMoleculeReadCifData(G, it->second, discrete, qu iet);
if (!obj) { if (!obj) {
PRINTFB(G, FB_ObjectMolecule, FB_Errors) PRINTFB(G, FB_ObjectMolecule, FB_Warnings)
" mmCIF-Error: no coordinates found in data_%s\n", it->first ENDFB(G); " mmCIF-Warning: no coordinates found in data_%s\n", it->first ENDFB(G);
continue; continue;
} }
#if !defined(_PYMOL_NOPY) && !defined(_PYMOL_NO_CXX11) #if !defined(_PYMOL_NOPY) && !defined(_PYMOL_NO_CXX11)
// we only provide access from the Python API so far // we only provide access from the Python API so far
if (SettingGetGlobal_b(G, cSetting_cif_keepinmemory)) { if (SettingGetGlobal_b(G, cSetting_cif_keepinmemory)) {
obj->m_cifdata = it->second; obj->m_cifdata = it->second;
obj->m_ciffile = cif; obj->m_ciffile = cif;
} }
#endif #endif
 End of changes. 14 change blocks. 
13 lines changed or deleted 89 lines changed or added
To the C++ Programs section of the PyMOL source changes report or the top of this page
Mainly generated by pkgdiff using rfcdiff
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