GlyCB.c

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/************************************************************************/
/**

   \file       GlyCB.c
   
   \version    V1.1
   \date       07.07.14
   \brief      Add C-beta atoms to glycines as pseudo-atoms for use
               in orientating residues
   \copyright  (c) Dr. Andrew C. R. Martin, UCL, 2006-2014
   \author     Dr. Andrew C. R. Martin
   \par
               Institute of Structural & Molecular Biology,
               University College London,
               Gower Street,
               London.
               WC1E 6BT.
   \par
               andrew@bioinf.org.uk
               andrew.martin@ucl.ac.uk
               
**************************************************************************

   This code is NOT IN THE PUBLIC DOMAIN, but it may be copied
   according to the conditions laid out in the accompanying file
   COPYING.DOC.

   The code may be modified as required, but any modifications must be
   documented so that the person responsible can be identified.

   The code may not be sold commercially or included as part of a 
   commercial product except as described in the file COPYING.DOC.

**************************************************************************

   Description:
   ============

   Based on the code from HAddPDB.c adds a C-beta to one or all glycine
   residues.

**************************************************************************

   Usage:
   ======

**************************************************************************

   Revision History:
   =================
-  04.01.06 V1.0   Original  By: ACRM
-  07.07.14 V1.1   Use bl prefix for functions By: CTP

*************************************************************************/
/* Doxygen
   -------
   #GROUP    Handling PDB Data
   #SUBGROUP Modifying the structure
   #FUNCTION  blAddCBtoGly()
   Adds a CB atom to a glycine. This is used when one needs to orientate
   a residue in a common frame of reference which makes use of the CB.

   #FUNCTION  blAddCBtoAllGly()
   Adds a CB atom to all glycines in a PDB linked list. This is used 
   when one needs to orientate a residue in a common frame of reference 
   which makes use of the CB.

   #FUNCTION  blStripGlyCB()
   Removes all Glycine CB pseudo-atoms added by AddGlyCB()
*/
/************************************************************************/
/* Includes
*/
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>

#include "MathType.h"
#include "SysDefs.h"
#include "pdb.h"
#include "macros.h"

/************************************************************************/
/* Defines and macros
*/
#define BONDLEN 1.524
#define ALPHA   54.7

/************************************************************************/
/* Globals
*/

/************************************************************************/
/* Prototypes
*/

/************************************************************************/
/*>BOOL blAddCBtoGly(PDB *pdb)
   ---------------------------
*//**

   \param[in,out] *pdb     The PDB linked list for a Glycine
   \return                   Success?

   Adds a CB atom to a glycine. This is used when one needs to orientate
   a residue in a common frame of reference which makes use of the CB.

-  04.01.06 Original   By: ACRM
-  07.07.14 Use bl prefix for functions By: CTP
*/
BOOL blAddCBtoGly(PDB *pdb)
{
   PDB *n       = NULL,
       *ca      = NULL,
       *cb      = NULL,
       *c       = NULL,
       *o       = NULL;

   REAL x1,y1,z1,x2,y2,z2,x3,y3,z3,xnew1,ynew1,znew1,
        x21,y21,z21,r21,x23,y23,z23,r23,
        cosa,sina,
        xa,ya,za,xb,yb,zb,xs,ys,zs,
        xab,yab,zab,rab,
        xmin,ymin,zmin,
        xapb,yapb,zapb,rapb,
        xplus,yplus,zplus,
        BondLen = BONDLEN, 
        alpha = ALPHA * PI / 180.0;
/* REAL xnew2,ynew2,znew2;                                              */
   
   if(strncmp(pdb->resnam, "GLY", 3))
      return(FALSE);
   
   if((n  = blFindAtomInRes(pdb, "N"))==NULL)
      return(FALSE);
      
   if((ca = blFindAtomInRes(pdb, "CA"))==NULL)
      return(FALSE);
   if((c  = blFindAtomInRes(pdb, "C"))==NULL)
      return(FALSE);
   if((o  = blFindAtomInRes(pdb, "O"))==NULL)
      return(FALSE);

   x1 = n->x;
   y1 = n->y;
   z1 = n->z;
   
   x2 = ca->x;
   y2 = ca->y;
   z2 = ca->z;
   
   x3 = c->x;
   y3 = c->y;
   z3 = c->z;
   
   x21=x2-x1;
   y21=y2-y1;
   z21=z2-z1;
   r21=(REAL)sqrt((double)(x21*x21 + y21*y21 + z21*z21));

