AddNTerHs.c

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

   \file       AddNTerHs.c
   
   \version    V1.11
   \date       23.06.15
   \brief      Routines to add N-terminal hydrogens and C-terminal
               oxygens.
   
   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1994-2014
   \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:
   ============


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

   Usage:
   ======

   int AddNTerHs(PDB **ppdb, BOOL Charmm)

   This routine is used to generate a set of N-terminal hydrogens.
   By default GROMOS naming is used; the Charmm flag changes this to
   Charmm format in which case an extra NTER residue will be created.
   Any pre-existing backbone H will be removed. Typically this
   routine would be called after calling HAddPDB()

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

   Revision History:
   =================
-  V1.0  24.08.94 Original    By: ACRM
-  V1.1  05.10.94 Removed unused variables
-  V1.2  12.11.96 If any of the antecedant coordinates are undefined, set
                  the terminal oxygen to NULL coordinates
-  V1.3  13.11.96 Also checks for missing CA,C and O1 records
-  V1.4  30.05.02 Changed PDB field from 'junk' to 'record_type'
-  V1.5  06.02.03 Handles atnam_raw
-  V1.6  03.06.05 Handles altpos
-  V1.7  04.02.14 Use CHAINMATCH By: CTP
-  V1.8  07.07.14 Use bl prefix for functions By: CTP
-  V1.9  17.02.15 Handles element and segid  By: ACRM
-  V1.10 05.03.15 Replaced blFindEndPDB() with blFindNextResidue()
-  V1.11 23.06.15 Added CLEAR_PDB() calls

*************************************************************************/
/* Doxygen
   -------
   #GROUP    Handling PDB Data
   #SUBGROUP Modifying the structure
   #FUNCTION  blAddNTerHs()
   Adds hydrogens onto the N-termini
*/
/************************************************************************/
/* Includes
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>

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

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

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

/************************************************************************/
/* Prototypes
*/
static PDB *KillNTerH(PDB *pdb);
static int doAddGromosNTer(PDB **ppdb, PDB *nter);
static int doAddCharmmNTer(PDB **ppdb, PDB *nter);

/************************************************************************/
/*>int blAddNTerHs(PDB **ppdb, BOOL Charmm)
   ----------------------------------------
*//**

   \param[in,out] **ppdb      Pointer to pointer to PDB linked list
   \param[in]     Charmm      Do Charmm style Nter
   \return                    Number of hydrogens added

   Adds hydrogens onto the N-termini

-  23.08.94 Original    By: ACRM
-  04.02.14 Use CHAINMATCH By: CTP
-  07.07.14 Use bl prefix for functions By: CTP
-  23.06.15 Added CLEAR_PDB() calls  By: ACRM
*/
int blAddNTerHs(PDB **ppdb, BOOL Charmm)
{
   PDB  *p;
   char chain[8] = "-";
   int  nhyd  = 0;
   
   for(p = *ppdb; p!=NULL; NEXT(p))
   {
      if(!CHAINMATCH(p->chain,chain))
      {
         strcpy(chain,p->chain);

         /* Kill the H if there is one. Makes the (safe...) assumption 
            that the H won't be the first atom (i.e. ignore the return)
         */
         KillNTerH(p);

         if(Charmm)
            nhyd += doAddCharmmNTer(ppdb, p);
         else
            nhyd += doAddGromosNTer(ppdb, p);
      }
   }
   
   return(nhyd);
}

/************************************************************************/
/*>static PDB *KillNTerH(PDB *pdb)
   -------------------------------
*//**

   \param[in,out] *pdb      PDB linked list
   \return                  New start of linked list

