"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer2/ObjectMolecule2.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.

ObjectMolecule2.cpp  (pymol-v2.1.0.tar.bz2)	:	ObjectMolecule2.cpp  (pymol-open-source-2.2.0)
skipping to change at line 35		skipping to change at line 35
#include"Base.h"		#include"Base.h"
#include"Debug.h"		#include"Debug.h"
#include"Parse.h"		#include"Parse.h"
#include"OOMac.h"		#include"OOMac.h"
#include"Vector.h"		#include"Vector.h"
#include"PConv.h"		#include"PConv.h"
#include"ObjectMolecule.h"		#include"ObjectMolecule.h"
#include"Feedback.h"		#include"Feedback.h"
#include"Util.h"		#include"Util.h"
		#include"Util2.h"
#include"AtomInfo.h"		#include"AtomInfo.h"
#include"Selector.h"		#include"Selector.h"
#include"ObjectDist.h"		#include"ObjectDist.h"
#include"Executive.h"		#include"Executive.h"
#include"P.h"		#include"P.h"
#include"ObjectCGO.h"		#include"ObjectCGO.h"
#include"Scene.h"		#include"Scene.h"
#include "Lex.h"		#include "Lex.h"
#include"AtomInfoHistory.h"		#include"AtomInfoHistory.h"
skipping to change at line 64		skipping to change at line 65
#define ntrim ParseNTrim		#define ntrim ParseNTrim
#define nextline ParseNextLine		#define nextline ParseNextLine
#define ncopy ParseNCopy		#define ncopy ParseNCopy
#define nskip ParseNSkip		#define nskip ParseNSkip
#define cResvMask 0x7FFF		#define cResvMask 0x7FFF
#define cMaxOther 6		#define cMaxOther 6
static int strstartswith(const char * s, const char * prefix) {		#define strstartswith p_strstartswith
while(*prefix)
if(*s++ != *prefix++)
return false;
return true;
}
static int strstartswithword(const char * s, const char * word) {		static int strstartswithword(const char * s, const char * word) {
while(*word)		while(*word)
if(*s++ != *word++)		if(*s++ != *word++)
return false;		return false;
switch(*s) {		switch(*s) {
case ' ':		case ' ':
case '\t':		case '\t':
case '\r':		case '\r':
case '\n':		case '\n':
skipping to change at line 605		skipping to change at line 601
test = diffsq3f(v, point);		test = diffsq3f(v, point);
if(sub_vdw) {		if(sub_vdw) {
test = sqrt1f(test);		test = sqrt1f(test);
test -= I->AtomInfo[cs->IdxToAtm[j]].vdw;		test -= I->AtomInfo[cs->IdxToAtm[j]].vdw;
if(test < 0.0F)		if(test < 0.0F)
test = 0.0F;		test = 0.0F;
test = test * test;		test = test * test;
}		}
if(test < cutoff2) {		if(test < cutoff2) {
float weight = cutoff - sqrt1f(test);		float weight = cutoff - sqrt1f(test);
float *at_col = ColorGet(I->Obj.G, I->AtomInfo[cs->IdxToAtm[j] ].color);		const float *at_col = ColorGet(I->Obj.G, I->AtomInfo[cs->IdxTo Atm[j]].color);
color[0] += at_col[0] * weight;		color[0] += at_col[0] * weight;
color[1] += at_col[1] * weight;		color[1] += at_col[1] * weight;
color[2] += at_col[2] * weight;		color[2] += at_col[2] * weight;
tot_weight += weight;		tot_weight += weight;
}		}
if(test <= nearest) {		if(test <= nearest) {
result = j;		result = j;
nearest = test;		nearest = test;
}		}
j = MapNext(map, j);		j = MapNext(map, j);
skipping to change at line 632		skipping to change at line 628
test = diffsq3f(v, point);		test = diffsq3f(v, point);
if(sub_vdw) {		if(sub_vdw) {
test = sqrt1f(test);		test = sqrt1f(test);
