"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer3/MoleculeExporter.cpp" between
pymol-v2.1.0.tar.bz2 and pymol-open-source-2.2.0.tar.gz

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.

MoleculeExporter.cpp  (pymol-v2.1.0.tar.bz2)	:	MoleculeExporter.cpp  (pymol-open-source-2.2.0)
skipping to change at line 30		skipping to change at line 30
#include "ObjectMolecule.h"		#include "ObjectMolecule.h"
#include "CoordSet.h"		#include "CoordSet.h"
#include "Mol2Typing.h"		#include "Mol2Typing.h"
#include "MmodTyping.h"		#include "MmodTyping.h"
#include "Color.h"		#include "Color.h"
#include "Util.h"		#include "Util.h"
#include "Lex.h"		#include "Lex.h"
#include "P.h"		#include "P.h"
#include "PConv.h"		#include "PConv.h"
#include "CifDataValueFormatter.h"		#include "CifDataValueFormatter.h"
		#include "MaeExportHelpers.h"
#ifdef _PYMOL_IP_EXTRAS		#ifdef _PYMOL_IP_EXTRAS
#include "Property.h"		#include "Property.h"
#endif		#endif
#ifdef _PYMOL_NO_CXX11		#ifdef _PYMOL_NO_CXX11
#define emplace_back push_back		#define emplace_back push_back
#endif		#endif
/*		/*
skipping to change at line 244		skipping to change at line 245
/*		/*
* Populates the "m_bonds" vector		* Populates the "m_bonds" vector
*/		*/
void populateBondRefs();		void populateBondRefs();
protected:		protected:
// functions to be implemented by derived classes		// functions to be implemented by derived classes
virtual int getMultiDefault() const = 0;		virtual int getMultiDefault() const = 0;
virtual bool isExcludedBond(int atm1, int atm2);		virtual bool isExcludedBond(int atm1, int atm2);
		virtual bool isExcludedBond(const BondType * bond);
virtual void writeAtom() = 0;		virtual void writeAtom() = 0;
virtual void writeBonds() = 0;		virtual void writeBonds() = 0;
virtual void beginObject();		virtual void beginObject();
virtual void beginCoordSet();		virtual void beginCoordSet();
virtual void endObject();		virtual void endObject();
virtual void endCoordSet();		virtual void endCoordSet();
virtual void beginMolecule() {}		virtual void beginMolecule() {}
virtual void beginFile() {}		virtual void beginFile() {}
};		};
/*		/*
* Return true if this bond should not be exported		* Return true if this bond should not be exported
*/		*/
bool MoleculeExporter::isExcludedBond(int atm1, int atm2) {		bool MoleculeExporter::isExcludedBond(int atm1, int atm2) {
return false;		return false;
}		}
		bool MoleculeExporter::isExcludedBond(const BondType * bond) {
		return isExcludedBond(bond->index[0], bond->index[1]);
		}
void MoleculeExporter::beginObject() {		void MoleculeExporter::beginObject() {
if (m_multi != cMolExportByCoordSet) {		if (m_multi != cMolExportByCoordSet) {
resetTmpIDs();		resetTmpIDs();
}		}
if (m_multi == cMolExportByObject) {		if (m_multi == cMolExportByObject) {
beginMolecule();		beginMolecule();
}		}
}		}
skipping to change at line 406		skipping to change at line 411
for (auto bond = obj->Bond, bond_end = obj->Bond + obj->NBond;		for (auto bond = obj->Bond, bond_end = obj->Bond + obj->NBond;
bond != bond_end; ++bond) {		bond != bond_end; ++bond) {
auto atm1 = bond->index[0];		auto atm1 = bond->index[0];
auto atm2 = bond->index[1];		auto atm2 = bond->index[1];
if (!(id1 = getTmpID(atm1)) ||		if (!(id1 = getTmpID(atm1)) ||
!(id2 = getTmpID(atm2)))		!(id2 = getTmpID(atm2)))
continue;		continue;
if (isExcludedBond(atm1, atm2))		if (isExcludedBond(bond))
continue;		continue;
if (id1 > id2)		if (id1 > id2)
std::swap(id1, id2);		std::swap(id1, id2);
// emit bond		// emit bond
m_bonds.emplace_back(BondRef { bond, id1, id2 });		m_bonds.emplace_back(BondRef { bond, id1, id2 });
}		}
}		}
skipping to change at line 877		skipping to change at line 882
void beginMolecule() {		void beginMolecule() {
MoleculeExporter::beginMolecule();		MoleculeExporter::beginMolecule();
m_offset += VLAprintf(m_buffer, m_offset,		m_offset += VLAprintf(m_buffer, m_offset,
"%s\n PyMOL%3.3s 3D 0\n\n",		"%s\n PyMOL%3.3s 3D 0\n\n",
getTitleOrName(), _PyMOL_VERSION);		getTitleOrName(), _PyMOL_VERSION);
m_chiral_flag = 0;		m_chiral_flag = 0;
}		}
		bool isExcludedBond(const BondType * bond) {
		// MOL format doesn't know zero order bonds. Writing them as order "0"
		// will produce a nonstandard file which may be rejected by other
		// applications (e.g. RDKit).
