fixed pdb2gmx behavior for nearly matching residue names and made the matching much...

[gromacs.git] / src / kernel / ter_db.c

/*
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.2.0
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
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 * 
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 * And Hey:
 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "sysstuff.h"
#include "smalloc.h"
#include "typedefs.h"
#include "symtab.h"
#include "futil.h"
#include "resall.h"
#include "h_db.h"
#include "string2.h"
#include "strdb.h"
#include "gmx_fatal.h"
#include "ter_db.h"
#include "toputil.h"
#include "gmxfio.h"
#include "fflibutil.h"


/* use bonded types definitions in hackblock.h */
#define ekwRepl ebtsNR+1
#define ekwAdd  ebtsNR+2
#define ekwDel  ebtsNR+3
#define ekwNR   3
const char *kw_names[ekwNR] = {
  "replace", "add", "delete" 
};

int find_kw(char *keyw)
{
  int i;
  
  for(i=0; i<ebtsNR; i++)
    if (gmx_strcasecmp(btsNames[i],keyw) == 0)
      return i;
  for(i=0; i<ekwNR; i++)
    if (gmx_strcasecmp(kw_names[i],keyw) == 0)
      return ebtsNR + 1 + i;
  
  return NOTSET;
}

#define FATAL() gmx_fatal(FARGS,"Reading Termini Database: not enough items on line\n%s",line)

static void read_atom(char *line, bool bAdd,
                      char **nname, t_atom *a, gpp_atomtype_t atype, int *cgnr)
{
  int    nr, i;
  char   buf[5][30],type[12];
  double m, q;
  
  /* This code is messy, because of support for different formats:
   * for replace: [new name] <atom type> <m> <q> [cgnr (old format)]
   * for add:                <atom type> <m> <q> [cgnr]
   */
  nr = sscanf(line,"%s %s %s %s %s",buf[0],buf[1],buf[2],buf[3],buf[4]);
  
  /* Here there an ambiguity due to the old replace format with cgnr,
   * which was read for years, but ignored in the rest of the code.
   * We have to assume that the atom type does not start with a digit
   * to make a line with 4 entries uniquely interpretable.
   */
  if (!bAdd && nr == 4 && isdigit(buf[1][0])) {
    nr = 3;
  }

  if (nr < 3 || nr > 4) {
    gmx_fatal(FARGS,"Reading Termini Database: expected %d or %d items of atom data in stead of %d on line\n%s", 3, 4, nr, line);
  }
  i = 0;
  if (!bAdd) {
    if (nr == 4) {
      *nname = strdup(buf[i++]);
    } else {
      *nname = NULL;
    }
  }
  a->type = get_atomtype_type(buf[i++],atype);
  sscanf(buf[i++],"%lf",&m);
  a->m = m;
  sscanf(buf[i++],"%lf",&q);
  a->q = q;
  if (bAdd && nr == 4) {
    sscanf(buf[i++],"%d", cgnr);
  } else {
    *cgnr = NOTSET;
  }
}

static void print_atom(FILE *out,t_atom *a,gpp_atomtype_t atype,char *newnm)
{
  fprintf(out,"\t%s\t%g\t%g\n",
          get_atomtype_name(a->type,atype),a->m,a->q);
}

static void print_ter_db(const char *ff,char C,int nb,t_hackblock tb[],
                         gpp_atomtype_t atype) 
{
  FILE *out;
  int i,j,k,bt,nrepl,nadd,ndel;
  char buf[STRLEN],nname[STRLEN];
  
  sprintf(buf,"%s-%c.tdb",ff,C);
  out = gmx_fio_fopen(buf,"w");
  
  for(i=0; (i<nb); i++) {
    fprintf(out,"[ %s ]\n",tb[i].name);
    
