/*
* XAUESelectRings
*
* Author: Christian Schafmeister (1991)
*
* Select all of the rings that have ATOMs selected.
*/
XtCallbackProc
XAUESelectRings( Widget wCur, caddr_t PAppData, caddr_t PArg )
{
LOOP lInternals, lAtoms;
int i;
INTERNAL iInt;
UNIT uUnit;
VARARRAY vaRings;
ATOM aFirst, aAtom;
Widget wTank;
PushCurrentPrintSink(ziXAUEPrintSink(wCur));
DisplayerAccumulateUpdates();
wTank = zwXAUETank( wCur );
uUnit = uTankUnit((TANK)wTank);
vaRings = vaVarArrayCreate(sizeof(INTERNAL));
/* Find all of the rings in the UNIT and search through the */
/* INTERNALs of the atom that the user selected for the INTERNAL */
/* that represents the smallest ring the ATOM is in */
GraphUtilFindAllSmallestRings(uUnit);
lAtoms = lLoop((OBJEKT) uUnit, ATOMS );
while ( (aFirst = (ATOM)oNext(&lAtoms)) ) {
if ( !bAtomFlagsSet( aFirst, ATOMSELECTED ) )
continue;
lInternals = lLoop((OBJEKT) aFirst, INTERNALS );
while ( (iInt = (INTERNAL)oNext(&lInternals)) ) {
if ( iInternalType(iInt) == INTERNALRING ) {
VarArrayAdd( vaRings, (GENP)&iInt );
}
}
}
for ( i=0; i<iVarArrayElementCount(vaRings); i++ ) {
iInt = *PVAI( vaRings, INTERNAL, i );
InternalRingLoopAtoms(iInt);
MESSAGE(( "Ring size: %d\n", iInternalRingSize(iInt) ));
while ( (aAtom = aInternalRingNextAtom(iInt)) ) {
MESSAGE(( "Selecting atom: %s\n", sAtomName(aAtom) ));
AtomSetFlags( aAtom, ATOMSELECTED );
}
}
lAtoms = lLoop((OBJEKT) uUnit, ATOMS );
BuildDestroyInternals(&lAtoms);
VarArrayDestroy( &vaRings );
TankRedisplayUnit((TANK)wTank);
DisplayerReleaseUpdates();
PopCurrentPrintSink();
return NULL;
}
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);
}
/*
* XAUEHideAllButSelection
*
* Author: Christian Schafmeister (1991)
*/
XtCallbackProc
XAUEHideAllButSelection( Widget wCur, caddr_t PAppData, caddr_t PArg )
{
LOOP lAtoms;
ATOM aAtom;
UNIT uUnit;
Widget wTank;
PushCurrentPrintSink(ziXAUEPrintSink(wCur));
DisplayerAccumulateUpdates();
wTank = zwXAUETank( wCur );
uUnit = uTankUnit((TANK)wTank);
if ( uUnit == NULL ) return NULL;
lAtoms = lLoop((OBJEKT) uUnit, ATOMS );
while ( (aAtom = (ATOM)oNext(&lAtoms)) ) {
if ( !bAtomFlagsSet( aAtom, ATOMSELECTED ) ) {
AtomSetFlags( aAtom, ATOMNOTDISPLAYED );
}
}
TankRedisplayUnit((TANK) wTank );
DisplayerReleaseUpdates();
PopCurrentPrintSink();
return NULL;
}
/*
* XAUESelectedAtomsFlipChirality
*
* Author: Christian Schafmeister (1991)
*/
XtCallbackProc
XAUESelectedAtomsFlipChirality( Widget wCur, caddr_t PAppData, caddr_t PArg )
{
UNIT uUnit;
LOOP lAtoms;
ATOM aAtom;
Widget wTank;
PushCurrentPrintSink(ziXAUEPrintSink(wCur));
DisplayerAccumulateUpdates();
wTank = zwXAUETank( wCur );
uUnit = uTankUnit((TANK)wTank);
if ( uUnit == NULL ) return(NULL);
lAtoms = lLoop((OBJEKT) uUnit, ATOMS );
while ( (aAtom = (ATOM)oNext(&lAtoms)) ) {
if ( bAtomFlagsSet( aAtom, ATOMSELECTED ) ) {
bBuildFlipChiralityFor( uUnit, aAtom );
}
}
TankRedisplayUnit((TANK) wTank );
DisplayerReleaseUpdates();
PopCurrentPrintSink();
return NULL;
}
/*
* XAUEMarkBuilt
*
* Author: Christian Schafmeister (1991)
*/
XtCallbackProc
XAUEMarkBuilt( Widget wCur, caddr_t PAppData, caddr_t PArg )
{
UNIT uTemp;
LOOP lAtoms;
Widget wTank;
ATOM aAtom;
PushCurrentPrintSink(ziXAUEPrintSink(wCur));
DisplayerAccumulateUpdates();
wTank = zwXAUETank( wCur );
uTemp = uTankUnit((TANK)wTank);
lAtoms = lLoop((OBJEKT) uTemp, ATOMS );
while ( (aAtom = (ATOM)oNext(&lAtoms)) ) {
if ( bAtomFlagsSet( aAtom, ATOMSELECTED ) ) {
AtomResetFlags( aAtom, ATOMPOSITIONDRAWN|ATOMNEEDSBUILD );
AtomSetFlags( aAtom, ATOMPOSITIONKNOWN );
}
}
TankRedisplayUnit((TANK)wTank);
DisplayerReleaseUpdates();
PopCurrentPrintSink();
return NULL;
}
/*
* XAUESelectMolecules
*
* Author: Christian Schafmeister (1991)
*
* Select all of the MOLECULEs that have ATOMs selected.