   Remove the backbone hydrogen from Nter residue

-  23.08.94 Original    By: ACRM
-  05.03.15 Replaced blFindEndPDB() with blFindNextResidue()
*/
static PDB *KillNTerH(PDB *pdb)
{
   PDB *p,
       *end,
       *prev = NULL;

   end = blFindNextResidue(pdb);
   
   for(p=pdb; p!=end; NEXT(p))
   {
      if(!strncmp(p->atnam,"H   ",4))
      {
         if(prev==NULL)         /* Is the first item in the list        */
         {
            prev = p->next;
            blDeleteAtomConects(p);
            free(p);
            return(prev);
         }
         else                   /* Is NOT the first item in the list    */
         {
            prev->next = p->next;
            blDeleteAtomConects(p);
            free(p);
            return(pdb);
         }
      }
      prev = p;
   }
   return(pdb);
}


/************************************************************************/
/*>static int doAddGromosNTer(PDB **ppdb, PDB *nter)
   -------------------------------------------------
*//**

   \param[in,out] **ppdb     Pointer to pointer to PDB linked list
   \param[in]     *nter      Pointer to an N-terminus
   \return                   Number of Hs added (0 if error)

   Does the actual work of adding the hydrogens onto an N terminus

-  23.08.94 Original    By: ACRM
-  24.08.94 Set B-values of Hs to 20.0
-  05.10.94 Removed unused variables
-  06.02.03 Handles atnam_raw
-  03.06.05 Handles altpos
-  17.02.15 Handles element and segid
*/
static int doAddGromosNTer(PDB **ppdb, PDB *nter)
{
   COOR coor[3];
   PDB  *prev = NULL,
        *H1, *H2, *H3;

   /* If not start of list find pointer to previous record              */
   if(*ppdb != nter)
   {
      for(prev = *ppdb; prev->next != nter; NEXT(prev));
   }

   if(blCalcTetraHCoords(nter, coor))
   {
      /* Initialise some space to store the 3 extra hydrogens           */
      INIT(H1, PDB);
      INIT(H2, PDB);
      INIT(H3, PDB);
      if(H1==NULL || H2==NULL || H3==NULL) return(0);
      
      CLEAR_PDB(H1);   /* 23.06.15                                      */
      CLEAR_PDB(H2);
      CLEAR_PDB(H3);

      /* Initialise the hydrogens with the res info, etc.               */
      blCopyPDB(H1, nter);
      blCopyPDB(H2, nter);
      blCopyPDB(H3, nter);
      H1->bval = H2->bval = H3->bval = (REAL)20.0;
      strcpy(H1->element," H");                    /* 17.02.15          */
      strcpy(H2->element," H");                    /* 17.02.15          */
      strcpy(H3->element," H");                    /* 17.02.15          */
      H1->formal_charge = 0;                       /* 17.02.15          */
      H2->formal_charge = 0;                       /* 17.02.15          */
      H3->formal_charge = 0;                       /* 17.02.15          */
      
      /* Link these extra records into the linked list                  */
      H3->next   = nter->next;
      H1->next   = H2;
      H2->next   = nter;
      nter->next = H3;

      /* Set the coordinates                                            */
      H1->x = coor[0].x;
      H1->y = coor[0].y;
      H1->z = coor[0].z;
      strcpy(H1->atnam, "H1  ");
      strcpy(H1->atnam_raw, " H1 ");
      H1->altpos = ' ';                   /* 03.06.05                   */
      
      H2->x = coor[1].x;
      H2->y = coor[1].y;
      H2->z = coor[1].z;
      strcpy(H2->atnam, "H2  ");
      strcpy(H2->atnam_raw, " H2 ");
      H2->altpos = ' ';                   /* 03.06.05                   */

      H3->x = coor[2].x;
      H3->y = coor[2].y;
      H3->z = coor[2].z;
      strcpy(H3->atnam, "H3  ");
      strcpy(H3->atnam_raw, " H3 ");
      H3->altpos = ' ';                   /* 03.06.05                   */

      /* Correctly link the new start into the whole linked list        */
      if(prev != NULL)
         prev->next = H1;
      else
         *ppdb = H1;
         
      return(3);
   }
   return(0);
}

/************************************************************************/
/*>static int doAddCharmmNTer(PDB **ppdb, PDB *nter)
   -------------------------------------------------
*//**

