ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/development/src/applications/atom2md/openmdformat.cpp

Comparing trunk/src/applications/atom2md/openmdformat.cpp (file contents):
Revision 1399 by gezelter, Thu Dec 24 05:45:30 2009 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 129 | Line 129 | namespace OpenBabel
129		return false;
130		}
131
132	+
133	+
134		WriteMDFile(mdMols, numMols, ofs, *pmol, indices);
135
136		for(vector<OBMol*>::iterator  i = mdMols.begin(); i != mdMols.end(); ++i) {
#	Line 171 | Line 173 | namespace OpenBabel
173		vector<int>& fragment) {
174
175		OBMol* newMol = new OBMol();
176	+	OBChainsParser* chainParser = new OBChainsParser();
177	+	bool molIsWater = false;
178	+
179		newMol->ReserveAtoms(fragment.size());
180		newMol->BeginModify();
181		for(vector<int>::iterator i = fragment.begin(); i != fragment.end(); ++i) {
#	Line 212 | Line 217 | namespace OpenBabel
217		OBMol* pmol = mols[i];
218		map<OBAtom*, int> atomMap;
219
220	+
221		//chainParser->PerceiveChains(*pmol, false);
222		molIsWater = false;
223		FOR_RESIDUES_OF_MOL(residue, *pmol) {
218	–	std::cerr << "residue = " << residue->GetName() << "\n";
224		if (residue->GetName().compare("HOH") == 0) {
225		molIsWater = true;
226		}
#	Line 351 | Line 356 | namespace OpenBabel
356		size_t endpos = str.find_last_not_of(" ");
357		str = str.substr( startpos, endpos-startpos+1 );
358		str1 = resName + "-" + str;
359	<	}
359	>	}
360		os << "  atom[" << ai << "] { ";
361		os << "type = " << "\"" << str1 << "\"" << "; ";
362		os << "position( " << (&*atom)->GetX() << ", " << (&*atom)->GetY() << ", " << (&*atom)->GetZ() << ");";
#	Line 390 | Line 395 | namespace OpenBabel
395		OBMol* pmol = mols[i];
396		os << "component{" << endl;
397		if (std::string(pmol->GetTitle()).compare("HOH") == 0) {
398	<	os << "  type = " << "HOH" << ";" << endl;
398	>	os << "  type = " << "\"HOH\"" << "; // change to appropriate water model" << endl;
399		} else {
400		sprintf(buffer, "%d", i);
401		os << "  type = " << molPrefix << buffer << ";" << endl;
#	Line 416 | Line 421 | namespace OpenBabel
421		os << buffer << endl;
422		os << "    </FrameData>" << endl;
423		os << "    <StuntDoubles>" << endl;
424	<
424	>
425		OBAtom *atom;
426	<
422	<	// still to do: intercept waters and recompute pvqj lines
423	<
426	>
427		for(vector<int>::iterator i = indices.begin();i != indices.end(); ++i) {
428	+
429		atom = mol.GetAtom(*i);
430		sprintf(buffer, "%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e", *i - 1,
431		"pv", atom->GetX(), atom->GetY(), atom->GetZ(), 0.0, 0.0, 0.0);

Comparing trunk/src/applications/atom2md/openmdformat.cpp (property svn:keywords):
Revision 1399 by gezelter, Thu Dec 24 05:45:30 2009 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines