/*
* DictionaryDescribe
*
* Author: Christian Schafmeister (1991)
*
* Describe the DICTIONARY.
*/
void
DictionaryDescribe( DICTIONARY dDict )
{
DICTLOOP dlLoop;
VP0(( "Dictionary with %d elements.\n",
iDictionaryElementCount(dDict) ));
dlLoop = ydlDictionaryLoop(dDict);
while ( yPDictionaryNext( dDict, &dlLoop ) ) {
VP0(( "%40s = %lX\n",
sDictLoopKey(dlLoop),
PDictLoopData(dlLoop) ));
}
}
LOOPOVERALL( aAtom, PROPERS, a1, ATOM, lTemp ) {
LoopGetTorsion( &lTemp, &a1, &a2, &a3, &a4 );
VP0(( "TORSION: %s - %s - %s - %s\n",
sContainerFullDescriptor((CONTAINER)a1,s1),
sContainerFullDescriptor((CONTAINER)a2,s2),
sContainerFullDescriptor((CONTAINER)a3,s3),
sContainerFullDescriptor((CONTAINER)a4,s4) ));
}
/*
* ListDescribe
*
* Author: Christian Schafmeister (1991)
*
* Fill the string with a description of the list.
* It is the callers responsibility to ensure that
* the string is long enough to store the description.
*/
void
ListDescribe( LIST lList )
{
OBJEKT oObj;
int iSize;
LISTLOOP llL;
iSize = iCollectionSize(lList);
VP0(( "List size=%d\n", iSize ));
llL = (LISTLOOP)PCollectionLoop( (COLLECTION)lList );
if ( llL == NULL )
return;
while ( (oObj = oCollectionNext( (COLLECTION)lList, (GENP *)&llL ))
!= NULL ) {
Describe( oObj );
}
VP0(( "--End of list\n" ));
}
/*
* XAUEPrintAllInternals
*
* Author: Christian Schafmeister (1991)
*
* List all of the bonds, angles, and torsions that are on the
* selected ATOMs.
*/
XtCallbackProc
XAUEPrintAllInternals( Widget wCur, caddr_t PAppData, caddr_t PArg )
{
UNIT uUnit;
ATOM aAtom;
LOOP lSelected;
LOOP lTemp;
ATOM a1, a2, a3, a4;
STRING s1, s2, s3, s4;
PushCurrentPrintSink(ziXAUEPrintSink(wCur));
DisplayerAccumulateUpdates();
/* Define where the output should go */
/* Get the UNIT being edited and put it */
/* in an ASSOC to pass it to the command */
/* handler */
VP0(( "--- Bonds, angles, torsions of selected ATOMs\n" ));
uUnit = zuXAUEUnit( wCur );
lSelected = lLoop((OBJEKT) uUnit, ATOMS );
LoopDefineVisibleAtoms( &lSelected, ATOMSELECTED );
while ( (aAtom = (ATOM)oNext(&lSelected)) ) {
VP0(( "Looking at atom: %s\n",
sContainerFullDescriptor((CONTAINER)aAtom,s1) ));
LOOPOVERALL( aAtom, BONDS, a1, ATOM, lTemp ) {
LoopGetBond( &lTemp, &a1, &a2 );
VP0(( "BOND: %s - %s\n",
sContainerFullDescriptor((CONTAINER)a1,s1),
sContainerFullDescriptor((CONTAINER)a2,s2) ));
}
LOOPOVERALL( aAtom, ANGLES, a1, ATOM, lTemp ) {
LoopGetAngle( &lTemp, &a1, &a2, &a3 );
VP0(( "ANGLE: %s - %s - %s\n",
sContainerFullDescriptor((CONTAINER)a1,s1),
sContainerFullDescriptor((CONTAINER)a2,s2),
sContainerFullDescriptor((CONTAINER)a3,s3) ));
}
/*
* XAHPTPopupTable (X, Athena, HydrogenBond Parameter Table)
*
* Popup a table for editing the parameter files.
* Register the callback to be called when the TABLE
* is destroyed.
*/
void
XAHPTPopupTable( Widget wCreated, Widget wWidget, PARMSET psParmSet,
VFUNCTION fCallback )
{
HBONDPARMTABLEt *hptPNew;
int iCount;
/* First create a place to put the PARM TABLE data */
MALLOC( hptPNew, HBONDPARMTABLEt*, sizeof(HBONDPARMTABLEt) );
hptPNew->fDestroyCallback = fCallback;
hptPNew->wTop = wWidget;
hptPNew->psParmSet = psParmSet;
/* First create the table for the PARM TABLE */
iCount = iParmSetTotalHBondParms( psParmSet );
XATPopupTable(
wCreated,
wWidget,
"hParmTableShell",
5, iCount,
"hParmRow",
"hParmAddRow",
zcPXAHPTGetElement,
zcPXAHPTVerifyElement,
zcPXAHPTVerifyRow,
zXAHPTAcceptRow,
NULL,
NULL,
zXAHPTDestroyTable,
0,
(GENP)hptPNew );
if ( !iCount ) {
VP0(( "There are no Hydrogen Bond parameters in this PARMSET.\n"));
VP0(("You may add some using the menu if you wish.\n" ));
}
}
OBJEKT AMBER_add_source(char *filename)
{
FILE *fCmds;
fCmds = FOPENCOMPLAIN( filename, "r" );
if ( fCmds != NULL )
{
if ( bINPUTMAXDEPTH() ) {
VP0(( "Source commands are nested too deep!\n" ));
} else {
/* Push the file onto the input file stack. The main */
/* parsing routine will continue parsing until there are */
/* no more files on the input file stack. */
VP0(( "----- Source: %s\n", GsBasicsFullName ));
INPUTPUSHFILE( fCmds );
VP0(( "----- Source of %s done\n", GsBasicsFullName ));
}
}
return(NULL);
}
/*
* ResidueCheck
*
* Author: Christian Schafmeister (1991)
*
* Check the RESIDUE and its contents as the whether or
* not calculations can be run on it.
