SelAtPDB.c

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

   \file       SelAtPDB.c
   
   \version    V1.11
   \date       19.04.15
   \brief      Select a subset of atom types from a PDB linked list
   
   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1990-2015
   \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:
   ============


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

   Usage:
   ======

\code
   pdbout = blSelectAtomsPDBAsCopy(pdbin,nsel,sel,natom)
\endcode

   This routine takes a linked list of type PDB and returns a list
   containing only those atom types specfied in the sel array.

   \param[in]   pdbin        Input list
   \param[in]   nsel         Number of atom types to keep
   \param[in]   sel          List of atom types to keep
   \param[out]  natom        Number of atoms kept
   \return                   PDB output list

   To set up the list of atoms to keep, define an array of pointers 
   to char:
   e.g.     char *sel[10]

   Then define the atoms in the list thus:

            SELECT(sel[0],"N   ");
            SELECT(sel[1],"CA  ");
            SELECT(sel[2],"C   ");
            SELECT(sel[3],"O   ");

   The SELECT macro returns a character pointer which will be NULL if
   the allocation it performs fails.

   N.B. The routines are non-destructive; i.e. the original PDB linked 
   list is intact after the selection process

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

   Revision History:
   =================
-  V1.0  01.03.90 Original   By: ACRM
-  V1.1  28.03.90 Modified to match new version of pdb.h
-  V1.2  24.05.90 Fixed so the variables passed in as sel[] don't 
                  *have* to be 4 chars.
-  V1.3  17.05.93 Modified for book. Returns BOOL.
-  V1.4  09.07.93 Modified to return PDB pointer. Changed allocation 
                  scheme. Changed back to sel[] variables *must* be 4
                  chars.
-  V1.5  01.11.94 Added HStripPDB()
-  V1.6  26.07.95 Removed unused variables
-  V1.7  16.10.96 Added SelectCaPDB()
-  V1.8  04.02.09 SelectAtomsPDB(): Initialize q for fussy compliers
-  V1.9  07.07.14 Use bl prefix for functions By: CTP
-  V1.10 19.08.14 Renamed function to blSelectAtomsPDBAsCopy(). By: CTP
-  V1.11 19.04.15 Added call to blCopyConect()   By: ACRM

*************************************************************************/
/* Doxygen
   -------
   #GROUP    Handling PDB Data
   #SUBGROUP Manipulating the PDB linked list
   #FUNCTION  blSelectAtomsPDBAsCopy()
   Take a PDB linked list and returns a list containing only those atom 
   types specified in the sel array.
*/
/************************************************************************/
/* Includes
*/
#include <string.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>

#include "SysDefs.h"
#include "MathType.h"

#include "pdb.h"
#include "macros.h"

/************************************************************************/
/* Defines and macros
*/

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

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

/************************************************************************/
/*>PDB *blSelectAtomsPDBAsCopy(PDB *pdbin, int nsel, char **sel,
                               int *natom)
   -------------------------------------------------------------
*//**

   \param[in]     *pdbin      Input list
   \param[in]     nsel        Number of atom types to keep
   \param[in]     **sel       List of atom types to keep
   \param[out]    *natom      Number of atoms kept
   \return                    Output list

   Take a PDB linked list and returns a list containing only those atom 
   types specified in the sel array.

   To set up the list of atoms to keep, define an array of pointers 
   to char:
   e.g.     char *sel[10]
   Then define the atoms in the list thus:


            SELECT(sel[0],"N   ");
            SELECT(sel[1],"CA  ");
            SELECT(sel[2],"C   ");
            SELECT(sel[3],"O   ");

   Ensure the spaces are used!!

   N.B. The routine is non-destructive; i.e. the original PDB linked 
        list is intact after the selection process

-  01.03.90 Original    By: ACRM
-  28.03.90 Modified to match new version of pdb.h
-  24.05.90 Fixed so the variables passed in as sel[] don't 
            *have* to be 4 chars.
-  17.05.93 Modified for book. Returns BOOL.
-  09.07.93 Modified to return PDB pointer. Changed allocation 
            scheme. Changed back to sel[] variables *must* be 4
            chars.
-  04.02.09 Initialize q for fussy compliers
-  07.07.14 Use bl prefix for functions By: CTP
-  19.08.14 Renamed function to blSelectAtomsPDBAsCopy(). By: CTP
*/
PDB *blSelectAtomsPDBAsCopy(PDB *pdbin, int nsel, char **sel, int *natom)
{
   PDB   *pdbout  = NULL,
         *p,
         *q = NULL;
   int   i;
    
   *natom = 0;
   
   /* Step through the input PDB linked list                            */
   for(p=pdbin; p!= NULL; NEXT(p))
   {
      /* Step through the selection list                                */
      for(i=0; i<nsel; i++)
      {
         /* See if there is a match                                     */
         if(!strncmp(p->atnam,sel[i],4))
         {
            /* Alloacte a new entry                                     */
            if(pdbout==NULL)
            {
               INIT(pdbout, PDB);
               q = pdbout;
            }
            else
            {
               ALLOCNEXT(q, PDB);
            }
            
            /* If failed, free anything allocated and return            */
            if(q==NULL)
            {
               if(pdbout != NULL) FREELIST(pdbout,PDB);
               *natom = 0;
               return(NULL);
            }
            
            /* Increment atom count                                     */
            (*natom)++;
            
            /* Copy the record to the output list (sets ->next to NULL) */
            blCopyPDB(q, p);
            
            break;
         }
      }
   }

   /* Copy CONECT data                                                  */
   if(!blCopyConects(pdbout, pdbin))
   {
      FREELIST(pdbout, PDB);
      *natom = 0;
      return(NULL);
   }

   /* Return pointer to start of output list                            */
   return(pdbout);
}