    /* first count: */
    nrepl=0;
    nadd=0;
    ndel=0;
    for(j=0; j<tb[i].nhack; j++) 
      if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname!=NULL )
        nrepl++;
      else if ( tb[i].hack[j].oname==NULL && tb[i].hack[j].nname!=NULL )
        nadd++;
      else if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname==NULL )
        ndel++;
      else if ( tb[i].hack[j].oname==NULL && tb[i].hack[j].nname==NULL )
        gmx_fatal(FARGS,"invalid hack (%s) in termini database",tb[i].name);
    if (nrepl) {
      fprintf(out,"[ %s ]\n",kw_names[ekwRepl-ebtsNR-1]);
      for(j=0; j<tb[i].nhack; j++) 
        if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname!=NULL ) {
          fprintf(out,"%s\t",tb[i].hack[j].oname);
          print_atom(out,tb[i].hack[j].atom,atype,tb[i].hack[j].nname);
        }
    }
    if (nadd) {
      fprintf(out,"[ %s ]\n",kw_names[ekwAdd-ebtsNR-1]);
      for(j=0; j<tb[i].nhack; j++) 
        if ( tb[i].hack[j].oname==NULL && tb[i].hack[j].nname!=NULL ) {
          print_ab(out,&(tb[i].hack[j]),tb[i].hack[j].nname);
          print_atom(out,tb[i].hack[j].atom,atype,tb[i].hack[j].nname);
        }
    }
    if (ndel) {
      fprintf(out,"[ %s ]\n",kw_names[ekwDel-ebtsNR-1]);
      for(j=0; j<tb[i].nhack; j++)
        if ( tb[i].hack[j].oname!=NULL && tb[i].hack[j].nname==NULL )
          fprintf(out,"%s\n",tb[i].hack[j].oname);
    }
    for(bt=0; bt<ebtsNR; bt++)
      if (tb[i].rb[bt].nb) {
        fprintf(out,"[ %s ]\n", btsNames[bt]);
        for(j=0; j<tb[i].rb[bt].nb; j++) {
          for(k=0; k<btsNiatoms[bt]; k++) 
            fprintf(out,"%s%s",k?"\t":"",tb[i].rb[bt].b[j].a[k]);
          if ( tb[i].rb[bt].b[j].s )
            fprintf(out,"\t%s",tb[i].rb[bt].b[j].s);
          fprintf(out,"\n");
        }
      }
    fprintf(out,"\n");
  }
  gmx_fio_fclose(out);
}

static void read_ter_db_file(char *fn,
                             int *ntbptr,t_hackblock **tbptr,
                             gpp_atomtype_t atype)
{
  char       filebase[STRLEN],*ptr;
  FILE       *in;
  char       header[STRLEN],buf[STRLEN],line[STRLEN];
  t_hackblock *tb;
  int        i,j,n,ni,kwnr,nb,maxnb,nh;

  fflib_filename_base(fn,filebase,STRLEN);
  /* Remove the C/N termini extension */
  ptr = strrchr(filebase,'.');
  if (ptr != NULL) {
    ptr[0] = '\0';
  }

  in = fflib_open(fn);
  if (debug)
    fprintf(debug,"Opened %s\n",fn);
  
  tb = *tbptr;
  nb = *ntbptr - 1;
  maxnb=0;
  kwnr=NOTSET;
  get_a_line(in,line,STRLEN);
  while (!feof(in)) {
    if (get_header(line,header)) {
      /* this is a new block, or a new keyword */
      kwnr=find_kw(header);
      
      if (kwnr == NOTSET) {
        nb++;
        /* here starts a new block */
        if ( nb >= maxnb ) {
          maxnb = nb + 100;
          srenew(tb,maxnb);
        }
        clear_t_hackblock(&tb[nb]);
        tb[nb].name     = strdup(header);
        tb[nb].filebase = strdup(filebase);
      }
    } else {
      if (nb < 0)
        gmx_fatal(FARGS,"reading termini database: "
                    "directive expected before line:\n%s\n"
                    "This might be a file in an old format.",line);
      /* this is not a header, so it must be data */
      if (kwnr >= ebtsNR) {
        /* this is a hack: add/rename/delete atoms */
        /* make space for hacks */
        if (tb[nb].nhack >= tb[nb].maxhack) {
          tb[nb].maxhack+=10;
          srenew(tb[nb].hack, tb[nb].maxhack);
        }
        nh=tb[nb].nhack;
        clear_t_hack(&(tb[nb].hack[nh]));
        for(i=0; i<4; i++)
          tb[nb].hack[nh].a[i]=NULL;
        tb[nb].nhack++;
        