   x23=x2-x3;
   y23=y2-y3;
   z23=z2-z3;
   r23=(REAL)sqrt((double)(x23*x23 + y23*y23 + z23*z23));
    
   cosa=(REAL)cos((double)alpha);
   sina=(REAL)sin((double)alpha);

   xa=x21/r21;
   ya=y21/r21;
   za=z21/r21;
   xb=x23/r23;
   yb=y23/r23;
   zb=z23/r23;
   xab=xa-xb;
   yab=ya-yb;
   zab=za-zb;
   rab=(REAL)sqrt((double)(xab*xab+yab*yab+zab*zab));
   xmin=xab/rab;
   ymin=yab/rab;
   zmin=zab/rab;
   xapb=xa+xb;
   yapb=ya+yb;
   zapb=za+zb;
   rapb=(REAL)sqrt((double)(xapb*xapb+yapb*yapb+zapb*zapb));
   xplus=xapb/rapb;
   yplus=yapb/rapb;
   zplus=zapb/rapb;
   xs=yplus*zmin-zplus*ymin;
   ys=zplus*xmin-xplus*zmin;
   zs=xplus*ymin-yplus*xmin;
   xnew1=x2+BondLen*(cosa*xplus-sina*xs);
   ynew1=y2+BondLen*(cosa*yplus-sina*ys);
   znew1=z2+BondLen*(cosa*zplus-sina*zs);

   /* Create a PDB record and initialize it to be the same as the O     */
   if((cb = (PDB *)malloc(sizeof(PDB)))==NULL)
   {
      return(FALSE);
   }
   blCopyPDB(cb,o);
   /* Put it into the linked list after the backbone oxygen             */
   cb->next = o->next;
   o->next = cb;
   /* Change it to a CB                                                 */
   strcpy(cb->atnam, "CB  ");
   strcpy(cb->atnam_raw, " CB ");
   /* And set the coordinates                                           */
   cb->x = xnew1;
   cb->y = ynew1;
   cb->z = znew1;

/* This is the position of the hydrogen
   xnew2=x2+BondLen*(cosa*xplus+sina*xs);
   ynew2=y2+BondLen*(cosa*yplus+sina*ys);
   znew2=z2+BondLen*(cosa*zplus+sina*zs);
*/

   return(TRUE);
}


/************************************************************************/
/*>BOOL blAddCBtoAllGly(PDB *pdb)
   ------------------------------
*//**

   \param[in,out] *pdb     The PDB linked list
   \return                   Success?

   Adds a CB atom to all glycines in a PDB linked list. This is used 
   when one needs to orientate a residue in a common frame of reference 
   which makes use of the CB.

-  04.01.06 Original   By: ACRM
-  07.07.14 Use bl prefix for functions By: CTP
*/
BOOL blAddCBtoAllGly(PDB *pdb)
{
   PDB *p;
   
   for(p=pdb; p!=NULL; p=blFindNextResidue(p))
   {
      if(!strncmp(p->resnam, "GLY", 3))
      {
         if(!blAddCBtoGly(p))
            return(FALSE);
      }
   }
   return(TRUE);
}


/************************************************************************/
/*>PDB *blStripGlyCB(PDB *pdb)
   ---------------------------
*//**

   \param[in,out] *pdb     The PDB linked list
   \return                    The modified linked list

   Removes all Glycine CB pseudo-atoms added by AddGlyCB()
   The linked list is modified in-place, but the return value
   should be used in case the very first item in the linked list
   is a Gly-CB which will be removed by the code.

-  04.01.06 Original   By: ACRM
-  07.07.14 Use bl prefix for functions By: CTP
*/
PDB *blStripGlyCB(PDB *pdb)
{
   PDB *p,
       *prev = NULL;
   
   for(p=pdb; p!=NULL; )
   {
      if(!strncmp(p->resnam, "GLY", 3))
      {
         if(!strncmp(p->atnam, "CB  ", 4))
         {
            if(prev!=NULL)
            {
               prev->next = p->next;
               free(p);
               p=prev->next;
            }
            else
            {
               PDB *q;
               q=p;
               NEXT(p);
               free(q);
               pdb = p;
            }
         }
         else
         {
            prev = p;
            NEXT(p);
         }
      }
      else
      {
         prev=p;
         NEXT(p);
      }
   }
   return(pdb);
}