minor fixes in ditribution files

[gromacs/qmmm-gamess-us.git] / src / tools / gmx_confrms.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
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
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 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "filenm.h"
#include "smalloc.h"
#include "macros.h"
#include "math.h"
#include "typedefs.h"
#include "xvgr.h"
#include "copyrite.h"
#include "statutil.h"
#include "tpxio.h"
#include "string2.h"
#include "vec.h"
#include "index.h"
#include "pbc.h"
#include "gmx_fatal.h"
#include "futil.h"
#include "confio.h"
#include "pdbio.h"
#include "txtdump.h"
#include "do_fit.h"
#include "viewit.h"
#include "rmpbc.h"
#include "gmx_ana.h"


void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
{
  int i,d;
  real tm,m;

  /* calculate and remove center of mass of reference structure */
  tm = 0;
  clear_rvec(xcm);
  for(i=0; i<isize; i++) {
    m = atoms->atom[index[i]].m;
    for(d=0; d<DIM; d++)
      xcm[d] += m*x[index[i]][d];
    tm += m;
  }
  svmul(1/tm,xcm,xcm);
  for(i=0; i<atoms->nr; i++)
    rvec_dec(x[i],xcm);
}

int build_res_index(int isize, atom_id index[], t_atom atom[], int rindex[])
{ 
  int i, r;
  
  r=0;
  rindex[r] = atom[index[0]].resind;
  r++;
  for(i=1; i<isize; i++)
    if (atom[index[i]].resind != rindex[r-1]) {
      rindex[r] = atom[index[i]].resind;
      r++;
    }
  
  return r;
}

int find_res_end(int i, int isize, atom_id index[], t_atoms *atoms)
{
  int rnr;
  
  rnr = atoms->atom[index[i]].resind;
  while(i<isize && atoms->atom[index[i]].resind==rnr)
    i++;
  return i;
}

int debug_strcmp(char s1[], char s2[])
{
  if (debug) fprintf(debug," %s-%s",s1,s2);
  return strcmp(s1, s2);
}

int find_next_match_atoms_in_res(int *i1,int isize1,atom_id index1[],
                                 int m1,char **atnms1[],
                                 int *i2,int isize2,atom_id index2[],
                                 int m2,char **atnms2[])
{
  int dx, dy, dmax, cmp;
  bool bFW=FALSE;
  
  dx=dy=0;
  cmp=NOTSET;
  dmax = max(m1-*i1, m2-*i2);
  for(dx=0; dx<dmax && cmp!=0; dx++) {
    for(dy=dx; dy<dmax && cmp!=0; dy++) {
      if (dx || dy) {
        if (debug) fprintf(debug, ".");
        cmp=NOTSET;
        if ( *i1+dx<m1 && *i2+dy<m2 ) {
          bFW=TRUE;
          cmp = debug_strcmp(*atnms1[index1[*i1+dx]],*atnms2[index2[*i2+dy]]);
          if (debug) fprintf(debug,"(%d %d)", *i1+dx, *i2+dy);
        }
        if ( cmp!=0 && *i1+dy<m1 && *i2+dx<m2 ) {
          bFW=FALSE;
          cmp = debug_strcmp(*atnms1[index1[*i1+dy]],*atnms2[index2[*i2+dx]]);
          if (debug) fprintf(debug,"(%d %d)", *i1+dy, *i2+dx);
        }
      }
    }
  }
  /* apparently, dx and dy are incremented one more time 
     as the loops terminate: we correct this here */
  dx--;
  dy--;
  if (cmp==0) {
    if (debug) fprintf(debug, "{%d %d}", *i1+bFW?dx:dy, *i2+bFW?dy:dx );
    if (bFW) { 
      *i1 += dx;
      *i2 += dy;
    } else {
      *i1 += dy;
      *i2 += dx;
    }
  }
  
  return cmp;
}

static int find_next_match_res(int *rnr1, int isize1,
                               int index1[], t_resinfo *resinfo1,
                               int *rnr2, int isize2,
                               int index2[], t_resinfo *resinfo2)
{
  int dx, dy, dmax, cmp, rr1, rr2;
  bool bFW=FALSE,bFF=FALSE;
  