   \param[in,out] **ppdb     Pointer to pointer to PDB linked list
   \param[in]     *nter      Pointer to an N-terminus
   \return                   Number of Hs added (0 if error)

   Does the actual work of adding the hydrogens onto an N terminus

-  23.08.94 Original    By: ACRM
-  24.08.94 Set B-values of H3 to 20.0
-  05.10.94 Removed unused variables
-  06.02.03 Handles atnam_raw
-  03.06.05 Handles altpos
-  17.02.15 Handles element, segid and formal charge
*/
static int doAddCharmmNTer(PDB **ppdb, PDB *nter)
{
   COOR coor[3];
   PDB  *prev = NULL,
        *H1, *H2, *H3;

   /* If not start of list find pointer to previous record              */
   if(*ppdb != nter)
   {
      for(prev = *ppdb; prev->next != nter; NEXT(prev));
   }

   if(blCalcTetraHCoords(nter, coor))
   {
      /* Initialise some space to store the 3 extra hydrogens           */
      INIT(H1, PDB);
      INIT(H2, PDB);
      INIT(H3, PDB);
      if(H1==NULL || H2==NULL || H3==NULL) return(0);
      
      /* Initialise the hydrogens with the res info, etc.               */
      H1->atnum  = 9998;
      H1->resnum = 9999;
      H1->occ    = 1.0;
      H1->bval   = 20.0;
      strcpy(H1->resnam,      "NTER");
      strcpy(H1->atnam,       "HT1 ");
      strcpy(H1->atnam_raw,   " HT1");
      strcpy(H1->record_type, "ATOM  ");
      strcpy(H1->chain,       nter->chain);
      strcpy(H1->insert,      " ");
      H1->altpos = ' ';                            /* 03.06.05          */
      strcpy(H1->element,     " H");               /* 17.02.15          */
      strcpy(H1->segid,       nter->segid);        /* 17.02.15          */
      H1->formal_charge = 0;                       /* 17.02.15          */
      
      H2->atnum  = 9999;
      H2->resnum = 9999;
      H2->occ    = 1.0;
      H2->bval   = 20.0;
      strcpy(H2->resnam,      "NTER");
      strcpy(H2->atnam,       "HT2 ");
      strcpy(H2->atnam_raw,   " HT2");
      strcpy(H2->record_type, "ATOM  ");
      strcpy(H2->chain,       nter->chain);
      strcpy(H2->insert,      " ");
      H2->altpos = ' ';                            /* 03.06.05          */
      strcpy(H2->element,     " H");               /* 17.02.15          */
      strcpy(H2->segid,       nter->segid);        /* 17.02.15          */
      H2->formal_charge = 0;                       /* 17.02.15          */
      
      blCopyPDB(H3, nter);
      strcpy(H3->atnam,  "HT3 ");
      strcpy(H3->atnam_raw,   " HT3");
      H3->bval   = 20.0;
      H3->altpos = ' ';                            /* 03.06.05          */
      strcpy(H3->element," H");                    /* 17.02.15          */
      H3->formal_charge = 0;                       /* 17.02.15          */

      /* Link these extra records into the linked list                  */
      H3->next   = nter->next;
      H1->next   = H2;
      H2->next   = nter;
      nter->next = H3;

      /* Set the coordinates                                            */
      H1->x = coor[0].x;
      H1->y = coor[0].y;
      H1->z = coor[0].z;

      H2->x = coor[1].x;
      H2->y = coor[1].y;
      H2->z = coor[1].z;

      H3->x = coor[2].x;
      H3->y = coor[2].y;
      H3->z = coor[2].z;

      /* Change the name of the Nter nitrogen                           */
      strcpy(nter->atnam, "NT  ");
      strcpy(nter->atnam_raw, " NT ");

      /* Correctly link the new start into the whole linked list        */
      if(prev != NULL)
         prev->next = H1;
      else
         *ppdb = H1;
         
      return(3);
   }
   return(0);
}