/*
* 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" ));
}
}
}
}