  dx=dy=0;
  rr1 = 0;
  while(rr1<isize1 && *rnr1 != index1[rr1])
    rr1++;
  rr2 = 0;
  while(rr2<isize2 && *rnr2 != index2[rr2])
    rr2++;
  
  cmp=NOTSET;
  dmax = max(isize1-rr1, isize2-rr2);
  if (debug) fprintf(debug," R:%d-%d:%d-%d:%d ",
                     rr1, isize1, rr2, isize2, dmax);
  for(dx=0; dx<dmax && cmp!=0; dx++)
    for(dy=0; dy<=dx && cmp!=0; dy++) 
      if ( dx!=dy ) {
        cmp=NOTSET;
        if ( rr1+dx<isize1 && rr2+dy<isize2 ) {
          bFW=TRUE;
          cmp=debug_strcmp(*resinfo1[index1[rr1+dx]].name,
                           *resinfo2[index2[rr2+dy]].name);
          if (debug) fprintf(debug,"(%d %d)", rr1+dx, rr2+dy);
        }
        if ( cmp!=0 && rr1+dy<isize1 && rr2+dx<isize2 ) {
          bFW=FALSE;
          cmp=debug_strcmp(*resinfo1[index1[rr1+dy]].name,
                           *resinfo2[index2[rr2+dx]].name);
          if (debug) fprintf(debug,"(%d %d)", rr1+dy, rr2+dx);
        }
        if ( dx!=0 && cmp!=0 && rr1+dx<isize1 && rr2+dx<isize2 ) {
          bFF=TRUE;
          cmp=debug_strcmp(*resinfo1[index1[rr1+dx]].name,
                           *resinfo2[index2[rr2+dx]].name);
          if (debug) fprintf(debug,"(%d %d)", rr1+dx, rr2+dx);
        } else
          bFF=FALSE;
      }
  /* apparently, dx and dy are incremented one more time 
     as the loops terminate: we correct this here */
  dx--;
  dy--;
  /* if we skipped equal on both sides, only skip one residue 
     to allow for single mutations of residues... */
  if (bFF) {
    if (debug) fprintf(debug, "%d.%d.%dX%sX%s",dx,rr1,rr2,
                       *resinfo1[index1[rr1+1]].name,
                       *resinfo2[index2[rr2+1]].name);
    dx=1;
  }
  if (cmp==0) {
    if (debug) fprintf(debug, "!");
    if (bFF) {
      rr1 += dx;
      rr2 += dx;
    } else
      if (bFW) { 
        rr1 += dx;
        rr2 += dy;
      } else {
        rr1 += dy;
        rr2 += dx;
      }
    *rnr1 = index1[rr1];
    *rnr2 = index2[rr2];
  }
  
  return cmp;
}

int find_first_atom_in_res(int rnr, int isize, atom_id index[], t_atom atom[])
{
  int i;
  
  i=0;
  while(i<isize && atom[index[i]].resind!=rnr)
    i++;
  
  if (atom[index[i]].resind==rnr)
    return i;
  else
    return NOTSET;
}

void find_matching_names(int *isize1, atom_id index1[], t_atoms *atoms1, 
                         int *isize2, atom_id index2[], t_atoms *atoms2)
{
  int i, i1, i2, ii1, ii2, m1, m2;
  int atcmp, rescmp;
  int r,rnr1, rnr2, prnr1, prnr2;
  int rsize1, rsize2;
  int *rindex1, *rindex2;
  char *resnm1, *resnm2, *atnm1, *atnm2;
  char ***atnms1,***atnms2;
  t_resinfo *resinfo1,*resinfo2;
  
  /* set some handy shortcuts */  
  resinfo1 = atoms1->resinfo;
  atnms1   = atoms1->atomname;
  resinfo2 = atoms2->resinfo;
  atnms2   = atoms2->atomname;
  
