OBJEKT AMBER_loadPrep(char *file_prep)
{
DICTIONARY dUnits;
DICTLOOP dlLoop ;
UNIT uUnit = NULL;
STRING sName;
LOOP lResidues;
RESIDUE rRes;
/* Read an AMBER PREP file into a dictionary.*/
dUnits = dAmberReadPrepFile(file_prep);
if ( dUnits != NULL )
{
dlLoop = ydlDictionaryLoop( dUnits );
uUnit=(UNIT)yPDictionaryNext( dUnits, &dlLoop );
strcpy( sName, sContainerName((CONTAINER) uUnit) );
PrintInfo(( "Loaded UNIT: %s", sName ));
/* Set the name for the UNIT */
ContainerSetName( (CONTAINER) uUnit, sName );
/* Set the name for the only residue in the unit */
lResidues = lLoop( (OBJEKT)uUnit, RESIDUES );
rRes = (RESIDUE)oNext(&lResidues);
ContainerSetName( (CONTAINER) rRes, sName );
VariableSet( sName, (OBJEKT) uUnit ); /* adds 1 REF */
return((OBJEKT)uUnit);
}
if (uUnit == NULL)
PrintError( ("-- no UNIT loaded \n"));
return(NULL);
}
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++;
}
}
static char *
zMol2FileWriteResidueContainer( MOL2WRITEt *pwPFile, CONTAINER cCont )
{
//const char C_TERMINAL_PREFIX = 'C';
//const char N_TERMINAL_PREFIX = 'N';
const int RESIDUE_NAME_LENGTH = 3;
//LOOP lContents;
char *cPTemp;
RESIDUE rRes;
cPTemp = sContainerName(cCont);
strncpy( pwPFile->sResidueName, cPTemp, RESIDUE_NAME_LENGTH );
/* The intentional side effect is to truncate long names. */
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 ));
}
rRes = (RESIDUE) cCont;
return(sContainerName(cCont));
}
OBJEKT AMBER_loadPrep(char*file_prep)
{
/* version of function oCmd_loadAmberPrep */
DICTIONARY dUnits;
DICTLOOP dlLoop ;
UNIT uUnit = NULL;
STRING sName;
LOOP lResidues;
RESIDUE rRes;
/* Read an AMBER PREP file into a dictionary.*/
dUnits = dAmberReadPrepFile(file_prep);
if ( dUnits != NULL ) {
dlLoop = ydlDictionaryLoop( dUnits );
/* for move3d version only one UNIT with one residue loaded */
uUnit=(UNIT)yPDictionaryNext( dUnits, &dlLoop );
strcpy( sName, sContainerName((CONTAINER) uUnit) );
printf( "Loaded UNIT: %s\n", sName );
/* Set the name for the UNIT */
ContainerSetName( (CONTAINER) uUnit, sName );
/* Set the name for the only residue in the unit */
lResidues = lLoop( (OBJEKT)uUnit, RESIDUES );
rRes = (RESIDUE)oNext(&lResidues);
ContainerSetName( (CONTAINER) rRes, sName );
VariableSet( (char*)sName, (OBJEKT) uUnit ); /* adds 1 REF */
if (uUnit != NULL)
return((OBJEKT)uUnit);
else{
printf ("-- no UNIT loaded \n");
return(NULL);
}
}
else
return(NULL);
}
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 );
}
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);
}
/* Main function, write the Mol3 file */
void
Mol3Write( FILE *fOut, UNIT uUnit, int choice ){
int i,j,iResNumber = 0;
VARARRAY vaRes;
STRING sName;
char* cPTemp;
Mol2Write( fOut, uUnit, choice );
fprintf(fOut, "@<TRIPOS>HEADTAIL\n") ;
/* Write the HEAD in the file */
if ( aUnitHead(uUnit) != NULL ){
iResNumber=(((CONTAINER)aUnitHead(uUnit))->cContainedBy)->iSequence;
cPTemp = ((CONTAINER)aUnitHead(uUnit))->sName;
strncpy( sName, cPTemp, 4 );
if ( strlen(cPTemp) > 4 ) {
VP0(( " Truncating residue name for PDB format: %s -> %s\n", ((CONTAINER)aUnitHead(uUnit))->sName, sName ));
fprintf(fOut,"%s %d\n",sName,iResNumber);
}
else {
fprintf(fOut,"%s %d\n",((CONTAINER)aUnitHead(uUnit))->sName,iResNumber);
}
}
else {
fprintf(fOut,"0 0\n");
}
/* Write the TAIL in the file */
if ( aUnitTail(uUnit) != NULL ){
iResNumber=(((CONTAINER)aUnitTail(uUnit))->cContainedBy)->iSequence;
cPTemp = ((CONTAINER)aUnitTail(uUnit))->sName;
strncpy( sName, cPTemp, 4 );
if ( strlen(cPTemp) > 4 ) {
VP0(( " Truncating residue name for PDB format: %s -> %s\n", ((CONTAINER)aUnitTail(uUnit))->sName, sName ));
fprintf(fOut,"%s %d\n",sName,iResNumber);
}
else{
fprintf(fOut,"%s %d\n",((CONTAINER)aUnitTail(uUnit))->sName,iResNumber);
}
}else{
fprintf(fOut,"0 0\n");
}
fprintf(fOut,"@<TRIPOS>RESIDUECONNECT\n");