*
* Arguments:
* rRes - Residue to check.
* iPErrors - Add the number of errors found.
* iPWarnings - Add the number of warnings found.
*/
void
ResidueCheck( RESIDUE rRes, int *iPErrors, int *iPWarnings )
{
LOOP lContents;
CONTAINER cCont;
STRING sTemp;
/* Print a warning if the residue is an unknown one */
if ( bResidueFlagsSet( rRes, RESIDUEUNKNOWN ) ) {
(*iPWarnings)++;
VP0(( "Warning: Unknown residue: %s\n",
sContainerFullDescriptor( (CONTAINER)rRes, sTemp ) ));
}
lContents = lLoop( (OBJEKT)rRes, DIRECTCONTENTS );
while ( cCont = (CONTAINER)oNext(&lContents) ) {
ContainerCheck( cCont, iPErrors, iPWarnings );
}
}
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));
}
/*
* zXABPTAcceptRow
*
* Accept/update table. Caller must check row 1st.
*/
static void
zXABPTAcceptRow( TABLE tTable, int iRow, STRING col[])
{
double dKb, dR0;
PARMSET psParmSet;
BONDPARMTABLEt *bptPCur;
bptPCur = (BONDPARMTABLEt*)PXATClientPointer(tTable);
psParmSet = bptPCur->psParmSet;
/*
* convert the numeric fields
*/
bStringToDouble( col[2], &dKb);
bStringToDouble( col[3], &dR0);
/*
* add or update row
*/
if ( iRow > iParmSetTotalBondParms( psParmSet ) )
DFATAL(( "programming err 1 in zXABPTAcceptRow\n" ));
if ( iRow == iParmSetTotalBondParms( psParmSet ) ) {
/*
* need to add row to table
*/
VP0(( "Adding bond parameter %s-%s.\n", col[0], col[1] ));
if ( iRow != iParmSetAddBond( psParmSet, col[0], col[1],
dKb, dR0, col[4] ) )
DFATAL(( "programming err 2 in zXABPTAcceptRow\n" ));
} else {
/*
* update row in place
*/
ParmSetUpdateBond( psParmSet, iRow, col[0], col[1], &dKb, &dR0, col[4]);
}
}
/* 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");
}
}
/*
* ResidueDescribe
*
* Author: Christian Schafmeister (1991)
*
* Call the specific routine for the class to print a description
* of the RESIDUE to the file fOut.
*
* Arguments:
* oObject - The object to describe.
*
*/
void
ResidueDescribe( RESIDUE rResidue )
{
int i;
LOOP lContents;
OBJEKT oObj;
STRING sTemp;
VP0(( "RESIDUE name: %s\n", rResidue->cHeader.sName ));
if ( bResidueFlagsSet( rResidue, RESIDUEUNKNOWN ) )
VP0(( "!!!This is an unknown residue!\n" ));
VP0(( "RESIDUE sequence number: %d\n",
iContainerSequence(rResidue) ));
VP0(( "RESIDUE PDB sequence number: %d\n",
iResiduePdbSequence(rResidue) ));
VP0(( "Type: %s\n",
sResidueTypeNameFromChar(cResidueType(rResidue)) ));
if ( cResidueType(rResidue) == RESTYPESOLVENT ) {
VP0(( "Solvent imaging atom: " ));
if ( aResidueImagingAtom(rResidue) == NULL ) {
VP0(( "None.\n" ));
} else {
VP0(( "%s\n",
sContainerDescriptor((CONTAINER)aResidueImagingAtom(rResidue),sTemp) ));
}
}
VP0(( "Connection atoms:\n" ));
for ( i=0; i<MAXCONNECT; i++ ) {
if ( bResidueConnectUsed(rResidue,i) ) {
VP0(( " Connect atom %d: %s\n", i,
sContainerDescriptor( (CONTAINER)rResidue->aaConnect[i], sTemp ) ));
}
}
if ( rResidue->vaImpropers ) {
VP0(( "No improper torsions\n" ));
} else {
VP0(( "Improper torsions:\n" ));
}
BasicsResetInterrupt();
VP0(( "Contents: \n" ));
lContents = lLoop( (OBJEKT)rResidue, DIRECTCONTENTS );
while ( oObj = oNext(&lContents ) ) {
VP0(( "%s\n", sContainerDescriptor( (CONTAINER)oObj, sTemp ) ));
if ( bBasicsInterrupt() ) {
BasicsResetInterrupt();
VP0(( "Interrupted\n" ));
break;
}
}
}
