/*>BOOL blAreResiduePointersBonded(PDB *res1, PDB *res2, REAL tol)
---------------------------------------------------------------
*//**
\param[in] *res1 Start of first residue
\param[in] *res2 Start of second residue
\param[in] tol Tolerance for distances
\return Are they bonded
Tests whether two residue are bonded using pointers to start of
residues
- 23.06.15 Original By: ACRM
*/
BOOL blAreResiduePointersBonded(PDB *res1, PDB *res2, REAL tol)
{
PDB *res1next,
*res2next,
*p,
*q;
if((res1 != NULL) && (res2 != NULL))
{
/* Find the following residues */
res1next = blFindNextResidue(res1);
res2next = blFindNextResidue(res2);
/* Step through the atoms in each residue and see if they are
bonded
*/
for(p=res1; p!=res1next; NEXT(p))
{
for(q=res2; q!=res2next; NEXT(q))
{
if(blIsBonded(p, q, tol))
return(TRUE);
}
}
}
return(FALSE);
}
/*>PDB *blFindAtomWildcardInRes(PDB *pdb, char *pattern)
-----------------------------------------------------
*//**
\param[in] *pdb Pointer to start of a residue
\param[in] *pattern Atom name pattern to find
\return Pointer to requested atom or NULL if not
found.
Finds an atom within the residue given as a PDB pointer. Allows
single character wildcards. Thus ?G? maybe used for any atom at the
gamma position.
Returns the first atom which matches
- 27.08.96 Original By: ACRM
- 07.07.14 Use bl prefix for functions By: CTP
*/
PDB *blFindAtomWildcardInRes(PDB *pdb, char *pattern)
{
PDB *p, *pNext;
int i;
BOOL ok;
pNext = blFindNextResidue(pdb);
for(p=pdb; p!=pNext; NEXT(p))
{
if(!strncmp(p->atnam,pattern,4))
return(p);
ok = TRUE;
for(i=0; i<4; i++)
{
if((pattern[i] != p->atnam[i]) && pattern[i] != '?')
{
ok = FALSE;
break;
}
}
if(ok)
return(p);
}
return(NULL);
}
/*>BOOL blBuildConectData(PDB *pdb, REAL tol)
------------------------------------------
*//**
\param[in,out] *pdb PDB linked list
\param[in] tol Tolerence for distance between atoms
\return Were all CONECTs added OK
Deletes all current connectivity data and rebuilds it using covalent
radii data. A return of FALSE indicates that there were too many
connections for an atom. If this happens, MAXCONECT needs to be
increased in pdb.h
- 19.02.15 Original By: ACRM
- 26.02.15 Added tol paramater
- 12.05.15 Conects are built involving backbone C and N if either atom
is a HETATM
*/
BOOL blBuildConectData(PDB *pdb, REAL tol)
{
PDB *p,
*q,
*res,
*nextRes;
BOOL retval=TRUE;
/* Clear all current connect data */
for(p=pdb; p!=NULL; NEXT(p))
{
p->nConect = 0;
}
for(res=pdb; res!=NULL; res=nextRes)
{
nextRes = blFindNextResidue(res);
/* Check for any HETATM connections within this residue */
for(p=res; p!=nextRes; NEXT(p))
{
for(q=p->next; q!=nextRes; NEXT(q))
{
if(!strncmp(p->record_type, "HETATM", 6) ||
!strncmp(q->record_type, "HETATM", 6))
{
if(blIsBonded(p, q, tol))
{
if(!blAddConect(p,q))
retval=FALSE;
}
}
}
}
/* Check for connections between residues which don't involve backbone
C or N, or do involve HETATMS
*/
for(p=res; p!=nextRes; NEXT(p))
{
for(q=nextRes; q!=NULL; NEXT(q))
{
if(strncmp(p->atnam, "C ", 4) ||
strncmp(q->atnam, "N ", 4) ||
!strncmp(p->record_type, "HETATM", 6) ||
!strncmp(q->record_type, "HETATM", 6))
{
if(blIsBonded(p, q, tol))
{
if(!blAddConect(p,q))
retval=FALSE;
}
}
}
}
}
return(retval);
}
/*>BOOL blRepOneSChain(PDB *pdb, char *ResSpec, char aa, char *ChiTable,
char *RefCoords)
---------------------------------------------------------------------
*//**
\param[in,out] *pdb PDB linked list to modify
\param[in] *ResSpec Residue spec for residue to replace in the
format [c]nnn[i]
\param[in] aa The 1-letter code for the new sidechain
\param[in] *ChiTable The equivalent Chi table
\param[in] *RefCoords The reference coordinates file
\return Success?
Replace a single sidechain. Takes a PDB linked list, a residues
specfication (in the form [c]nnn[i] where [c] is an optional chain
name, nnn is a residue number and [i] is an optional insert code)
and a 1-letter code of the required sidechain and does a simple
maximum overlap replacement of the sidechain. Also requires filenames
of the two datafiles.
- 12.08.96 Original based on RepSChain()
- 15.08.96 Removed unused variables
- 07.07.14 Use bl prefix for functions By: CTP
- 23.02.15 Modified for new blRenumAtomsPDB() which takes an offset
*/
BOOL blRepOneSChain(PDB *pdb, char *ResSpec, char aa, char *ChiTable,
char *RefCoords)
{
PDB *ResStart, /* Start of residue */
*NextRes; /* Start of next residue */
BOOL noenv = FALSE; /* Flag for no env. var. found */
if(sFirstCall)
{
FILE *fp_ChiTable;
/* Allocate 2D array for equivalent torsions */
if((sChiTab = (int **)blArray2D(sizeof(int), NUMAAKNOWN, NUMAAKNOWN))
== NULL)
return(FALSE);
/* Open files */
if((fp_ChiTable = blOpenFile(ChiTable,"DATADIR","r",&noenv)) == NULL)
{
if(noenv)
{
sprintf(gRSCError,"DATADIR environment variable not set\n");
}
else
{
sprintf(gRSCError,"Unable to open chi link table: %s\n",
ChiTable);
}
return(FALSE);
}
if((sFp_RefCoords = blOpenFile(RefCoords,"DATADIR","r",&noenv)) ==
NULL)
{
if(noenv)
{
sprintf(gRSCError,"DATADIR environment variable not set\n");
}
else
{
sprintf(gRSCError,"Unable to open reference coordinates: \
%s\n", RefCoords);
}
return(FALSE);
}
/* Read the equivalent chi table and the atom table */
ReadChiTable(fp_ChiTable, sChiTab);
/* Close the table files */
fclose(fp_ChiTable);
sFirstCall = FALSE;
}
/* Find the specified residue and the one following */
if((ResStart = blFindResidueSpec(pdb, ResSpec))==NULL)
{
sprintf(gRSCError,"Residue specification not in PDB list\n");
return(FALSE);
}
NextRes = blFindNextResidue(ResStart);
/* If there is a sequence mismatch, replace the residue */
if(aa != blThrone(ResStart->resnam))
{
if(DoReplace(ResStart, NextRes, aa, sChiTab, sFp_RefCoords) ==
NULL)
{
return(FALSE);
}
}
blRenumAtomsPDB(pdb, 1);
return(TRUE);
}
PDB *FindNextResidue(PDB *pdb)
{
DEPRECATED("FindNextResidue()","blFindNextResidue()");
return(blFindNextResidue(pdb));
}
PDB *FindEndPDB(PDB *start)
{
DEPRECATED("FindEndPDB()","blFindNextResidue()");
return(blFindNextResidue(start));
}