test -= I->AtomInfo[cs->IdxToAtm[j]].vdw;		test -= I->AtomInfo[cs->IdxToAtm[j]].vdw;
if(test < 0.0F)		if(test < 0.0F)
test = 0.0F;		test = 0.0F;
test = test * test;		test = test * test;
}		}
if(test < cutoff2) {		if(test < cutoff2) {
float weight = cutoff - sqrt1f(test);		float weight = cutoff - sqrt1f(test);
float *color = ColorGet(I->Obj.G, I->AtomInfo[cs->IdxToAtm[j]].color		const float *at_col = ColorGet(I->Obj.G, I->AtomInfo[cs->IdxToAtm[j]
);		].color);
color[0] += color[0] * weight;		color[0] += at_col[0] * weight;
color[1] += color[1] * weight;		color[1] += at_col[1] * weight;
color[2] += color[2] * weight;		color[2] += at_col[2] * weight;
tot_weight += weight;		tot_weight += weight;
}		}
if(test <= nearest) {		if(test <= nearest) {
result = j;		result = j;
nearest = test;		nearest = test;
}		}
v += 3;		v += 3;
}		}
}		}
if(result >= 0)		if(result >= 0)
skipping to change at line 1661		skipping to change at line 1657
static void ObjectMoleculePDBStr2CoordSetPASS1(PyMOLGlobals * G, int *ok,		static void ObjectMoleculePDBStr2CoordSetPASS1(PyMOLGlobals * G, int *ok,
const char **restart_model, const char *p, int n_tags, const char* const* ta g_start,		const char **restart_model, const char *p, int n_tags, const char* const* ta g_start,
int *nAtom, char cc[], int quiet, int *bogus_name_alignment,		int *nAtom, char cc[], int quiet, int *bogus_name_alignment,
int *ssFlag, const char **next_pdb, PDBInfoRec *info, int only_read_one_mode l,		int *ssFlag, const char **next_pdb, PDBInfoRec *info, int only_read_one_mode l,
int *ignore_conect, int *bondFlag, M4XAnnoType * m4x, int *have_bond_order) {		int *ignore_conect, int *bondFlag, M4XAnnoType * m4x, int *have_bond_order) {
int seen_end_of_atoms = false;		int seen_end_of_atoms = false;
*restart_model = NULL;		*restart_model = NULL;
while(*ok && *p) {		while(*ok && *p) {
AddOrthoOutputIfMatchesTags(G, n_tags, *nAtom, tag_start, p, cc, quiet);		AddOrthoOutputIfMatchesTags(G, n_tags, *nAtom, tag_start, p, cc, quiet);
if((strstartswith(p, "ATOM ") ||		if((strstartswith(p, "ATOM ") ||
strstartswith(p, "HETATM")) && (!*restart_model)) {		strstartswith(p, "HETATM")) && (!*restart_model)) {
if(!seen_end_of_atoms)		if(!seen_end_of_atoms)
(*nAtom)++;		(*nAtom)++;
if(*bogus_name_alignment) {		if(*bogus_name_alignment) {
ncopy(cc, nskip(p, 12), 4); /* copy the atom field */		ncopy(cc, nskip(p, 12), 4); /* copy the atom field */
if((cc[0] == 32) && (cc[1] != 32)) { /* check to see if indentation was followed correctly, 32 - space */		if((cc[0] == 32) && (cc[1] != 32)) { /* check to see if indentation was followed correctly, 32 - space */
*bogus_name_alignment = false;		*bogus_name_alignment = false;
}		}
}		}
} else if(strstartswith(p, "HELIX ")){		} else if(strstartswith(p, "HELIX ")){
skipping to change at line 1944		skipping to change at line 1940
&& (ai->resv != sst->resv2 || ai->inscode <= sst->inscode2))		&& (ai->resv != sst->resv2 || ai->inscode <= sst->inscode2))
{		{
ai->ssType[0] = sst->type;		ai->ssType[0] = sst->type;
return;		return;
}		}
ssi = sst->next;		ssi = sst->next;
}		}
}		}
}		}
		/*
		* PQR atom line parsing
		*
		* Try to parse columns white space delimited (10 columns with optional
		* chain, 9 without).