		if (bond->order == 0) {
		return !SettingGetGlobal_b(G, cSetting_sdf_write_zero_order_bonds);
		}
		return false;
		}
};		};
// ----------------------------------------------------------------------------- ----- //		// ----------------------------------------------------------------------------- ----- //
struct MoleculeExporterSDF : public MoleculeExporterMOL {		struct MoleculeExporterSDF : public MoleculeExporterMOL {
int getMultiDefault() const {		int getMultiDefault() const {
// multi-entry format		// multi-entry format
return cMolExportByCoordSet;		return cMolExportByCoordSet;
}		}
skipping to change at line 1030		skipping to change at line 1046
}		}
};		};
// ----------------------------------------------------------------------------- ----- //		// ----------------------------------------------------------------------------- ----- //
struct MoleculeExporterMAE : public MoleculeExporter {		struct MoleculeExporterMAE : public MoleculeExporter {
int m_n_atoms;		int m_n_atoms;
int m_n_atoms_offset;		int m_n_atoms_offset;
int m_n_arom_bonds;		int m_n_arom_bonds;
		std::map<int, const AtomInfoType *> m_atoms;
// quasi constructor		// quasi constructor
void init(PyMOLGlobals * G_) {		void init(PyMOLGlobals * G_) {
MoleculeExporter::init(G_);		MoleculeExporter::init(G_);
m_n_arom_bonds = 0;		m_n_arom_bonds = 0;
}		}
int getMultiDefault() const {		int getMultiDefault() const {
// multi-entry format		// multi-entry format
skipping to change at line 1052		skipping to change at line 1069
void beginFile() {		void beginFile() {
m_offset += VLAprintf(m_buffer, m_offset,		m_offset += VLAprintf(m_buffer, m_offset,
"{ s_m_m2io_version ::: 2.0.0 }\n"		"{ s_m_m2io_version ::: 2.0.0 }\n"
"# created with PyMOL " _PyMOL_VERSION " #\n");		"# created with PyMOL " _PyMOL_VERSION " #\n");
}		}
void beginMolecule() {		void beginMolecule() {
MoleculeExporter::beginMolecule();		MoleculeExporter::beginMolecule();
		std::string groupid = MaeExportGetSubGroupId(G, reinterpret_cast<CObject*>(m
		_iter.obj));
m_offset += VLAprintf(m_buffer, m_offset,		m_offset += VLAprintf(m_buffer, m_offset,
"\nf_m_ct {\n"		"\nf_m_ct {\n"
		"s_m_subgroupid\n"
"s_m_title\n"		"s_m_title\n"
":::\n"		":::\n"
		"\"%s\"\n"
"\"%s\"\n",		"\"%s\"\n",
		groupid.c_str(),
getTitleOrName());		getTitleOrName());
// defer until number of atoms known		// defer until number of atoms known
m_n_atoms_offset = m_offset;		m_n_atoms_offset = m_offset;
m_offset += VLAprintf(m_buffer, m_offset,		m_offset += VLAprintf(m_buffer, m_offset,
"m_atom[X] {\n" // place holder		"m_atom[X] {\n" // place holder
"# First column is atom index #\n"		"# First column is atom index #\n"
"i_m_mmod_type\n"		"i_m_mmod_type\n"
"r_m_x_coord\n"		"r_m_x_coord\n"
skipping to change at line 1080		skipping to change at line 1102
"s_m_insertion_code\n"		"s_m_insertion_code\n"
"s_m_chain_name\n"		"s_m_chain_name\n"
"s_m_pdb_residue_name\n"		"s_m_pdb_residue_name\n"
"s_m_pdb_atom_name\n"		"s_m_pdb_atom_name\n"
"i_m_atomic_number\n"		"i_m_atomic_number\n"
"i_m_formal_charge\n"		"i_m_formal_charge\n"
"s_m_color_rgb\n"		"s_m_color_rgb\n"
"i_m_secondary_structure\n"		"i_m_secondary_structure\n"
"r_m_pdb_occupancy\n"		"r_m_pdb_occupancy\n"
"i_pdb_PDB_serial\n"		"i_pdb_PDB_serial\n"
		"i_m_visibility\n"
		"i_m_representation\n"
		"i_m_ribbon_style\n"
		"i_m_ribbon_color\n"
		"s_m_ribbon_color_rgb\n"
		"s_m_label_format\n"
		"i_m_label_color\n"
