/**
* Writes a the shortest paths of a list of virtual cross-links into a PDB formated file.
*
* @param pathFileName - String object holding the path to the PDB file to be written.
* @param crossLinkList - List of cross-link objects holding each the the shortest path
*/
public final void writeSASDpdbFile(final String pathFileName, final CrossLinkList crossLinkList) {
StringBuffer content = new StringBuffer();
for (CrossLink crossLink : crossLinkList) {
if (crossLink.getPath() != null) {
Atom atom1 = crossLink.getPreAtom();
Atom atom2 = crossLink.getPostAtom();
String distName =
crossLink.getIndex()
+ "_"
+ this.decFormat.format(crossLink.getSolventPathDistance())
+ "_"
+ atom1.getResidueName().trim()
+ ""
+ atom1.getResidueNumber()
+ ""
+ atom1.getChainId()
+ "-"
+ atom2.getResidueName().trim()
+ ""
+ atom2.getResidueNumber()
+ ""
+ atom2.getChainId()
+ "_solventPath";
content.append("HEADER " + distName + Constants.LINE_SEPERATOR);
content.append(crossLink.getPath().toString(crossLink.getIndex()));
content.append("END" + Constants.LINE_SEPERATOR);
}
}
WriteFile file = new WriteFile();
file.setFile(pathFileName);
file.write(content.toString());
}