		*
		* Where PQR files come from:
		*
		* pdb2pqr -> writes PDB-like fixed colums. APBS will fail to read those files
		* if columns are too wide.
		*
		* pdb2pqr --whitespace -> puts extra whitespace, starting at column 2, but
		* not between chain and resi! PyMOL <= 2.1 fails to read those files.
		*
		* APBS Tools Plugin by Michael Lerner adds extra whitespace before negative
		* coordinates (assuming -100.0 is the most likely source of error).
		*
		* @param[in,out] p Pointer to parse from, points after the ATOM field.
		* Will move the pointer to the end of the line if
		* parsing was successful.
		* @param[out] ai Atom to populate with data
		* @param[out] coord Coordinates to populate
		* @return true on success, false otherwise.
		*/
		static bool parse_pqr_atom_line(PyMOLGlobals * G,
		const char * &p,
		AtomInfoType * ai,
		float * coord)
		{
		auto p_eol = nskip(p, 999); // end of line pointer
		std::string cc(p, p_eol); // line (starting after ATOM field)
		// whitespace splitting
		auto columns = strsplit(cc);
		// insert chain column if missing
		if (columns.size() == 9) {
		columns.insert(columns.begin() + 3, "");
		// check for concatenated chain + resi
		if (columns[4].size() > 4 && !isdigit(columns[4][0])) {
		columns[3] = columns[4].substr(0, 1);
		columns[4] = columns[4].substr(1);
		}
		}
		// for validation: if number parsing consumes the entire string, then dummy
		// will never be populated (sscanf(...) == 1, not 2)
		char dummy[2];
		// validate numeric fields and populate atom info and coordinates
		if (columns.size() == 10 &&
		sscanf(columns[0].c_str(), "%d%1s", &ai->id, dummy) == 1 &&
		sscanf(columns[5].c_str(), "%f%1s", coord + 0, dummy) == 1 &&
		sscanf(columns[6].c_str(), "%f%1s", coord + 1, dummy) == 1 &&
		sscanf(columns[7].c_str(), "%f%1s", coord + 2, dummy) == 1 &&
		sscanf(columns[8].c_str(), "%f%1s", &ai->partialCharge, dummy) == 1 &&
		sscanf(columns[9].c_str(), "%f%1s", &ai->elec_radius, dummy) == 1) {
		LexAssign(G, ai->name, columns[1].c_str());
		LexAssign(G, ai->resn, columns[2].c_str());
		LexAssign(G, ai->chain, columns[3].c_str());
		ai->setResi(columns[4].c_str());
		// move parser to next line
		p = p_eol;
		return true;
		}
		return false;
		}
CoordSet *ObjectMoleculePDBStr2CoordSet(PyMOLGlobals * G,		CoordSet *ObjectMoleculePDBStr2CoordSet(PyMOLGlobals * G,
const char *buffer,		const char *buffer,
AtomInfoType ** atInfoPtr,		AtomInfoType ** atInfoPtr,
const char **restart_model,		const char **restart_model,
char *segi_override,		char *segi_override,
M4XAnnoType * m4x,		M4XAnnoType * m4x,
char *pdb_name,		char *pdb_name,
const char **next_pdb,		const char **next_pdb,
PDBInfoRec * info, int quiet, int *model _number)		PDBInfoRec * info, int quiet, int *model _number)
{		{
skipping to change at line 2095		skipping to change at line 2163
a = 0; /* WATCHOUT */		a = 0; /* WATCHOUT */
atomCount = 0;		atomCount = 0;
/* PASS 2 */		/* PASS 2 */
seen_model = false;		seen_model = false;
while(ok && *p) {		while(ok && *p) {
/* printf("%c%c%c%c%c%c\n",p[0],p[1],p[2],p[3],p[4],p[5]); */		/* printf("%c%c%c%c%c%c\n",p[0],p[1],p[2],p[3],p[4],p[5]); */
AFlag = false;		AFlag = false;
SSCode = 0;		SSCode = 0;
if(strstartswith(p, "ATOM"))		if(strstartswith(p, "ATOM "))
AFlag = 1;		AFlag = 1;
else if(strstartswith(p, "HETATM"))		else if(strstartswith(p, "HETATM"))
AFlag = 2;		AFlag = 2;
else if(strstartswith(p, "HEADER")) {		else if(strstartswith(p, "HEADER")) {
if(pdb_name) {		if(pdb_name) {
if(atomCount > 0) {		if(atomCount > 0) {
/* have we already read atoms? then this is probably a new PDB file * /		/* have we already read atoms? then this is probably a new PDB file * /
(*next_pdb) = p; /* found another PDB file after this one... */		(*next_pdb) = p; /* found another PDB file after this one... */
break;		break;
skipping to change at line 2632		skipping to change at line 2700
if(ok && SSCode) {		if(ok && SSCode) {
ss_found = sshash_register_rec(ss_hash,		ss_found = sshash_register_rec(ss_hash,
ss_chain1, ss_resv1, ss_inscode1,		ss_chain1, ss_resv1, ss_inscode1,
ss_chain2, ss_resv2, ss_inscode2, SSCode);		ss_chain2, ss_resv2, ss_inscode2, SSCode);
}		}
/* Atom records */		/* Atom records */
if(ok && AFlag && (!*restart_model)) {		if(ok && AFlag && (!*restart_model)) {
ai = atInfo + atomCount;		ai = atInfo + atomCount;
p = nskip(p, 6);		p = nskip(p, 6);
		ai->rank = atomCount;
		if(info && info->is_pqr_file()) {
		if (parse_pqr_atom_line(G, p, ai, coord + a)) {
		goto pqr_done;
		}
		}
p = ncopy(cc, p, 5);		p = ncopy(cc, p, 5);
if(!sscanf(cc, "%d", &ai->id))		if(!sscanf(cc, "%d", &ai->id))
ai->id = 0;		ai->id = 0;
ai->rank = atomCount;
p = nskip(p, 1); /* to 12 */		p = nskip(p, 1); /* to 12 */
p = ncopy(literal_name, p, 4);		p = ncopy(literal_name, p, 4);
if(literal_names) {		if(literal_names) {
LexAssign(G, ai->name, literal_name);		LexAssign(G, ai->name, literal_name);
} else {		} else {
ParseNTrim(cc, literal_name, 4);		ParseNTrim(cc, literal_name, 4);
LexAssign(G, ai->name, cc);		LexAssign(G, ai->name, cc);
}		}
skipping to change at line 2724		skipping to change at line 2800
break;		break;
case 4: /* simply read trim and write back out with 3-let ter names starting from the		case 4: /* simply read trim and write back out with 3-let ter names starting from the
second column, and four-letter names starting in the first */		second column, and four-letter names starting in the first */
ntrim(cc, ai_name, 4);		ntrim(cc, ai_name, 4);
LexAssign(G, ai->name, cc);		LexAssign(G, ai->name, cc);
break;		break;
}		}
}		}
p = ncopy(cc, p, 1);		p = ncopy(cc, p, 1);
		if (ai->chain){
		LexDec(G, ai->chain);
		}
if(*cc == ' ') {		if(*cc == ' ') {
ss_chain1 = 0;		ss_chain1 = 0;
ai->chain = 0;		ai->chain = 0;
} else {		} else {
ss_chain1 = *cc;		ss_chain1 = *cc;
ai->chain = LexIdx(G, cc);		ai->chain = LexIdx(G, cc);
}		}
p = ncopy(cc, p, 4);		p = ncopy(cc, p, 4);
if(!sscanf(cc, "%d", &ai->resv))		if(!sscanf(cc, "%d", &ai->resv))
ai->resv = 0;		ai->resv = 0;
ai->setInscode(*p);		ai->setInscode(*p);
p = nskip(p, 1);		p = nskip(p, 1);
if(ssFlag) { /* get secondary structure information (if avail ) */		if(ssFlag) { /* get secondary structure information (if avail ) */