		"s_m_label_user_text\n"
":::\n");		":::\n");
m_n_atoms = 0;		m_n_atoms = 0;
}		}
void beginObject() {		void beginObject() {
MoleculeExporter::beginObject();		MoleculeExporter::beginObject();
ObjectMoleculeVerifyChemistry(m_iter.obj, m_iter.state);		ObjectMoleculeVerifyChemistry(m_iter.obj, m_iter.state);
}		}
skipping to change at line 1125		skipping to change at line 1155
name,		name,
ai->protons,		ai->protons,
ai->formalCharge,		ai->formalCharge,
int(rgb[0] * 255),		int(rgb[0] * 255),
int(rgb[1] * 255),		int(rgb[1] * 255),
int(rgb[2] * 255),		int(rgb[2] * 255),
ai->ssType[0] == 'H' ? 1 : ai->ssType[0] == 'S' ? 2 : 0,		ai->ssType[0] == 'H' ? 1 : ai->ssType[0] == 'S' ? 2 : 0,
ai->q,		ai->q,
ai->id);		ai->id);
		char ribbon_color_rgb[7] = "<>";
		MaeExportGetRibbonColor(G, m_iter, ribbon_color_rgb);
		std::string label_user_text = MaeExportGetLabelUserText(G, ai);
		m_offset += VLAprintf(m_buffer, m_offset,
		"%d %d %d %d %s \"%s\" 2 \"%s\"\n",
		(ai->visRep & ~(cRepCartoonBit | cRepRibbonBit)) ? 1 : 0,
		MaeExportGetAtomStyle(G, m_iter),
		MaeExportGetRibbonStyle(ai),
		ribbon_color_rgb[0] == '<' ? 3 /* calphaatom */ : 0 /* constant */,
		ribbon_color_rgb,
		label_user_text.empty() ? "" : "%UT",
		label_user_text.c_str());
		m_atoms[getTmpID()] = ai;
++m_n_atoms;		++m_n_atoms;
}		}
void writeBonds() {		void writeBonds() {
// atom count		// atom count
m_n_atoms_offset += sprintf(m_buffer + m_n_atoms_offset, "m_atom[%d]", m_n_a toms);		m_n_atoms_offset += sprintf(m_buffer + m_n_atoms_offset, "m_atom[%d]", m_n_a toms);
m_buffer[m_n_atoms_offset] = ' '; // overwrite terminator		m_buffer[m_n_atoms_offset] = ' '; // overwrite terminator
if (!m_bonds.empty()) {		if (!m_bonds.empty()) {
// table with zero rows not allowed		// table with zero rows not allowed
m_offset += VLAprintf(m_buffer, m_offset,		m_offset += VLAprintf(m_buffer, m_offset,
":::\n"		":::\n"
"}\n" // end atoms table		"}\n" // end atoms table
"m_bond[%d] {\n"		"m_bond[%d] {\n"
"# First column is bond index #\n"		"# First column is bond index #\n"
"i_m_from\n"		"i_m_from\n"
"i_m_to\n"		"i_m_to\n"
"i_m_order\n"		"i_m_order\n"
		"i_m_from_rep\n"
		"i_m_to_rep\n"
":::\n", (int) m_bonds.size());		":::\n", (int) m_bonds.size());
int b = 0;		int b = 0;
for (auto bond_it = m_bonds.begin(); bond_it != m_bonds.end(); ++bond_it) {		for (auto bond_it = m_bonds.begin(); bond_it != m_bonds.end(); ++bond_it) {
const auto& bond = *bond_it;		const auto& bond = *bond_it;
int order = bond.ref->order;		int order = bond.ref->order;
if (order > 3) {		if (order > 3) {
++m_n_arom_bonds;		++m_n_arom_bonds;
order = 1; // aromatic bonds not supported		order = 1; // aromatic bonds not supported
}		}
m_offset += VLAprintf(m_buffer, m_offset, "%d %d %d %d\n", ++b,		m_offset += VLAprintf(m_buffer, m_offset, "%d %d %d %d\n", ++b,
bond.id1,		bond.id1,
bond.id2,		bond.id2,
order);		order);
		int style = MaeExportGetBondStyle(m_atoms[bond.id1], m_atoms[bond.id2]);
		m_offset += VLAprintf(m_buffer, m_offset, "%d %d\n", style, style);
}		}
m_bonds.clear();		m_bonds.clear();
}		}
// end molecule		// end molecule
m_offset += VLAprintf(m_buffer, m_offset,		m_offset += VLAprintf(m_buffer, m_offset,
":::\n"		":::\n"
"}\n" // end bonds (or atoms) table		"}\n" // end bonds (or atoms) table
"}\n");		"}\n");
End of changes. 14 change blocks.
1 lines changed or deleted		53 lines changed or added

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