void
zMol2FileWriteAtomRecord( MOL2WRITEt *pwPFile, ATOM aAtom, int choice )
{
pdb_record p;
#ifdef DEBUG
STRING sElement;
#endif
STRING sName, sTemp, sTypeAt;
p.pdb.atom.serial_num = pwPFile->iRecordNumber++;
strcpy( p.pdb.atom.residue.name, pwPFile->sResidueName );
strcpy( sName, sAtomType(aAtom) );
strcpy( sTemp, sContainerName((CONTAINER)aAtom) );
if (choice == 0) {
strcpy( sTypeAt, sTemp);
sTypeAt[1] = '\0';
strcpy( p.pdb.atom.type_at, sTypeAt );
}
if (choice == 1) {
strcpy( sTypeAt, sName);
strcpy( p.pdb.atom.type_at, sTypeAt );
}
strcpy( p.pdb.atom.name, sTemp );
MESSAGE(( "Element: |%s| pdb_name=|%s|\n", sElement, sName ));
p.pdb.atom.residue.chain_id = ' ';
p.pdb.atom.residue.seq_num = pwPFile->iResidueSeq;
p.pdb.atom.residue.insert_code=' ';
/* p.pdb.atom.alt_loc = ' ' ; */
p.pdb.atom.x = dVX(&vAtomPosition(aAtom));
p.pdb.atom.y = dVY(&vAtomPosition(aAtom));
p.pdb.atom.z = dVZ(&vAtomPosition(aAtom));
p.pdb.atom.occupancy = 1.0;
p.pdb.atom.temp_factor = dAtomCharge(aAtom);
p.pdb.atom.ftnote_num = 0;
p.record_type = MOL2_ATOM;
pdb_write_record( pwPFile->fPdbFile, &p, NULL, 0 );
}
/*
* ResidueMutate
*
* Author: Christian Schafmeister (1991)
*
* Mutate the RESIDUE (rOld) into the RESIDUE (rNew).
* Do this by superimposing the coordinates from rOld onto
* rNew, breaking all the bonds from rOld to other residues,
* and rejoining them to identically named atoms in rNew,
* then building the coordinates for the rest of the atoms in rNew.
* The new RESIDUE rNew should not be bonded to anything else, it
* should also have EXTERNAL coordinates defined, but no INTERNALS.
*
*/
void
ResidueMutate( RESIDUE rNew, RESIDUE rOld )
{
LOOP lAtoms, lSpan;
ATOM aNew, aNeighbor, aOld, aAtom, aSpan, aTemp;
STRING sTemp, sSpan;
int i, iDum;
FLAGS fBondFlags;
MESSAGE(( "Mutating: %s to: %s\n", sContainerName( rOld ),
sContainerName(rNew) ));
/* Build internal coordinates for the new RESIDUE */
lAtoms = lLoop( (OBJEKT)rNew, ATOMS );
BuildInternalsUsingFlags( &lAtoms,
ATOMPOSITIONKNOWN,
0,
0,
ATOMPOSITIONKNOWN,
&iDum, &iDum, &iDum );
/* Define the coordinates, and the flags */
/* if there are bonds out of the old RESIDUE, break them */
/* and rejoin them to identically named atoms in the new */
/* RESIDUE */
lAtoms = lLoop( (OBJEKT)rOld, ATOMS );
FOREACH( aOld, ATOM, lAtoms ) {
MESSAGE(( "Searching for atom in new residue with name: %s\n",
sContainerName(aOld) ));
aNew = (ATOM)cContainerFindName( (CONTAINER)rNew, ATOMid,
sContainerName(aOld) );
/* If there is a cooresponding ATOM with the same name */
/* then define its flags and coordinates */
if ( aNew != NULL ) {
MESSAGE(( "--- Found one\n" ));
AtomSetPosition( aNew, vAtomPosition(aOld) );
AtomDefineFlags( aNew, fAtomFlags(aOld) );
} else {
MESSAGE(( "--- No atom found\n" ));
}
/* Search for bonds out of the old RESIDUE */
for ( i=0; i<iAtomCoordination(aOld); i++ ) {
aNeighbor = aAtomBondedNeighbor( aOld, i );
MESSAGE(( "--- Looking at neighbor: %s\n",
sContainerFullDescriptor( (CONTAINER)aNeighbor, sTemp ) ));
if ( rOld != (RESIDUE)cContainerWithin(aNeighbor) ) {
fBondFlags = fAtomBondFlags( aOld, i );
AtomRemoveBond( aOld, aNeighbor );
MESSAGE(( "Removing a bond to: %s\n",
sContainerFullDescriptor( (CONTAINER)aNeighbor, sTemp ) ));
if ( aNew != NULL ) {
MESSAGE(( "--- And rejoining it to: %s\n",
sContainerFullDescriptor( (CONTAINER)aNew, sTemp ) ));
AtomBondToFlags( aNew, aNeighbor, fBondFlags );
} else {
MESSAGE(( "--- Not rejoining it to anything.\n" ));
VP1(( "There is no atom in residue: %s with the name: %s.\n" ));
VP1(( "--- No bond could be made to the missing atom.\n" ));
}
}
}
}
