"Fossies" - the Fresh Open Source Software Archive  

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

CoordSet.cpp  (pymol-v1.8.6.0.tar.bz2)	:	CoordSet.cpp  (pymol-v2.1.0.tar.bz2)
skipping to change at line 758		skipping to change at line 758
* matrix: 4x4 homogenous transformation matrix from model space to output		* matrix: 4x4 homogenous transformation matrix from model space to output
* space (view matrix * state matrix). Used for ANISOU.		* space (view matrix * state matrix). Used for ANISOU.
*/		*/
{		{
char *aType;		char *aType;
AtomName name;		AtomName name;
ResName resn;		ResName resn;
ov_word chain;		ov_word chain;
char formalCharge[4];		char formalCharge[4];
int literal = SettingGetGlobal_b(G, cSetting_pdb_literal_names);
int reformat = SettingGetGlobal_i(G, cSetting_pdb_reformat_names_mode);
int ignore_pdb_segi = SettingGetGlobal_b(G, cSetting_ignore_pdb_segi);		int ignore_pdb_segi = SettingGetGlobal_b(G, cSetting_ignore_pdb_segi);
WordType x, y, z;		WordType x, y, z;
		AtomInfoGetAlignedPDBResidueName(G, ai, resn);
		AtomInfoGetAlignedPDBAtomName(G, ai, resn, name);
formalCharge[0] = 0;		formalCharge[0] = 0;
sprintf(resn, "%3.4s", LexStr(G, ai->resn));
if(SettingGetGlobal_b(G, cSetting_pdb_truncate_residue_name)) {
resn[3] = 0; /* enforce 3-letter residue name in PDB files */
}
if(SettingGetGlobal_b(G, cSetting_pdb_formal_charges)) {		if(SettingGetGlobal_b(G, cSetting_pdb_formal_charges)) {
if((ai->formalCharge > 0) && (ai->formalCharge < 10)) {		if((ai->formalCharge > 0) && (ai->formalCharge < 10)) {
sprintf(formalCharge, "%d+", ai->formalCharge);		sprintf(formalCharge, "%d+", ai->formalCharge);
} else if((ai->formalCharge < 0) && (ai->formalCharge > -10)) {		} else if((ai->formalCharge < 0) && (ai->formalCharge > -10)) {
sprintf(formalCharge, "%d-", -ai->formalCharge);		sprintf(formalCharge, "%d-", -ai->formalCharge);
}		}
}		}
if(ai->hetatm)		if(ai->hetatm)
aType = sHETATM;		aType = sHETATM;
else		else
aType = sATOM;		aType = sATOM;
char inscode = ai->getInscode(true);		char inscode = ai->getInscode(true);
VLACheck(*charVLA, char, (*c) + 1000);		VLACheck(*charVLA, char, (*c) + 1000);
const char * ai_name = LexStr(G, ai->name);
auto ai_name_len = strlen(ai_name);
bool start_column_1 = false;
UtilNCopy(name, ai_name, 5);
if(!ai->name) {
if(!ai->elem[1])
sprintf(name, " %s", ai->elem);
else
sprintf(name, "%s", ai->elem);
} else if(!literal) {
if(ai_name_len < 4) { /* atom name less than length 4 */
if(!isdigit(name[0])) { /* doesn't start with a number */
if((toupper(ai->elem[0]) == toupper(name[0])) && ((!ai->elem[1]) || /* s
ymbol len = 1 */
(toupper(ai->elem[1]) == toupper(name[1])))) { /* matched l
en 2 */
/* starts with corrent atomic symbol, so */
if(!ai->elem[1]) { /* symbol len = 1 */
switch (reformat) {
case 1: /* pdb with internal pdb */
case 3: /* pdb with internal iupac */
if((ai->elem[0] == 'H') && ai_name_len > 2) {
AtomInfoGetPDB3LetHydroName(G, resn, ai_name, name);
break;
}
default: /* otherwise, start in column 1 */
start_column_1 = true;
break;
}
}
} else { /* name doesn't start with atomic symbol */
/* then just place it in column 1 as usual */
start_column_1 = true;
}
} else { /* name starts with a number */
switch (reformat) {
case 2: /* make Amber compliant */
if((ai->elem[0] == name[1]) &&
((!ai->elem[1]) || (toupper(ai->elem[1]) == toupper(name[2])))) {
/* rotate the name to place atom symbol in column 0 to comply with A
mber PDB format */
name[3] = name[0];
name[0] = ' ';
}
break;
}
} /* just stick it in column 0 and hope for the be
st */
} else { /* if name is length 4 */
if((ai->elem[0] == name[0]) && ((!ai->elem[1]) || /* symbol len = 1 */
(toupper(ai->elem[1]) == toupper(name[
1])))) { /* matched len 2 */
/* name starts with the atomic symbol */
if((!ai->elem[1]) && (ai->elem[0])) { /* but if element is one letter.
.. */
switch (reformat) {
case 1: /* retaining PDB compliance throughout, or */
case 3: /* saving as PDB compliant, but use IUPAC within
PyMOL */
if(isdigit(name[3])) { /* and last character is a number */
/* rotate the name to place atom symbol in column 1 to comply with
PDB format */
name[0] = ai_name[3];
name[1] = ai_name[0];
name[2] = ai_name[1];
name[3] = ai_name[2];
name[4] = 0;
}
break;
}
}
} else { /* name does not start with the symbol... */
if(reformat == 2) { /* AMBER compliance mode */
if(isdigit(name[0])) {
if((ai->elem[0] == name[1]) &&
((!(ai->elem[1])) || (toupper(ai->elem[1]) == toupper(name[2]))))
{
/* rotate the name to place atom symbol in column 0 to comply with
Amber PDB format */
name[0] = ai_name[1];
name[1] = ai_name[2];
name[2] = ai_name[3];
name[3] = ai_name[0];
name[4] = 0;
}
}
}
}
}
} else { /* LITERAL mode: preserve what was in the origin
al PDB as best PyMOL can
this should enable people to open and save am
ber pdb files without issues */
if (ai_name_len < 4 && !(ai->elem[1] && /* elem len = 2 */
toupper(ai->elem[0]) == toupper(name[0]) &&
toupper(ai->elem[1]) == toupper(name[1]))) {
start_column_1 = true;
}
}
if (start_column_1) {
name[0] = ' ';
UtilNCopy(name + 1, ai_name, 4);
}
if(SettingGetGlobal_b(G, cSetting_pdb_retain_ids)) {		if(SettingGetGlobal_b(G, cSetting_pdb_retain_ids)) {
cnt = ai->id - 1;		cnt = ai->id - 1;
}		}
if(cnt > 99998)		if(cnt > 99998)
cnt = 99998;		cnt = 99998;
name[4] = 0;
if((!pdb_info) || (!pdb_info->is_pqr_file())) { /* relying upon short-circuit */		if((!pdb_info) || (!pdb_info->is_pqr_file())) { /* relying upon short-circuit */
short linelen;		short linelen;
sprintf(x, "%8.3f", v[0]);		sprintf(x, "%8.3f", v[0]);
x[8] = 0;		x[8] = 0;
sprintf(y, "%8.3f", v[1]);		sprintf(y, "%8.3f", v[1]);
y[8] = 0;		y[8] = 0;
sprintf(z, "%8.3f", v[2]);		sprintf(z, "%8.3f", v[2]);
z[8] = 0;		z[8] = 0;
linelen =		linelen =
sprintf((*charVLA) + (*c),		sprintf((*charVLA) + (*c),
End of changes. 5 change blocks.
115 lines changed or deleted		3 lines changed or added

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