static void
zMol2FileWriteContainer( MOL2WRITEt *pwPFile, CONTAINER cCont, int choice )
{
//const char C_TERMINAL_PREFIX = 'C';
//const char N_TERMINAL_PREFIX = 'N';
const int RESIDUE_NAME_LENGTH = 4;
LOOP lContents;
ATOM aAtom;
char *cPTemp;
cPTemp = sContainerName(cCont);
strncpy( pwPFile->sResidueName, cPTemp, RESIDUE_NAME_LENGTH );
pwPFile->sResidueName[ RESIDUE_NAME_LENGTH ] = '\0';
if ( strlen(cPTemp) > RESIDUE_NAME_LENGTH ) {
VP0(( " Truncating residue name for PDB format: %s -> %s\n",
sContainerName(cCont), pwPFile->sResidueName ));
}
/* }
*/
if ( iObjectType(cCont) == ATOMid ) {
zMol2FileWriteAtomRecord( pwPFile, (ATOM)cCont, choice);
pwPFile->iResidueSeq++;
} else if ( iObjectType(cCont) == RESIDUEid ) {
RESIDUE rRes = (RESIDUE) cCont;
pwPFile->iResidueSeq = rRes->iTemp;
if ( pwPFile->iResidueSeq == 0 )
pwPFile->iResidueSeq = 1;
lContents = lLoop( (OBJEKT)cCont, DIRECTCONTENTSBYSEQNUM );
while ( (aAtom = (ATOM)oNext(&lContents)) ) {
zMol2FileWriteAtomRecord( pwPFile, aAtom, choice);
}
} else if ( iObjectType(cCont) == MOLECULEid ) {
lContents = lLoop( (OBJEKT)cCont, ATOMS );
while ( (aAtom = (ATOM)oNext(&lContents)) ) {
zMol2FileWriteAtomRecord( pwPFile, aAtom, choice );
}
pwPFile->iResidueSeq++;
}
}
OBJEKT
AMBER_Combine(OBJEKT objProt, OBJEKT objLig)
{
// version of function oCmd_combine
UNIT uCombined, uCurrent;
LOOP lTemp;
RESIDUE rRes = NULL;
OBJEKT oObj;
/* add only one uCurrent unit (Ligand) to uCombined unit (Protein) */
uCombined = (UNIT)objProt;
oObj = objLig;
if ( iObjectType( oObj ) != UNITid ) {
printf( "%s: is type %s\n",
"Ligand", sObjectType(oObj) );
}
uCurrent = (UNIT)objLig;
printf( " Ligand: %s\n", sContainerName((CONTAINER) uCurrent) );
if ( uCombined == NULL ) {
printf( "--- no Protein unit \n" );
} else {
printf( "Joining Protein and Ligand \n" );
UnitJoin( uCombined, uCurrent );
}
if ( uCombined == NULL ) {
printf( "No UNITS, so no combine performed\n" );
return(NULL);
}
/* Define PDB sequence */
lTemp = lLoop( (OBJEKT)uCombined, RESIDUES );
while ( rRes == (RESIDUE)oNext(&lTemp) ) {
ResidueSetPdbSequence( rRes, iContainerSequence((CONTAINER) rRes) );
}
return((OBJEKT)uCombined);
}
OBJEKT AMBER_Combine(OBJEKT objProt, OBJEKT objLig)
{
UNIT uCombined, uCurrent;
LOOP lTemp;
RESIDUE rRes = NULL;
OBJEKT oObj;
uCombined = (UNIT)objProt;
oObj = objLig;
if ( iObjectType( oObj ) != UNITid )
{
PrintInfo(( "%s: is type %s", "Ligand", sObjectType(oObj) ));
}
uCurrent = (UNIT)oCopy(oObj );
PrintInfo(( " Sequence: %s", sContainerName((CONTAINER) uCurrent) ));
if ( uCombined == NULL )
{
printf( "Copying the first UNIT\n" );
uCombined = uCurrent;
} else
{
printf( "Copied a subsequent UNIT\n" );
printf( "Joining two UNITS \n" );
UnitJoin( uCombined, uCurrent );
}
if ( uCombined == NULL )
{
printf( "No UNITS, so no combine performed\n" );
return(NULL);
}
lTemp = lLoop( (OBJEKT)uCombined, RESIDUES );
while ( rRes == (RESIDUE)oNext(&lTemp) )
{
ResidueSetPdbSequence( rRes, iContainerSequence((CONTAINER) rRes) );
}
return((OBJEKT)uCombined);
}