*/
XtCallbackProc
XAUESelectMolecules( Widget wCur, caddr_t PAppData, caddr_t PArg )
{
UNIT uUnit;
LOOP lAtoms, lSpan;
ATOM aFirst, aAtom;
Widget wTank;
PushCurrentPrintSink(ziXAUEPrintSink(wCur));
DisplayerAccumulateUpdates();
wTank = zwXAUETank( wCur );
uUnit = uTankUnit((TANK)wTank);
if ( uUnit == NULL ) return NULL;
/* First turn off the ATOMTOUCHED flags for all ATOMs */
ContainerResetAllAtomsFlags((CONTAINER) uUnit, ATOMTOUCHED );
/* Look over all the ATOMs that are selected and select */
/* all of the ATOMs within the RESIDUEs that they are */
/* part of. Use the ATOMTOUCHED to prevent duplicating */
/* work. */
lAtoms = lLoop((OBJEKT) uUnit, ATOMS );
while ( (aFirst = (ATOM)oNext(&lAtoms)) ) {
if ( bAtomFlagsSet( aFirst, ATOMSELECTED ) &&
!bAtomFlagsSet( aFirst, ATOMTOUCHED ) ) {
lSpan = lLoop((OBJEKT) aFirst, SPANNINGTREE );
while ( (aAtom = (ATOM)oNext(&lSpan)) ) {
AtomSetFlags( aAtom, ATOMSELECTED|ATOMTOUCHED );
}
}
}
TankRedisplayUnit((TANK) wTank );
DisplayerReleaseUpdates();
PopCurrentPrintSink();
return NULL;
}
/*
* SelectMoleculeWithAtom
*
* Author: Christian Schafmeister (1991)
*
* Select the molecule that contains the ATOM.
* Do this by generating a spanning tree.
*/
void
SelectMoleculeWithAtom( UNIT uUnit, ATOM aAtom, BOOL bOn )
{
LOOP lSpan;
lSpan = lLoop( (OBJEKT)aAtom, SPANNINGTREE );
while ( (aAtom = (ATOM)oNext(&lSpan)) ) {
if ( bOn ) AtomSetFlags( aAtom, ATOMSELECTED );
else AtomResetFlags( aAtom, ATOMSELECTED );
}
}
/*
* SelectResidueWithAtom
*
* Author: Christian Schafmeister (1991)
*
* Select the RESIDUE that contains the ATOM.
*/
void
SelectResidueWithAtom( UNIT uUnit, ATOM aAtom, BOOL bOn )
{
LOOP lAtoms;
ATOM aCur;
lAtoms = lLoop( (OBJEKT)cContainerWithin((CONTAINER)aAtom), ATOMS );
while ( (aCur = (ATOM)oNext(&lAtoms)) ) {
if ( bOn ) AtomSetFlags( aCur, ATOMSELECTED );
else AtomResetFlags( aCur, ATOMSELECTED );
}
}
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++;
}
}
/*
* SelectEverything
*
* Author: Christian Schafmeister (1991)
*
* Select all of the ATOMs in the UNIT.
*/
void
SelectEverything( UNIT uUnit, BOOL bOn )
{
LOOP lAtoms;
ATOM aAtom;
MESSAGE(( "Selecting everything. Select=%s\n", sBOOL(bOn) ));
lAtoms = lLoop( (OBJEKT)uUnit, ATOMS );
while ( (aAtom = (ATOM)oNext(&lAtoms)) ) {
if ( bOn ) AtomSetFlags( aAtom, ATOMSELECTED );
else AtomResetFlags( aAtom, ATOMSELECTED );
}
}
/*
* 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;
}
}
}
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);
}
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);
}
/*
* 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 );
}
}
/*
* 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) ));
}
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);
}
/*
* bSelectChainBetween
*
* Author: Christian Schafmeister (1991)
*
* Select the shortest chain of ATOMs between aA and aB.
* Return FALSE if no chain was found.