/* Write Atoms Connect for every Residue */
vaRes=uUnit->vaResidues;
for (i = 0; i < iVarArrayElementCount((VARARRAY)vaRes); i++) {
SAVERESIDUEt prRes = *PVAI(vaRes, SAVERESIDUEt, i);
fprintf(fOut,"%d",prRes.iSequenceNumber);
for (j = 0; j <= 5; j++) {
if ( prRes.rResidue->aaConnect[j] != NULL ){
cPTemp = sContainerName(prRes.rResidue->aaConnect[j]);
strncpy( sName, cPTemp, 4 );
if ( strlen(cPTemp) > 4 ) {
VP0(( " Truncating residue name for PDB format: %s -> %s\n", sContainerName(prRes.rResidue->aaConnect[j]), sName ));
fprintf(fOut," %s",sName);
}else{
fprintf(fOut," %s",sContainerName(prRes.rResidue->aaConnect[j]) );
}
}else{
fprintf(fOut," 0");
}
}
fprintf(fOut,"\n");
}
}
void
Mol2Write( FILE *fOut, UNIT uUnit, int choice )
{
// int i, iResidueCount, iAtomCount = 0, iAtom, iBondCount, iCount;
int i, iResidueCount, iAtomCount = 0, iBondCount, iCount;
//` int j,k,l,m,n;
int j,k;
LOOP lContents,lTemp,lResidues;
SAVERESIDUEt *srPResidue;
SAVECONNECTIVITYt *scPCon;
MOL2WRITEt pwFile;
STRING sTemp;
char *sName;
ATOM aAtom1,aAtom2;
RESIDUE rRes1;
BOOL bPert,bFailedGeneratingParameters;
// STRING sAtom1, sAtom2, sDesc;
zMol2FileBegin( &pwFile, fOut );
/* @<TRIPOS>MOLECULE Bloc */
fprintf(fOut, "@<TRIPOS>MOLECULE\n") ;
iResidueCount = zUnitIOAmberOrderResidues( uUnit );
strcpy( sTemp, sContainerName((CONTAINER) uUnit));
iCount = 0;
bPert = FALSE;
lTemp = lLoop((OBJEKT) uUnit, BONDS);
while (oNext(&lTemp) != NULL)
iCount++;
iAtomCount = 0;
lTemp = lLoop((OBJEKT) uUnit, ATOMS);
while (oNext(&lTemp) != NULL)
iAtomCount++;
iBondCount = iCount;
fprintf(fOut, "%s\n", sTemp) ;
fprintf(fOut, "%5d %5d %5d 0 1 \n", iAtomCount,iBondCount,iResidueCount) ;
fprintf(fOut, "SMALL\n");
fprintf(fOut, "USER_CHARGES\n");
/* @<TRIPOS>ATOM Bloc */
fprintf(fOut, "@<TRIPOS>ATOM\n") ;
srPResidue = PVAI(uUnit->vaResidues, SAVERESIDUEt, 0);
for (i = 0; i < iResidueCount; srPResidue++, i++) {
RESIDUE rRes = srPResidue->rResidue;
rRes->iTemp = i + 1;
zMol2FileWriteContainer( &pwFile, (CONTAINER) rRes, choice);
}
fprintf(fOut, "@<TRIPOS>BOND\n") ;
/* Now generate the connectivity table */
/* Inspired by zUnitIOBuildTables in unitio.c */
/*zbUnitIOIndexBondParameters(plParameters, uUnit, bPert); */
iAtomCount = 0;
lTemp = lLoop((OBJEKT) uUnit, ATOMS);
while (oNext(&lTemp) != NULL)
iAtomCount++;
if (iAtomCount) {
uUnit->vaAtoms = vaVarArrayCreate(sizeof(SAVEATOMt));
VarArraySetSize((uUnit->vaAtoms), iAtomCount);
i = 0;
lResidues = lLoop((OBJEKT) uUnit, DIRECTCONTENTSBYSEQNUM);
while ((rRes1 = (RESIDUE) oNext(&lResidues)) != NULL) {
zUnitDoAtoms(uUnit, NULL, rRes1, &i, &bFailedGeneratingParameters, bPert);
}
}
iCount = 0;
lTemp = lLoop((OBJEKT) uUnit, BONDS);
while (oNext(&lTemp) != NULL)
iCount++;
uUnit->vaConnectivity = vaVarArrayCreate(sizeof(SAVECONNECTIVITYt));
VarArraySetSize((uUnit->vaConnectivity), iCount);
if (iCount) {
i = 0;
lTemp = lLoop((OBJEKT) uUnit, BONDS);
scPCon = PVAI(uUnit->vaConnectivity, SAVECONNECTIVITYt, 0);
while (oNext(&lTemp) != NULL) {
/*LoopGetBond(&lTemp, &aAtom1, &aAtom2); */
(*(&aAtom1))=(ATOM)(&lTemp)->oaObj[0] ;
(*(&aAtom2))=(ATOM)(&lTemp)->oaObj[1] ;
i++;
scPCon++;
fprintf(fOut, "%5d %5d %5d 1\n", i,(((CONTAINER)(aAtom1))->iTempInt),(((CONTAINER)(aAtom2))->iTempInt));
}
}
fprintf(fOut, "@<TRIPOS>SUBSTRUCTURE\n") ;
srPResidue = PVAI(uUnit->vaResidues, SAVERESIDUEt, 0);
k=0;
for (i = 0; i < iResidueCount; srPResidue++, i++) {
ATOM aAtom;
RESIDUE rRes = srPResidue->rResidue;
j=0;
sName = zMol2FileWriteResidueContainer( &pwFile, (CONTAINER) rRes);
lContents = lLoop((OBJEKT)rRes, DIRECTCONTENTSBYSEQNUM );
while((aAtom = (ATOM)oNext(&lContents)) )
j=j+1 ;
k=k+j;
fprintf(fOut, "%7d %4s %14d **** 0 **** **** \n", i+1, sName, k-j+1);
}
}
/*
* 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" ));
}
}
}
}