  /* build indexes of selected residues */
  snew(rindex1,atoms1->nres);
  rsize1=build_res_index(*isize1, index1, atoms1->atom, rindex1);
  snew(rindex2,atoms2->nres);
  rsize2=build_res_index(*isize2, index2, atoms2->atom, rindex2);
  
  i1=i2=0;
  ii1=ii2=0;
  atcmp=rescmp=0;
  prnr1=prnr2=NOTSET;
  if (debug) fprintf(debug, "Find matching names: %d, %d\n", *isize1, *isize2);
  while ( atcmp==0 && i1<*isize1 && i2<*isize2 ) {
    /* prologue */
    rnr1 = atoms1->atom[index1[i1]].resind;
    rnr2 = atoms2->atom[index2[i2]].resind;
    if (rnr1!=prnr1 || rnr2!=prnr2) {
      if (debug) fprintf(debug, "R: %s%d %s%d\n", 
                         *resinfo1[rnr1].name,rnr1,*resinfo2[rnr2].name,rnr2);
      rescmp=strcmp(*resinfo1[rnr1].name, *resinfo2[rnr2].name);
    }
    if (debug) fprintf(debug, "comparing %d %d", i1, i2);
    atcmp=debug_strcmp(*atnms1[index1[i1]], *atnms2[index2[i2]]);
    
    /* the works */
    if (atcmp!=0) { /* no match -> find match within residues */
      m1 = find_res_end(i1, *isize1, index1, atoms1);
      m2 = find_res_end(i2, *isize2, index2, atoms2);
      if (debug) fprintf(debug, " [%d<%d %d<%d]", i1,m1, i2,m2);
      atcmp = find_next_match_atoms_in_res(&i1,*isize1,index1,m1,atnms1,
                                           &i2,*isize2,index2,m2,atnms2);
      if (debug) fprintf(debug, " -> %d %d %s-%s", i1, i2,
                         *atnms1[index1[i1]],*atnms2[index2[i2]]);
      
    }
    if (atcmp!=0) { /* still no match -> next residue(s) */
      prnr1=rnr1;
      prnr2=rnr2;
      rescmp = find_next_match_res(&rnr1,rsize1,rindex1,resinfo1,
                                   &rnr2,rsize2,rindex2,resinfo2);
      if (rnr1!=prnr1) 
        i1 = find_first_atom_in_res(rnr1, *isize1, index1, atoms1->atom);
      if (rnr2!=prnr2) 
        i2 = find_first_atom_in_res(rnr2, *isize2, index2, atoms2->atom);
      if (debug) fprintf(debug, " -> %s%d-%s%d %s%d-%s%d",
                         *resinfo1[rnr1].name,rnr1,
                         *atnms1[index1[i1]],index1[i1],
                         *resinfo2[rnr2].name,rnr2,
                         *atnms2[index2[i2]],index2[i2]);
      m1 = find_res_end(i1, *isize1, index1, atoms1);
      m2 = find_res_end(i2, *isize2, index2, atoms2);
      if (debug) fprintf(debug, " [%d<%d %d<%d]", i1,m1, i2,m2);
      atcmp = find_next_match_atoms_in_res(&i1,*isize1,index1,m1,atnms1,
                                           &i2,*isize2,index2,m2,atnms2);
      if (debug) fprintf(debug, " -> %d %d %s-%s", i1, i2,
                         *atnms1[index1[i1]],*atnms2[index2[i2]]);
    }
    if (debug)
      fprintf(debug, "(%d %d): %d %d\n", ii1, ii2, atcmp, rescmp);
    if (atcmp==0) { /* if match -> store indices */
      index1[ii1++]=index1[i1];
      index2[ii2++]=index2[i2];
    }
    i1++;
    i2++;
    