        /* get data */
        n=0;
        if ( kwnr==ekwRepl || kwnr==ekwDel ) {
          if (sscanf(line, "%s%n", buf, &n) != 1) 
            gmx_fatal(FARGS,"Reading Termini Database '%s': "
                      "expected atom name on line\n%s",fn,line);
          tb[nb].hack[nh].oname = strdup(buf);
          /* we only replace or delete one atom at a time */
          tb[nb].hack[nh].nr = 1;
        } else if ( kwnr==ekwAdd ) {
          read_ab(line, fn, &(tb[nb].hack[nh]));
          get_a_line(in, line, STRLEN);
        } else
          gmx_fatal(FARGS,"unimplemented keyword number %d (%s:%d)",
                      kwnr,__FILE__,__LINE__);
        if ( kwnr==ekwRepl || kwnr==ekwAdd ) {
          snew(tb[nb].hack[nh].atom, 1);
          read_atom(line+n,kwnr==ekwAdd,
                    &tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype, 
                    &tb[nb].hack[nh].cgnr);
          if (tb[nb].hack[nh].nname == NULL) {
            if (tb[nb].hack[nh].oname != NULL) {
              tb[nb].hack[nh].nname = strdup(tb[nb].hack[nh].oname);
            } else {
              gmx_fatal(FARGS,"Reading Termini Database '%s': don't know which name the new atom should have on line\n%s",fn,line);
            }
          }
        }
      } else if (kwnr >= 0 && kwnr < ebtsNR) {
        /* this is bonded data: bonds, angles, dihedrals or impropers */
        srenew(tb[nb].rb[kwnr].b,tb[nb].rb[kwnr].nb+1);
        n=0;
        for(j=0; j<btsNiatoms[kwnr]; j++) {
          if ( sscanf(line+n, "%s%n", buf, &ni) == 1 )
            tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = strdup(buf);
          else
            gmx_fatal(FARGS,"Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
          n+=ni;
        }
        for(   ; j<MAXATOMLIST; j++)
          tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
        strcpy(buf, "");
        sscanf(line+n, "%s", buf);
        tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = strdup(buf);
        tb[nb].rb[kwnr].nb++;
      } else
        gmx_fatal(FARGS,"Reading Termini Database: Expecting a header at line\n"
                    "%s",line);
    }
    get_a_line(in,line,STRLEN);
  }
  nb++;
  srenew(tb,nb);
  
  ffclose(in);
  
  *ntbptr = nb;
  *tbptr  = tb;
}

int read_ter_db(const char *ffdir,char ter,
                t_hackblock **tbptr,gpp_atomtype_t atype)
{
  char ext[STRLEN];
  int  ntdbf,f;
  char **tdbf;
  int  ntb;

  sprintf(ext,".%c.tdb",ter);

  /* Search for termini database files.
   * Do not generate an error when none are found.
   */
  ntdbf = fflib_search_file_end(ffdir,ext,FALSE,&tdbf);
  ntb    = 0;
  *tbptr = NULL;
  for(f=0; f<ntdbf; f++) {
    read_ter_db_file(tdbf[f],&ntb,tbptr,atype);
    sfree(tdbf[f]);
  }
  sfree(tdbf);

