"Fossies" - the Fresh Open Source Software Archive  

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

AtomInfo.cpp  (pymol-v2.1.0.tar.bz2)	:	AtomInfo.cpp  (pymol-open-source-2.2.0)
skipping to change at line 2346		skipping to change at line 2346
if (lookup.empty()) {		if (lookup.empty()) {
for (int i = 0; i < ElementTableSize; i++)		for (int i = 0; i < ElementTableSize; i++)
lookup[ElementTable[i].symbol] = i;		lookup[ElementTable[i].symbol] = i;
lookup["Q"] = cAN_H;		lookup["Q"] = cAN_H;
lookup["D"] = cAN_H;		lookup["D"] = cAN_H;
}		}
// check second letter for lower case		// check second letter for lower case
if (isupper(symbol[1]) && strcmp(symbol, "LP") != 0) {		if (symbol[0] && isupper(symbol[1]) && strcmp(symbol, "LP") != 0) {
UtilNCopy(titleized, symbol, 4);		UtilNCopy(titleized, symbol, 4);
titleized[1] = tolower(symbol[1]);		titleized[1] = tolower(symbol[1]);
symbol = titleized;		symbol = titleized;
}		}
// find in lookup dictionary		// find in lookup dictionary
auto it = lookup.find(symbol);		auto it = lookup.find(symbol);
if (it != lookup.end()) {		if (it != lookup.end()) {
return it->second;		return it->second;
skipping to change at line 2829		skipping to change at line 2829
/*		/*
* Set stereochemistry. Valid are: R, S, N[one], E[ven], O[dd]		* Set stereochemistry. Valid are: R, S, N[one], E[ven], O[dd]
*/		*/
void AtomInfoSetStereo(AtomInfoType * ai, const char * stereo) {		void AtomInfoSetStereo(AtomInfoType * ai, const char * stereo) {
switch (toupper(stereo[0])) {		switch (toupper(stereo[0])) {
case 'R': ai->mmstereo = 1; ai->stereo = 0; break; // MMSTEREO_CHIRALITY_R		case 'R': ai->mmstereo = 1; ai->stereo = 0; break; // MMSTEREO_CHIRALITY_R
case 'S': ai->mmstereo = 2; ai->stereo = 0; break; // MMSTEREO_CHIRALITY_S		case 'S': ai->mmstereo = 2; ai->stereo = 0; break; // MMSTEREO_CHIRALITY_S
case 'E': ai->mmstereo = 0; ai->stereo = SDF_CHIRALITY_EVEN; break;		case 'E': ai->mmstereo = 0; ai->stereo = SDF_CHIRALITY_EVEN; break;
case 'O': ai->mmstereo = 0; ai->stereo = SDF_CHIRALITY_ODD; break;		case 'O': ai->mmstereo = 0; ai->stereo = SDF_CHIRALITY_ODD; break;
		case 'A': // ANS (s), ANR (r) pseudochirality
case 'N': case 0: ai->mmstereo = ai->stereo = 0; break;		case 'N': case 0: ai->mmstereo = ai->stereo = 0; break;
default: ai->mmstereo = ai->stereo = 3; break;		default: ai->mmstereo = ai->stereo = 3; break;
}		}
}		}
/*		/*
* Get column aligned (left space padded) PDB residue name		* Get column aligned (left space padded) PDB residue name
*		*
* resn: output buffer		* resn: output buffer
*/		*/
End of changes. 2 change blocks.
1 lines changed or deleted		2 lines changed or added

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