    /* epilogue */
    prnr1=rnr1;
    prnr2=rnr2;
  }
  
  if (ii1 != ii2)
    gmx_fatal(FARGS, "DEATH HORROR: non-equal number of matching atoms!\n");
  if ( ii1==i1 && ii2==i2 )
    printf("All atoms in index groups 1 and 2 match\n");
  else {
    if ( i1==i2 && ii1==ii2 )
      printf("Both index groups modified from %d to %d atoms\n", i1, ii1);
    else {
      if (ii1 != i1)
        printf("Index group 1 modified from %d to %d atoms\n",i1, ii1);
      if (ii2 != i2)
        printf("Index group 2 modified from %d to %d atoms\n",i2, ii2);
    }
    *isize1 = ii1;
    *isize2 = ii2;
  }
}
/* 1 */

int gmx_confrms(int argc,char *argv[])
{
  const char *desc[] = {
    "g_confrms computes the root mean square deviation (RMSD) of two",
    "structures after LSQ fitting the second structure on the first one.",
    "The two structures do NOT need to have the same number of atoms,",
    "only the two index groups used for the fit need to be identical.",
    "With [TT]-name[tt] only matching atom names from the selected groups",
    "will be used for the fit and RMSD calculation. This can be useful ",
    "when comparing mutants of a protein."
    "[PAR]",
    "The superimposed structures are written to file. In a [TT].pdb[tt] file",
    "the two structures will be written as separate models",
    "(use [TT]rasmol -nmrpdb[tt]). Also in a [TT].pdb[tt] file, B-factors",
    "calculated from the atomic MSD values can be written with [TT]-bfac[tt].",
  };
  static bool bOne=FALSE,bRmpbc=FALSE,bMW=TRUE,bName=FALSE,
    bBfac=FALSE,bFit=TRUE,bLabel=FALSE;
  
  t_pargs pa[] = {
    { "-one", FALSE, etBOOL, {&bOne},   "Only write the fitted structure to file" },
    { "-mw",  FALSE, etBOOL, {&bMW},    "Mass-weighted fitting and RMSD" },
    { "-pbc", FALSE, etBOOL, {&bRmpbc}, "Try to make molecules whole again" },
    { "-fit", FALSE, etBOOL, {&bFit},   
      "Do least squares superposition of the target structure to the reference" },
    { "-name", FALSE,etBOOL,{&bName},
      "Only compare matching atom names" },
    { "-label",FALSE,etBOOL,{&bLabel},
      "Added chain labels A for first and B for second structure"},
    { "-bfac", FALSE,etBOOL,{&bBfac},
      "Output B-factors from atomic MSD values" }
  };
  t_filenm fnm[] = {
    { efTPS, "-f1",  "conf1.gro", ffREAD  },
    { efSTX, "-f2",  "conf2",     ffREAD  },
    { efSTO, "-o",   "fit.pdb",   ffWRITE },
    { efNDX, "-n1" , "fit1.ndx",  ffOPTRD },
    { efNDX, "-n2", "fit2.ndx",  ffOPTRD },
    { efNDX, "-no", "match.ndx", ffOPTWR }
  };
#define NFILE asize(fnm)
  
  /* the two structure files */
  const char *conf1file, *conf2file, *matchndxfile, *outfile;
  FILE    *fp;
  char    title1[STRLEN],title2[STRLEN],*name1,*name2;
  t_topology *top1,*top2;
  int     ePBC1,ePBC2;
  t_atoms *atoms1,*atoms2;
  int     warn=0;
  atom_id at;
  real    *w_rls,mass,totmass;
  rvec    *x1,*v1,*x2,*v2,*fit_x;
  matrix  box1,box2;

  output_env_t oenv;
  
  /* counters */
  int     i,j,m;
  
  /* center of mass calculation */
  real    tmas1,tmas2;
  rvec    xcm1,xcm2;
  
  /* variables for fit */
  char    *groupnames1,*groupnames2;
  int     isize1,isize2;
  atom_id *index1,*index2;
  real    rms,msd,minmsd,maxmsd;
  real    *msds;

  
  CopyRight(stderr,argv[0]);
  parse_common_args(&argc,argv,PCA_BE_NICE | PCA_CAN_VIEW,
                    NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
  matchndxfile = opt2fn_null("-no",NFILE,fnm);
  conf1file = ftp2fn(efTPS,NFILE,fnm);
  conf2file = ftp2fn(efSTX,NFILE,fnm);
  
  /* reading reference structure from first structure file */
  fprintf(stderr,"\nReading first structure file\n");
  snew(top1,1);
  read_tps_conf(conf1file,title1,top1,&ePBC1,&x1,&v1,box1,TRUE);
  atoms1 = &(top1->atoms);
  fprintf(stderr,"%s\nContaining %d atoms in %d residues\n",
          title1,atoms1->nr,atoms1->nres);
  
  if ( bRmpbc ) 
    rm_gropbc(atoms1,x1,box1);

  fprintf(stderr,"Select group from first structure\n");
  get_index(atoms1,opt2fn_null("-n1",NFILE,fnm),
            1,&isize1,&index1,&groupnames1);
  printf("\n");
  
  if (bFit && (isize1 < 3))
    gmx_fatal(FARGS,"Need >= 3 points to fit!\n");
  
  /* reading second structure file */
  fprintf(stderr,"\nReading second structure file\n");
  snew(top2,1);
  read_tps_conf(conf2file,title2,top2,&ePBC2,&x2,&v2,box2,TRUE);
  atoms2 = &(top2->atoms);
  fprintf(stderr,"%s\nContaining %d atoms in %d residues\n",
          title2,atoms2->nr,atoms2->nres);
  
  if ( bRmpbc ) 
    rm_gropbc(atoms2,x2,box2);
  
  fprintf(stderr,"Select group from second structure\n");
  get_index(atoms2,opt2fn_null("-n2",NFILE,fnm),
            1,&isize2,&index2,&groupnames2);
  
  if (bName) {
    find_matching_names(&isize1, index1, atoms1, &isize2, index2, atoms2);
    if (matchndxfile) {
      fp = ffopen(matchndxfile,"w");
      fprintf(fp, "; Matching atoms between %s from %s and %s from %s\n",
              groupnames1, conf1file, groupnames2, conf2file);
      fprintf(fp, "[ Match_%s_%s ]\n", conf1file, groupnames1);
      for(i=0; i<isize1; i++)
        fprintf(fp, "%4u%s", index1[i]+1, (i%15==14 || i==isize1-1)?"\n":" ");
      fprintf(fp, "[ Match_%s_%s ]\n", conf2file, groupnames2);
      for(i=0; i<isize2; i++)
        fprintf(fp, "%4u%s", index2[i]+1, (i%15==14 || i==isize2-1)?"\n":" ");
    }
  }
  
  /* check isizes, must be equal */
  if ( isize2 != isize1 )
    gmx_fatal(FARGS,"You selected groups with differen number of atoms.\n");
  
  for(i=0; i<isize1; i++) {
    name1=*atoms1->atomname[index1[i]];
    name2=*atoms2->atomname[index2[i]];
    if (strcmp(name1,name2)) {
      if (warn < 20)
        fprintf(stderr,
                "Warning: atomnames at index %d don't match: %u %s, %u %s\n",
                i+1,index1[i]+1,name1,index2[i]+1,name2);
      warn++;
    }
    if (!bMW) {
      atoms1->atom[index1[i]].m = 1;
      atoms2->atom[index2[i]].m = 1;
    }
  }
  if (warn)
    fprintf(stderr,"%d atomname%s did not match\n",warn,(warn==1) ? "":"s");
  
  if (bFit) {  
    /* calculate and remove center of mass of structures */
    calc_rm_cm(isize1, index1, atoms1, x1, xcm1);
    calc_rm_cm(isize2, index2, atoms2, x2, xcm2);
    
    snew(w_rls,atoms2->nr);
    snew(fit_x,atoms2->nr);
    for(at=0; (at<isize1); at++) {
      w_rls[index2[at]] = atoms1->atom[index1[at]].m;
      copy_rvec(x1[index1[at]],fit_x[index2[at]]);
    }
    