  if (debug) {
    print_ter_db("new",ter,ntb,*tbptr,atype);
  }

  return ntb;
}

t_hackblock **filter_ter(int nrtp,t_restp rtp[],
                         int nb,t_hackblock tb[],
                         const char *resname,
                         const char *rtpname,
                         int *nret)
{
    /* Since some force fields (e.g. OPLS) needs different
     * atomtypes for different residues there could be a lot
     * of entries in the databases for specific residues
     * (e.g. GLY-NH3+, SER-NH3+, ALA-NH3+).
     * 
     * To reduce the database size, we assume that a terminus specifier liker
     *
     * [ GLY|SER|ALA-NH3+ ]
     *
     * would cover all of the three residue types above. 
     * Wildcards (*,?) are not OK. Don't worry about e.g. GLU vs. GLUH since 
     * pdb2gmx only uses the first 3 letters when calling this routine.
     * 
     * To automate this, this routines scans a list of termini 
     * for the residue name "resname" and returns an allocated list of 
     * pointers to the termini that could be applied to the 
     * residue in question. The variable pointed to by nret will
     * contain the number of valid pointers in the list.
     * Remember to free the list when you are done with it...
     */ 

    t_restp *   restp;
    int         i,j,n,len,none_idx;
    bool        found;
    char        *rtpname_match,*s,*s2,*c;
    t_hackblock **list;
    
    rtpname_match = search_rtp(rtpname,nrtp,rtp);
    restp = get_restp(rtpname_match,nrtp,rtp);
    
    n=0;
    list=NULL;
    
    for(i=0;i<nb;i++) 
    {
        s=tb[i].name;
        found=FALSE;
        do 
        {
            /* The residue name should appear in a tdb file with the same base name
             * as the file containing the rtp entry.
             * This makes termini selection for different molecule types
             * much cleaner.
             */
            if (gmx_strcasecmp(restp->filebase,tb[i].filebase) == 0 &&
                gmx_strncasecmp(resname,s,3) == 0) 
            {
                found=TRUE;
                srenew(list,n+1);
                list[n]=&(tb[i]);
                n++;
            }
            else 
            {
                /* advance to next |-separated field */
                s=strchr(s,'|');
                if(s!=NULL)
                {
                    s++;
                }
            }
        }
        while(!found && s!=NULL);
    }
    
    /* All residue-specific termini have been added. See if there
     * are some generic ones by searching for the occurence of
     * '-' in the name prior to the last position (which indicates charge).
     * The [ None ] alternative is special since we don't want that
     * to be the default, so we put it last in the list we return.
     */
    none_idx=-1;
    for(i=0;i<nb;i++) 
    {
        s=tb[i].name;
        /* The residue name should appear in a tdb file with the same base name
         * as the file containing the rtp entry.
         * This makes termini selection for different molecule types
         * much cleaner.
         */
        if(gmx_strcasecmp(restp->filebase,tb[i].filebase) == 0)
        {
            if(!gmx_strcasecmp("None",s)) 
            {
                none_idx=i;
            }
            else 
            {
                c=strchr(s,'-');
                if(c==NULL || ((c-s+1)==strlen(s))) 
                {
                    /* Check that we haven't already added a residue-specific version 
                     * of this terminus.
                     */
                    for(j=0;j<n && strstr((*list[j]).name,s)==NULL;j++);
                    if(j==n) 
                    {
                        srenew(list,n+1);
                        list[n]=&(tb[i]);
                        n++;
                    }
                }
            }
        } 
    }
    if(none_idx>=0) 
    {
        srenew(list,n+1);
        list[n]=&(tb[none_idx]);
        n++;
    }    
    
    *nret=n;
    return list;
}


t_hackblock *choose_ter(int nb,t_hackblock **tb,const char *title)
{
  int i,sel,ret;
  
  printf("%s\n",title);
  for(i=0; (i<nb); i++) 
    printf("%2d: %s\n",i,(*tb[i]).name);
  do {
    ret=fscanf(stdin,"%d",&sel);
  } while ((ret != 1) || (sel < 0) || (sel >= nb));
  
  return tb[sel];
}