throne.c

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

   \file       throne.c
   
   \version    V1.9
   \date       07.07.14
   \brief      Convert between 1 and 3 letter aa codes
   
   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1993-2014
   \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:
   ======

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

   Revision History:
   =================
-  V1.0  29.09.92 Original    By: ACRM   
-  V1.1  11.03.94 Added PCA, ASX and GLX to translation table.
                  PCA translates to E
                  Added routines to handle asx/glx
-  V1.2  25.07.95 handles nucleic acids
                  Sets the gBioplibSeqNucleicAcid flag if it's a 
                  nucleic acid.
-  V1.3  08.03.07 Added PGA (Pyroglutamate) to translation table 
                  (same as PCA: pyrrolidone carboxylic acid).
                  Note that it isn't clear whether this should translate
                  to Glu or Gln
-  V1.4  21.07.08 Added CGN (5-OXO-PYRROLIDINE-2-CARBALDEHYDE) which
                  is again the same as PCA
-  V1.5  19.12.08 Corrected NUMAAKNOWN - wasn't looking at U or X as
                  these were > NUMAAKNOWN!
-  V1.6  04.02.09 onethr() was not properly working from end of list
                  for nucleic acids
-  V1.7  18.02.09 Fixed for new PDB files which have "  DT" etc for DNA
                  sequences
-  V1.8  30.01.14 Added pyrrolysine and selenocysteine to translation 
                  table. By: CTP
                  PYL translates to O, SEC translates to U.
-  V1.9  07.07.14 Use bl prefix for functions By: CTP

*************************************************************************/
/* Doxygen
   -------
   #GROUP    Handling Sequence Data
   #SUBGROUP Conversions
   #FUNCTION  blThrone()
   Converts 3-letter code to 1-letter code.
   Handles ASX and GLX as X

   #FUNCTION  blThronex()
   Converts 3-letter code to 1-letter code.
   Handles ASX and GLX as B and Z.

   #FUNCTION  blOnethr()
   Converts 1-letter code to 3-letter code (actually as 4 chars).
*/
/************************************************************************/
/* Includes
*/
#include <string.h>
#include "SysDefs.h"

/************************************************************************/
/* Defines and macros
*/
#define NUMAAKNOWN 39

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

/* N.B. The order in sTab1[] and sTab3[] must be the same and they must
   end with X/UNK.
   Also, nucleic acids must come *after* amino acids.
*/
/* Don't forget to fix NUMAAKNOWN if adding to this table!              */
static char sTab1[]    = {'A','C','D','E','F',
                          'G','H','I','K','L',
                          'M','N','P','Q','R',
                          'S','T','V','W','Y',
                          'E','B','Z','E','E',
                          'O','U',
                          'A','T','C','G','U','I',
                          'A','T','C','G','I','X'
                         };
/* Don't forget to fix NUMAAKNOWN if adding to this table!              */
static char sTab3[][8] = {"ALA ","CYS ","ASP ","GLU ","PHE ",
                          "GLY ","HIS ","ILE ","LYS ","LEU ",
                          "MET ","ASN ","PRO ","GLN ","ARG ",
                          "SER ","THR ","VAL ","TRP ","TYR ",
                          "PCA ","ASX ","GLX ","PGA ","CGN ",
                          "PYL ","SEC ",
                          "  A ","  T ","  C ","  G ","  U ","  I ",
                          " DA "," DT "," DC "," DG "," DI ","UNK "
                         };
/* Don't forget to fix NUMAAKNOWN if adding to this table!              */

BOOL gBioplibSeqNucleicAcid = FALSE;

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


/************************************************************************/
/*>char blThrone(char *three)
   --------------------------
*//**

   \param[in]     *three    Three letter code
   \return                    One letter code

   Converts 3-letter code to 1-letter code.
   Handles ASX and GLX as X
   
-  29.09.92 Original    By: ACRM
-  11.03.94 Modified to handle ASX and GLX in the tables
-  25.07.95 Added handling of gBioplibSeqNucleicAcid
-  07.07.14 Use bl prefix for functions By: CTP
*/
char blThrone(char *three)
{
   int j;

   if(three[0] == ' ' && three[1] == ' ')
      gBioplibSeqNucleicAcid = TRUE;
   else
      gBioplibSeqNucleicAcid = FALSE;

   if(three[2] == 'X')
      return('X');

   for(j=0;j<NUMAAKNOWN;j++)
      if(!strncmp(sTab3[j],three,3)) return(sTab1[j]);

   /* Only get here if the three letter code was not found              */
   return('X');
}


/************************************************************************/
/*>char blThronex(char *three)
   ---------------------------
*//**

   \param[in]     *three    Three letter code
   \return                    One letter code

   Converts 3-letter code to 1-letter code.
   Handles ASX and GLX as B and Z.
   
-  29.09.92 Original    By: ACRM
-  25.07.95 Added handling of gBioplibSeqNucleicAcid
-  07.07.14 Use bl prefix for functions By: CTP
*/
char blThronex(char *three)
{
   int j;

   if(three[0] == ' ' && three[1] == ' ')
      gBioplibSeqNucleicAcid = TRUE;
   else
      gBioplibSeqNucleicAcid = FALSE;

   for(j=0;j<NUMAAKNOWN;j++)
      if(!strncmp(sTab3[j],three,3)) return(sTab1[j]);

   /* Only get here if the three letter code was not found              */
   return('X');
}


/************************************************************************/
/*>char *blOnethr(char one)
   ------------------------
*//**

   \param[in]     one     One letter code
   \return                Three letter code (padded to 4 chars with a 
                          space)

   Converts 1-letter code to 3-letter code (actually as 4 chars).

-  07.06.93 Original    By: ACRM
-  25.07.95 If the gBioplibSeqNucleicAcid flag is set, assumes nucleic
            acids rather than amino acids
-  03.02.09 Fixed nucleic search - j was incrementing instead of 
            decrementing!
-  07.07.14 Use bl prefix for functions By: CTP
*/
char *blOnethr(char one)
{
   int j;

   if(gBioplibSeqNucleicAcid) /* Work from end of table                 */
   {
      for(j=NUMAAKNOWN-1;j>=0;j--)
         if(sTab1[j] == one) return(sTab3[j]);
   }
   else                       /* Work from start of table               */
   {
      for(j=0;j<NUMAAKNOWN;j++)
         if(sTab1[j] == one) return(sTab3[j]);
   }

   /* Only get here if the one letter code was not found                */
   return(sTab3[NUMAAKNOWN-1]);
}