/**
* Returns true if ligand specified by either 3-letter ligand id (i.e. HEM) or chain/residue
* number (i.e. A156) matches the passed in residue.
*
* @param residue
* @param initialLigand Specification of ligand to be highlighted in Ligand Explorer upon startup
* @return
*/
private boolean isInitialLigandResidue(Residue residue, String initialLigand) {
if (residue.getCompoundCode().equalsIgnoreCase(initialLigand)) {
return true;
}
String chainId = initialLigand.substring(0, 1);
int residueNumber;
try {
residueNumber = Integer.parseInt(initialLigand.substring(1));
} catch (NumberFormatException e) {
return false;
}
if (residue.getAuthorChainId().equalsIgnoreCase(chainId)
&& residue.getAuthorResidueId() == residueNumber) {
return true;
}
return false;
}
/**
* Returns true if the initialLigand matches a PRD ID (i.e., PRD_000223)
*
* @param residue
* @param initialLigand Specification of PRD molecule to be highlighted in Ligand Explorer upon
* startup
* @return
*/
private boolean isInitialBirdChain(Chain chain, String initialLigand) {
if (chain.getClassification() == Classification.BIRD) {
Residue r = chain.getResidue(0);
if (r != null) {
Bird bird = r.getBird();
if (bird == null) {
return false;
}
if (initialLigand.toUpperCase().startsWith("PRD_")) {
return bird.getPrdId().equalsIgnoreCase(initialLigand);
} else {
String chainId = initialLigand.substring(0, 1);
String prdId = initialLigand.substring(2, initialLigand.length());
return chain.getAuthorChainId().equalsIgnoreCase(chainId)
&& bird.getPrdId().equalsIgnoreCase(prdId);
}
}
}
return false;
}