"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer3/MoleculeExporter.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.

MoleculeExporter.cpp  (pymol-v1.8.6.0.tar.bz2)	:	MoleculeExporter.cpp  (pymol-v2.1.0.tar.bz2)
/*		/*
* Molecular file formats export		* Molecular file formats export
*		*
* (c) 2016 Schrodinger, Inc.		* (c) 2016 Schrodinger, Inc.
*/		*/
#include <vector>		#include <vector>
#include <map>		#include <map>
#include <algorithm>		#include <algorithm>
#include <cstdarg>		#include <cstdarg>
		#include <clocale>
#include "os_std.h"		#include "os_std.h"
#include "MoleculeExporter.h"		#include "MoleculeExporter.h"
#include "Selector.h"		#include "Selector.h"
#include "SelectorDef.h"		#include "SelectorDef.h"
#include "Executive.h"		#include "Executive.h"
#include "Vector.h"		#include "Vector.h"
#include "ObjectMolecule.h"		#include "ObjectMolecule.h"
#include "CoordSet.h"		#include "CoordSet.h"
skipping to change at line 157		skipping to change at line 158
std::vector<int> m_tmpids;		std::vector<int> m_tmpids;
public:		public:
// quasi constructor (easier to inherit than a real constructor)		// quasi constructor (easier to inherit than a real constructor)
virtual void init(PyMOLGlobals * G_) {		virtual void init(PyMOLGlobals * G_) {
G = G_;		G = G_;
m_buffer = VLAlloc(char, 1280);		m_buffer = VLAlloc(char, 1280);
m_buffer[0] = '\0';		m_buffer[0] = '\0';
		m_mat_ref.ptr = NULL;
m_offset = 0;		m_offset = 0;
m_last_cs = NULL;		m_last_cs = NULL;
m_last_obj = NULL;		m_last_obj = NULL;
m_last_state = -1;		m_last_state = -1;
m_retain_ids = false;		m_retain_ids = false;
m_id = 0;		m_id = 0;
setMulti(getMultiDefault());		setMulti(getMultiDefault());
}		}
skipping to change at line 215		skipping to change at line 217
* Get the running index for the given atom.		* Get the running index for the given atom.
*/		*/
int getTmpID(int atm) {		int getTmpID(int atm) {
return m_tmpids[atm];		return m_tmpids[atm];
}		}
/*		/*
* Get the current state title if not empty, or the object name otherwise.		* Get the current state title if not empty, or the object name otherwise.
*/		*/
const char * getTitleOrName() {		const char * getTitleOrName() {
		if (!m_iter.cs)
		return "untitled";
return m_iter.cs->Name[0] ? m_iter.cs->Name : m_iter.obj->Obj.Name;		return m_iter.cs->Name[0] ? m_iter.cs->Name : m_iter.obj->Obj.Name;
}		}
public:		public:
/*		/*
* Set the reference coordinate frame to the inverse of the given		* Set the reference coordinate frame to the inverse of the given
* object's transformation matrix.		* object's transformation matrix.
*/		*/
void setRefObject(const char * ref_object, int ref_state);		void setRefObject(const char * ref_object, int ref_state);
skipping to change at line 344		skipping to change at line 348
m_coord = m_coord_tmp;		m_coord = m_coord_tmp;
}		}
writeAtom();		writeAtom();
}		}
if (m_last_cs)		if (m_last_cs)
endCoordSet();		endCoordSet();
if (m_last_obj)		if (m_last_obj)
endObject();		endObject();
		else if (m_multi == cMolExportGlobal)
		// empty selection
		beginMolecule();
if (m_multi == cMolExportGlobal) {		if (m_multi == cMolExportGlobal) {
writeBonds();		writeBonds();
}		}
}		}
void MoleculeExporter::setRefObject(const char * ref_object, int ref_state) {		void MoleculeExporter::setRefObject(const char * ref_object, int ref_state) {
double matrix[16];		double matrix[16];
m_mat_ref.ptr = NULL;		m_mat_ref.ptr = NULL;
skipping to change at line 684		skipping to change at line 691
ai->resv,		ai->resv,
cifrepr(ai->inscode, "?"),		cifrepr(ai->inscode, "?"),
m_coord[0], m_coord[1], m_coord[2],		m_coord[0], m_coord[1], m_coord[2],
ai->q, ai->b, ai->formalCharge,		ai->q, ai->b, ai->formalCharge,
cifrepr(LexStr(G, ai->chain)),		cifrepr(LexStr(G, ai->chain)),
m_iter.state + 1);		m_iter.state + 1);
}		}
void writeBonds() {		void writeBonds() {
// TODO		// TODO
		// Bond categories:
		// 1) within residue -> _chem_comp_bond
		// 2) polymer links -> implicit
		// 3) others -> _struct_conn
m_bonds.clear();		m_bonds.clear();
}		}
bool isExcludedBond(int atm1, int atm2) {		bool isExcludedBond(int atm1, int atm2) {
// TODO		// TODO
		// polymer links
return true;		return true;
}		}
};		};
// ----------------------------------------------------------------------------- ----- //		// ----------------------------------------------------------------------------- ----- //
		/*
		* Experimental PyMOL style annotated mmCIF. Exports colors, representation,
		* and secondary structure.
		*/
		struct MoleculeExporterPMCIF : public MoleculeExporterCIF {
		void beginMolecule() {
		MoleculeExporterCIF::beginMolecule();
		m_offset += VLAprintf(m_buffer, m_offset, "#\n"
		"_atom_site.pymol_color\n"
		"_atom_site.pymol_reps\n"
		"_atom_site.pymol_ss\n");
		}
		void writeAtom() {
		MoleculeExporterCIF::writeAtom();
		const AtomInfoType * ai = m_iter.getAtomInfo();
		m_offset += VLAprintf(m_buffer, m_offset,
		"%d %d %s\n",
		ai->color,
		ai->visRep,
		cifrepr(ai->ssType));
		}
		void writeBonds() {
		if (m_bonds.empty())
		return;
		m_offset += VLAprintf(m_buffer, m_offset, "#\n"
		"loop_\n"
		"_pymol_bond.atom_site_id_1\n"
		"_pymol_bond.atom_site_id_2\n"
		"_pymol_bond.order\n");
		for (auto bond_it = m_bonds.begin(); bond_it != m_bonds.end(); ++bond_it) {
		const auto& bond = *bond_it;
		m_offset += VLAprintf(m_buffer, m_offset, "%d %d %d\n",
		bond.id1, bond.id2, bond.ref->order);
		}
		m_bonds.clear();
		}
		bool isExcludedBond(int atm1, int atm2) {
		return false;
		}
		};
		// -----------------------------------------------------------------------------
		----- //
struct MoleculeExporterMOL : public MoleculeExporter {		struct MoleculeExporterMOL : public MoleculeExporter {
int m_chiral_flag;		int m_chiral_flag;
std::vector<AtomRef> m_atoms;		std::vector<AtomRef> m_atoms;
ElemCanonicalizer elemGetter;		ElemCanonicalizer elemGetter;
int getMultiDefault() const {		int getMultiDefault() const {
// single entry format		// single entry format
return cMolExportGlobal;		return cMolExportGlobal;
}		}
skipping to change at line 808		skipping to change at line 872
writeCTabV3000();		writeCTabV3000();
} else {		} else {
writeCTabV2000();		writeCTabV2000();
}		}
}		}
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%03d 3D 0\n\n",		"%s\n PyMOL%3.3s 3D 0\n\n",
getTitleOrName(), (_PyMOL_VERSION_int / 10) % 1000);		getTitleOrName(), _PyMOL_VERSION);
m_chiral_flag = 0;		m_chiral_flag = 0;
}		}
};		};
// ----------------------------------------------------------------------------- ----- //		// ----------------------------------------------------------------------------- ----- //
struct MoleculeExporterSDF : public MoleculeExporterMOL {		struct MoleculeExporterSDF : public MoleculeExporterMOL {
int getMultiDefault() const {		int getMultiDefault() const {
skipping to change at line 1035		skipping to change at line 1099
void writeAtom() {		void writeAtom() {
const auto ai = m_iter.getAtomInfo();		const auto ai = m_iter.getAtomInfo();
const float * rgb = ColorGet(G, ai->color);		const float * rgb = ColorGet(G, ai->color);
char inscode[3] = { ai->inscode, 0 };		char inscode[3] = { ai->inscode, 0 };
if (!inscode[0]) {		if (!inscode[0]) {
strcpy(inscode, "<>");		strcpy(inscode, "<>");
}		}
		ResName resn = "";
		AtomName name = "X";
		if (ai->resn)
		AtomInfoGetAlignedPDBResidueName(G, ai, resn);
		if (ai->name)
		AtomInfoGetAlignedPDBAtomName(G, ai, resn, name);
m_offset += VLAprintf(m_buffer, m_offset,		m_offset += VLAprintf(m_buffer, m_offset,
"%d %d %.3f %.3f %.3f %d %s %s %s %s %d %d %02X%02X%02X %d %.2f %d\n", / / %d %d\n",		"%d %d %.3f %.3f %.3f %d %s %s \"%-4s\" \"%-4s\" %d %d %02X%02X%02X %d % .2f %d\n",
getTmpID(),		getTmpID(),
getMacroModelAtomType(ai),		getMacroModelAtomType(ai),
m_coord[0], m_coord[1], m_coord[2],		m_coord[0], m_coord[1], m_coord[2],
ai->resv,		ai->resv,
inscode,		inscode,
ai->chain ? LexStr(G, ai->chain) : "\" \"",		ai->chain ? LexStr(G, ai->chain) : "\" \"",
ai->resn ? LexStr(G, ai->resn) : "\"\"",		resn,
ai->name ? LexStr(G, ai->name) : "X",		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);
++m_n_atoms;		++m_n_atoms;
skipping to change at line 1199		skipping to change at line 1270
if (ref_state < -1)		if (ref_state < -1)
ref_state = state;		ref_state = state;
// do "effective" current states		// do "effective" current states
if (state == -2)		if (state == -2)
state = -3;		state = -3;
if (strcmp(format, "pdb") == 0) {		if (strcmp(format, "pdb") == 0) {
exporter = new MoleculeExporterPDB;		exporter = new MoleculeExporterPDB;
		} else if (strcmp(format, "pmcif") == 0) {
		exporter = new MoleculeExporterPMCIF;
} else if (strcmp(format, "cif") == 0) {		} else if (strcmp(format, "cif") == 0) {
exporter = new MoleculeExporterCIF;		exporter = new MoleculeExporterCIF;
} else if (strcmp(format, "sdf") == 0) {		} else if (strcmp(format, "sdf") == 0) {
exporter = new MoleculeExporterSDF;		exporter = new MoleculeExporterSDF;
} else if (strcmp(format, "pqr") == 0) {		} else if (strcmp(format, "pqr") == 0) {
exporter = new MoleculeExporterPQR;		exporter = new MoleculeExporterPQR;
} else if (strcmp(format, "mol2") == 0) {		} else if (strcmp(format, "mol2") == 0) {
exporter = new MoleculeExporterMOL2;		exporter = new MoleculeExporterMOL2;
} else if (strcmp(format, "mol") == 0) {		} else if (strcmp(format, "mol") == 0) {
exporter = new MoleculeExporterMOL;		exporter = new MoleculeExporterMOL;
} else if (strcmp(format, "xyz") == 0) {		} else if (strcmp(format, "xyz") == 0) {
exporter = new MoleculeExporterXYZ;		exporter = new MoleculeExporterXYZ;
} else if (strcmp(format, "mae") == 0) {		} else if (strcmp(format, "mae") == 0) {
exporter = new MoleculeExporterMAE;		exporter = new MoleculeExporterMAE;
} else {		} else {
PRINTFB(G, FB_ObjectMolecule, FB_Errors)		PRINTFB(G, FB_ObjectMolecule, FB_Errors)
" Error: unknown format: '%s'\n", format ENDFB(G);		" Error: unknown format: '%s'\n", format ENDFB(G);
return NULL;		return NULL;
}		}
		// Ensure "." decimal point in printf. It's possible to change this from
		// Python, so don't rely on a persistent global value.
		std::setlocale(LC_NUMERIC, "C");
exporter->init(G);		exporter->init(G);
exporter->setMulti(multi);		exporter->setMulti(multi);
exporter->setRefObject(ref_object, ref_state);		exporter->setRefObject(ref_object, ref_state);
exporter->execute(sele, state);		exporter->execute(sele, state);
char * charVLA = NULL;		char * charVLA = NULL;
std::swap(charVLA, exporter->m_buffer);		std::swap(charVLA, exporter->m_buffer);
delete exporter;		delete exporter;
return charVLA;		return charVLA;
}		}
/*========================================================================*/		/*========================================================================*/
#ifndef _PYMOL_NOPY		#ifndef _PYMOL_NOPY
/*		/*
		* See MoleculeExporterGetPyBonds
		*/
		struct MoleculeExporterPyBonds : public MoleculeExporter {
		PyObject *m_bond_list; // out
		protected:
		int getMultiDefault() const {
		// single-entry format
		return cMolExportGlobal;
		}
		void writeAtom() {}
		void writeBonds() {
		size_t nBond = m_bonds.size();
		m_bond_list = PyList_New(nBond);
		for (size_t b = 0; b < nBond; ++b) {
		const auto& bond = m_bonds[b];
		PyList_SetItem(m_bond_list, b, Py_BuildValue("iii",
		bond.id1 - 1, bond.id2 - 1, bond.ref->order));
		}
		m_bonds.clear();
		}
		};
		/*========================================================================*/
		/*
		* Get all bonds within the given selection.
		*
		* Returns a list of (atm1, atm2, order) tuples, where atm1 and atm2 are
		* the 0-based atom indices within the selection.
		*
		* Return value: New reference
		*/
		PyObject *MoleculeExporterGetPyBonds(PyMOLGlobals * G,
		const char *selection, int state)
		{
		SelectorTmp tmpsele1(G, selection);
		int sele = tmpsele1.getIndex();
		if (sele < 0)
		return NULL;
		int unblock = PAutoBlock(G);
		MoleculeExporterPyBonds exporter;
		exporter.init(G);
		exporter.execute(sele, state);
		if (PyErr_Occurred())
		PyErr_Print();
		PAutoUnblock(G, unblock);
		return exporter.m_bond_list;
		}
		/*========================================================================*/
		/*
* Creates a `chempy.models.Indexed` instance from a selection.		* Creates a `chempy.models.Indexed` instance from a selection.
*		*
* Changes from the old implementation (SelectorGetChemPyModel):		* Changes from the old implementation (SelectorGetChemPyModel):
* - drops support for `cs->Spheroid`		* - drops support for `cs->Spheroid`
*		*
*/		*/
struct MoleculeExporterChemPy : public MoleculeExporter {		struct MoleculeExporterChemPy : public MoleculeExporter {
PyObject *m_model; // out		PyObject *m_model; // out
protected:		protected:
End of changes. 14 change blocks.
5 lines changed or deleted		145 lines changed or added

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