sshash_lookup(ss_hash, ai, ss_chain1);		sshash_lookup(ss_hash, ai, ss_chain1);
} else {		} else {
ai->cartoon = cCartoon_tube;		ai->cartoon = cCartoon_tube;
}		}
if((!info) || (!info->is_pqr_file())) { /* standard PDB file */
		{
p = nskip(p, 3);		p = nskip(p, 3);
p = ncopy(cc, p, 8);		p = ncopy(cc, p, 8);
sscanf(cc, "%f", coord + a);		sscanf(cc, "%f", coord + a);
p = ncopy(cc, p, 8);		p = ncopy(cc, p, 8);
sscanf(cc, "%f", coord + (a + 1));		sscanf(cc, "%f", coord + (a + 1));
p = ncopy(cc, p, 8);		p = ncopy(cc, p, 8);
sscanf(cc, "%f", coord + (a + 2));		sscanf(cc, "%f", coord + (a + 2));
		}
		if((!info) || (!info->is_pqr_file())) { /* standard PDB file */
p = ncopy(cc, p, 6);		p = ncopy(cc, p, 6);
if(!sscanf(cc, "%f", &ai->q))		if(!sscanf(cc, "%f", &ai->q))
ai->q = 1.0;		ai->q = 1.0;
p = ncopy(cc, p, 6);		p = ncopy(cc, p, 6);
if(!sscanf(cc, "%f", &ai->b))		if(!sscanf(cc, "%f", &ai->b))
ai->b = 0.0;		ai->b = 0.0;
if (info->variant == PDB_VARIANT_PDBQT) {		if (info->variant == PDB_VARIANT_PDBQT) {
ignore_pdb_segi = true;		ignore_pdb_segi = true;
skipping to change at line 2846		skipping to change at line 2927
/* only read formal charge when sign is present */		/* only read formal charge when sign is present */
char ctmp = cc[0];		char ctmp = cc[0];
cc[0] = cc[1];		cc[0] = cc[1];
cc[1] = ctmp;		cc[1] = ctmp;
if(!sscanf(cc, "%hhi", &ai->formalCharge))		if(!sscanf(cc, "%hhi", &ai->formalCharge))
ai->formalCharge = 0;		ai->formalCharge = 0;
}		}
/* end normal PDB */		/* end normal PDB */
} else if(info && info->is_pqr_file()) {		} else if(info && info->is_pqr_file()) {
/* PQR file format...not well defined, but basically PDB
with charge and radius instead of B and Q. Right now,
we insist on PDB column format through the chain ID,
and then switch over to whitespace delimited parsing
for the coordinates, charge, and radius */
p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
sscanf(cc, "%f", coord + a);
p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
sscanf(cc, "%f", coord + (a + 1));
p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
sscanf(cc, "%f", coord + (a + 2));
p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);		p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
if(!sscanf(cc, "%f", &ai->partialCharge))		if(!sscanf(cc, "%f", &ai->partialCharge))
ai->partialCharge = 0.0F;		ai->partialCharge = 0.0F;
p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);		p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
if(sscanf(cc, "%f", &ai->elec_radius) != 1)		if(sscanf(cc, "%f", &ai->elec_radius) != 1)
ai->elec_radius = 0.0F;		ai->elec_radius = 0.0F;
}		}
		pqr_done:
ai->visRep = auto_show;		ai->visRep = auto_show;
if(AFlag == 1)		if(AFlag == 1)
ai->hetatm = 0;		ai->hetatm = 0;
else {		else {
ai->hetatm = 1;		ai->hetatm = 1;
ai->flags = cAtomFlag_ignore;		ai->flags = cAtomFlag_ignore;
}		}
AtomInfoAssignParameters(G, ai);		AtomInfoAssignParameters(G, ai);
End of changes. 16 change blocks.
29 lines changed or deleted		99 lines changed or added

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