Residue ResidueSubstitutionTable::replaceResidue(Residue &_res) {
// If this residue isn't in our list of residues to be replaced,
// just return it!
if( !isResidueInSubstitutionTable(_res) )
return _res;
// Clone the current residue, and find the replacement info.
Residue newRes;
ReplacementInfo ri = find( _res.getResidueName() )->second;
string newName = ri.first;
AtomHash ah = ri.second;
// Loop over all of the atoms in the residue.
for(int i=0; i < _res.size(); ++i ){
Atom &currAtom = _res.getAtom(i);
string currAtomName = currAtom.getName();
// If the current atom is in the list of atoms we should keep,
// add it.
if( ah.find(currAtomName) != ah.end() )
newRes.addAtom( currAtom );
}
// Set the new name of the residue.
newRes.setResidueNumber( _res.getResidueNumber() );
newRes.setResidueIcode( _res.getResidueIcode() );
newRes.setChainId( _res.getChainId() );
newRes.setResidueName( newName );
return newRes;
}
Structure* PDBReader::readStructure(Alphabet* alphabet, char* filename, const char* backboneAtomName) {
FILE* infile = fopen(filename, "r");
if (infile == NULL) {
return 0;
}
Structure* structure = new Structure(alphabet, filename);
// Create the entries from the PDB file.
char recordType[7];
char serialNumber[6];
char atomName[5];
char altLoc[2];
char residueName[4];
char chain[2];
char resID[5];
char insertion[2];
char x[9];
char y[9];
char z[9];
// Go through the file and parse out the records.
char line[1024];
Coordinate3D backboneCoord;
Residue* currentResidue = NULL;
while (!feof(infile)) {
// Get the next line.
if (fgets(line, 1023, infile) == NULL)
break;
// Make sure this is an atom or hetatom record.
parseField(recordType, line, 0, 6);
if (strcmp(recordType, "ATOM") == 0 || strcmp(recordType, "HETATOM") == 0)
{
// Parse the fields.
parseField(serialNumber, line, 6, 5);
parseField(atomName, line, 12, 4);
parseField(altLoc, line, 16, 1);
parseField(residueName, line, 17, 3);
parseField(chain, line, 21, 1);
parseField(resID, line, 22, 4);
parseField(insertion, line, 26, 1);
parseField(x, line, 30, 8);
parseField(y, line, 38, 8);
parseField(z, line, 46, 8);
// If this is a new residue, save the old one (if we have one) and start over.
if (currentResidue == NULL || (strcmp(resID, currentResidue->getResID()) != 0 || strcmp(insertion, currentResidue->getInsertionName()) != 0))
{
if (currentResidue != NULL)
{
structure->addResidue(currentResidue->getName(), backboneCoord, currentResidue);
}
// Start the new residue.
backboneCoord.unset();
currentResidue = new Residue(residueName, resID, insertion);
}
// If this is a backbone atom, save it.
if (strcmp(atomName, backboneAtomName) == 0)
{
backboneCoord.set(charToFloat(x), charToFloat(y), charToFloat(z));
}
// Add the atom to the list.
currentResidue->addAtom(new Atom(atomName, charToFloat(x),charToFloat(y),charToFloat(z)));
}
else if (strcmp(recordType, "TER") == 0)
{
break;
}
}
// If we have one last residue, save it.
if (currentResidue != NULL)
{
structure->addResidue(currentResidue->getName(), backboneCoord, currentResidue);
}
fclose(infile);
return structure;
}