    /* do the least squares fit to the reference structure */
    do_fit(atoms2->nr,w_rls,fit_x,x2);
    
    sfree(fit_x);
    sfree(w_rls);
    w_rls = NULL;
  }
  else {
    clear_rvec(xcm1);
    clear_rvec(xcm2);
    w_rls = NULL;
  }
  
  /* calculate the rms deviation */
  rms     = 0;
  totmass = 0;
  maxmsd  = -1e18;
  minmsd  =  1e18;
  snew(msds, isize1);
  for(at=0; at<isize1; at++) {
    mass = atoms1->atom[index1[at]].m;
    for(m=0; m<DIM; m++) {
      msd = sqr(x1[index1[at]][m] - x2[index2[at]][m]);
      rms += msd*mass;
      msds[at] += msd;
    }
    maxmsd = max(maxmsd, msds[at]);
    minmsd = min(minmsd, msds[at]);
    totmass += mass;
  }
  rms = sqrt(rms/totmass);
  
  printf("Root mean square deviation after lsq fit = %g\n",rms);
  if (bBfac)
    printf("Atomic MSD's range from %g to %g\n",minmsd, maxmsd);
  
  if (bFit) {
    /* reset coordinates of reference and fitted structure */
    for(i=0; i<atoms1->nr; i++)
      for(m=0; m<DIM; m++)
        x1[i][m]+=xcm1[m];
    for(i=0; i<atoms2->nr; i++)
      for(m=0; m<DIM; m++)
        x2[i][m]+=xcm1[m];
  }

  outfile = ftp2fn(efSTO,NFILE,fnm);
  switch (fn2ftp(outfile)) {
  case efPDB:
  case efBRK:
  case efENT:
    if (bBfac || bLabel) {
      snew(atoms1->pdbinfo, atoms1->nr);
      snew(atoms1->atom, atoms1->nr);
      for(i=0; i<isize1; i++) {
        atoms1->pdbinfo[index1[i]].type = eptAtom;
        atoms1->pdbinfo[index1[i]].bAnisotropic = FALSE;
        if (bBfac)
          atoms1->pdbinfo[index1[i]].bfac = 800*M_PI*M_PI/3.0*msds[i]/100;
        if (bLabel)
          atoms1->resinfo[atoms1->atom[index1[i]].resind].chain = 'A';
      }
      snew(atoms2->pdbinfo, atoms2->nr);
      snew(atoms2->atom, atoms2->nr);
      for(i=0; i<isize2; i++) {
        atoms2->pdbinfo[index2[i]].type = eptAtom;
        atoms2->pdbinfo[index2[i]].bAnisotropic = FALSE;
        if (bBfac)
          atoms2->pdbinfo[index2[i]].bfac = 800*M_PI*M_PI/3.0*msds[i]/100;
        if (bLabel)
          atoms2->resinfo[atoms2->atom[index2[i]].resind].chain = 'B';
      }
    }
    fp=ffopen(outfile,"w");
    if (!bOne)
      write_pdbfile(fp,title1,atoms1,x1,ePBC1,box1,0,1,NULL);
    write_pdbfile(fp,title2,atoms2,x2,ePBC2,box2,0,bOne ? -1 : 2,NULL);
    ffclose(fp);
    break;
  case efGRO:
    if (bBfac)
      fprintf(stderr,"WARNING: cannot write B-factor values to gro file\n");
    fp=ffopen(outfile,"w");
    if (!bOne)
      write_hconf_p(fp,title1,atoms1,3,x1,v1,box1);
    write_hconf_p(fp,title2,atoms2,3,x2,v2,box2);
    ffclose(fp);
    break;
  default:
    if (bBfac)
      fprintf(stderr,"WARNING: cannot write B-factor values to %s file\n",
              ftp2ext(fn2ftp(outfile)));
    if (!bOne)
      fprintf(stderr,
              "WARNING: cannot write the reference structure to %s file\n",
              ftp2ext(fn2ftp(outfile))); 
    write_sto_conf(outfile,title2,atoms2,x2,v2,ePBC2,box2);
    break;
  }
  
  view_all(oenv,NFILE, fnm);
  
  thanx(stderr);
  
  return 0;
}