*/
BOOL
bSelectChainBetween( UNIT uUnit, ATOM aA, ATOM aB, BOOL bOn )
{
LOOP lSpan;
ATOM aCur;
/* Span out from aA looking for aB */
lSpan = lLoop( (OBJEKT)aA, SPANNINGTREE );
while ( (aCur = (ATOM)oNext(&lSpan)) ) {
if ( aCur == aB ) break;
}
if ( aCur == NULL ) return(FALSE);
/* Select the chain back to aA */
for ( aCur = aB; aCur; aCur = aAtomBackSpan(aCur) ) {
if ( bOn ) AtomSetFlags( aCur, ATOMSELECTED );
else AtomResetFlags( aCur, ATOMSELECTED );
}
return(TRUE);
}
/*
* XAUEAddHydrogensBuildExternals
*
* Author: Christian Schafmeister (1991)
*
* Add missing hydrogens and build the external coordinates
* for the UNIT.
*/
XtCallbackProc
XAUEAddHydrogensAndBuildExternals( Widget wCur, caddr_t PAppData, caddr_t PArg )
{
LOOP lAtom, lSpan;
ATOM aAtom, aStart;
UNIT uUnit;
Widget wTank;
int iDum;
PushCurrentPrintSink(ziXAUEPrintSink(wCur));
DisplayerAccumulateUpdates();
wTank = zwXAUETank( wCur );
uUnit = uTankUnit((TANK)wTank);
if ( uUnit == NULL ) return NULL;
MESSAGE(( "Building external coordinates for the UNIT\n" ));
/* Add hydrogens */
ModelAddHydrogens( uUnit );
/* Try to build geometries for simple rings */
BuildInternalsForSimpleRings( uUnit );
/* Assign internal coordinates for all internals that */
/* include atoms that need building */
lAtom = lLoop((OBJEKT) uUnit, ATOMS );
BuildInternalsUsingFlags( &lAtom, ATOMPOSITIONDRAWN, 0,
ATOMNEEDSBUILD,
ATOMPOSITIONDRAWN );
/* Build spanning trees for all atoms that need building */
/* and build external coordinates for those atoms */
lAtom = lLoop((OBJEKT) uUnit, ATOMS );
while ( (aAtom = (ATOM)oNext(&lAtom)) ) {
if ( bAtomFlagsSet( aAtom, ATOMNEEDSBUILD ) ) {
/* Look for a collision with an ATOM that has */
/* already been built */
/* Then start building from there */
lSpan = lLoop((OBJEKT) aAtom, SPANNINGTREE );
LoopDefineVisibleAtoms( &lSpan, ATOMNEEDSBUILD );
while ( oNext(&lSpan) );
if ( iLoopInvisibleCollisionCount(&lSpan) > 0 ) {
aStart = aLoopLastCollisionAtom(&lSpan);
lSpan = lLoop((OBJEKT) aStart, SPANNINGTREE );
} else {
lSpan = lLoop((OBJEKT) aAtom, SPANNINGTREE );
}
LoopDefineVisibleAtoms( &lSpan, ATOMNEEDSBUILD );
iDum = 0; /* for purify */
BuildExternalsUsingFlags( &lSpan, ATOMNEEDSBUILD, 0,
ATOMPOSITIONKNOWN,
ATOMNEEDSBUILD,
&iDum, &iDum, &iDum, TRUE );
}
}
/* Destroy all of the INTERNALs */
lAtom = lLoop((OBJEKT) uUnit, ATOMS );
BuildDestroyInternals( &lAtom );
TankRedisplayUnit((TANK) wTank );
DisplayerReleaseUpdates();
PopCurrentPrintSink();
return NULL;
}
/*
* 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" ));
}
}
}
}
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);
}
}
VP1(( "There is no atom in residue: %s with the name: %s.\n" ));
VP1(( "--- No bond could be made to the missing atom.\n" ));
}
}
}
}
/* Build the coordinates for ATOMs that do not have them */
BuildFixInternals( rNew );
/* Loop through all ATOMs looking for those that */
/* do not have positions known and build externals */
/* for them and neighbors that are bonded to them */
lAtoms = lLoop( (OBJEKT)rNew, ATOMS );
while ( aAtom = (ATOM)oNext(&lAtoms) ) {
if ( !bAtomFlagsSet( aAtom, ATOMPOSITIONKNOWN ) ) {
lSpan = lLoop( (OBJEKT)aAtom, SPANNINGTREE );
LoopDefineInvisibleAtoms( &lSpan, ATOMPOSITIONKNOWN );
/* Look for a collision with an ATOM whos */
/* ATOMPOSITIONKNOWN flag is set */
aSpan = NULL;
while ( aTemp = (ATOM)oNext(&lSpan) ) {
if ( aSpan == NULL ) aSpan = aTemp;
if ( aLoopLastCollisionAtom(&lSpan) != NULL ) {
aSpan = aLoopLastCollisionAtom(&lSpan);
break;
}
}
