Пример #1
0
/*==========================================================================*/
void search_base_vps(char filename[],CVPS *cvps_typ,
                     DICT_WORD fun_dict[],int num_fun_dict,
                     DICT_WORD *vps_dict_tmp[],
                     DICT_WORD vps_dict[],int num_vps_dict_ret,int *ifound)
{/*begin routine*/
  /*=======================================================================*/
  /*             Local variable declarations                               */
  int nline,nkey,i,num;
  int ifirst,nfun_key;
  int num_vps_dict = num_vps_dict_ret;
  NAME fun_key;
  DICT_WORD word;
  FILE *fp;
  /*========================================================================*/
  fp       = cfopen(filename,"r");
  *ifound  = 0;
  ifirst   = 0;
  nline    = 0;
  nkey     = 0;
  nfun_key = 0;
  while(get_fun_key(fp,fun_key,&nline,&nfun_key,filename)){
    get_fun_key_index(fun_key,num_fun_dict,fun_dict,nline,
                      nfun_key,filename,&num);
    if(num==6){
      set_potvps_dict(vps_dict_tmp,&num_vps_dict,ifirst);
      while(get_word(fp,&word,&nline,&nkey,nfun_key,filename)){
        put_word_dict(&word,*vps_dict_tmp,num_vps_dict,
                      fun_key,nline,nkey,nfun_key,filename);
      }/*endwhile*/
      if(strcasecmp((*vps_dict_tmp)[1].keyarg,cvps_typ->atm1)==0){
        *ifound = 1;
        dict_save(*vps_dict_tmp,vps_dict,num_vps_dict);
      }
    }else{
        close_fun_key_cnt(fp,fun_key,&nline,nfun_key,filename);      
    }/*endif*/
  }/*end while*/
  fclose(fp);
  if(*ifound==1){
    for(i=1;i<=num_vps_dict;i++){
      if((vps_dict[i].iuset==0)&&(vps_dict[i].key_type==1)){
        keyword_miss(vps_dict,filename,fun_key,i);}
    }/*endfor*/
  }/*endif*/
} /*end routine*/
Пример #2
0
void control_set_mol_params(ATOMMAPS *atommaps,CPOPTS *cpopts,
                         CPCOEFFS_INFO *cpcoeffs_info,CP_PARSE *cp_parse,
                         CLASS_PARSE *class_parse,
                         BONDED *bonded,SURFACE *surface,
                         FILENAME_PARSE *filename_parse,
                         FREE_PARSE *free_parse,
                         DICT_MOL *dict_mol,DICT_WORD *word,
                         char *fun_key,int *nfun_key,
                         int iextend,double t_ext,int ifirst,int pi_beads)
/*=======================================================================*/
{/*begin routine*/
/*=======================================================================*/
/*             Local variable declarations                               */

  int   nline,nkey,i,num,ierr;
  FILE *fp;
  int  *mol_ind_chk;                                 /* Index check      */
  int  *ifound;

  int nmol_typ            = atommaps->nmol_typ;
  int *nmol_jmol_typ      = atommaps->nmol_jmol_typ;
  int *nres_1mol_jmol_typ = atommaps->nres_1mol_jmol_typ;

  int num_fun_dict        = dict_mol->num_fun_dict;
  char *molsetname        = filename_parse->molsetname;

  int bond_free_num       = bonded->bond_free.num;
  int bend_free_num       = bonded->bend_free.num;
  int tors_free_num       = bonded->tors_free.num;
  int rbar_sig_free_iopt  = bonded->rbar_sig_free.iopt;

  int *imoltyp_rbar1_free;
  int *imoltyp_rbar2_free;
  int *imol_rbar1_free;
  int *imol_rbar2_free;
  int *ires_rbar1_free;
  int *ires_rbar2_free;
  int nbar_bond;

  int *imoltyp_bond_free = free_parse->imoltyp_bond_free;
  int *imol_bond_free     = free_parse->imol_bond_free;
  int *ires_bond_free    = free_parse->ires_bond_free;
  int *iatm_bond_free    = free_parse->iatm_bond_free;

  int *imoltyp_bend_free = free_parse->imoltyp_bend_free;
  int *imol_bend_free     = free_parse->imol_bend_free;
  int *ires_bend_free    = free_parse->ires_bend_free;
  int *iatm_bend_free    = free_parse->iatm_bend_free;

  int *imoltyp_tors_free = free_parse->imoltyp_tors_free;
  int *imol_tors_free     = free_parse->imol_tors_free;
  int *ires_tors_free    = free_parse->ires_tors_free; 
  int *iatm_tors_free    = free_parse->iatm_tors_free;

/*=======================================================================*/
/* 0) Set up molecular index checking memory                             */

  mol_ind_chk     = (int *) cmalloc(nmol_typ*sizeof(int))-1;
  ifound          = (int *) cmalloc(num_fun_dict*sizeof(int))-1;
  for(i=1;i<=nmol_typ;i++){ mol_ind_chk[i]=0;}
  for(i=1;i<=num_fun_dict;i++){ ifound[i]=0;}

/*=======================================================================*/
/* I) Fetch a valid functional key word from molset file                 */

  fp = cfopen(molsetname,"r");

  nline          = 1;
  *nfun_key      = 0;
  word->iuset    = 0;
  word->key_type = 0;
  while(get_fun_key(fp,fun_key,&nline,nfun_key,molsetname)){
    get_fun_key_index(fun_key,dict_mol->num_fun_dict,dict_mol->fun_dict,
                      nline,*nfun_key,molsetname,&num);

/*=======================================================================*/
/* II) Fetch the key words and key args of the functional key word       */
/*     and stick them into the correct dictionary                        */

    if(num==1){
      set_mol_dict(&(dict_mol->mol_dict),&(dict_mol->num_mol_dict),
                 iextend,class_parse->tau_nhc_def,t_ext,ifirst);
    }
    nkey=0;
    while(get_word(fp,word,&nline,&nkey,*nfun_key,molsetname)){
      switch(num){
      case 1:
       put_word_dict(word,dict_mol->mol_dict,dict_mol->num_mol_dict,
                    fun_key,nline,nkey,*nfun_key,molsetname);
       break;
      case 2:
       put_word_dict(word,dict_mol->wave_dict,
                    dict_mol->num_wave_dict,fun_key,nline,nkey,
                    *nfun_key,molsetname);
       break;
      case 3:
       put_word_dict(word,dict_mol->bond_free_dict,
                    dict_mol->num_bond_free_dict,fun_key,nline,
                    nkey,*nfun_key,molsetname);
       break;
      case 4:
       put_word_dict(word,dict_mol->bend_free_dict,
                    dict_mol->num_bend_free_dict,fun_key,nline,
                    nkey,*nfun_key,molsetname);
       break;
      case 5:
       put_word_dict(word,dict_mol->tors_free_dict,
                    dict_mol->num_tors_free_dict,fun_key,nline,
                    nkey,*nfun_key,molsetname);
       break;
      case 6:
       put_word_dict(word,dict_mol->def_base_dict,
                    dict_mol->num_def_base_dict,fun_key,nline,
                    nkey,*nfun_key,molsetname);
       break;
      case 7:
       put_word_dict(word,dict_mol->user_base_dict,
                    dict_mol->num_user_base_dict,fun_key,nline,
                    nkey,*nfun_key,molsetname);
       break;
      case 8:
       put_word_dict(word,dict_mol->rbar_free_dict,
                    dict_mol->num_rbar_free_dict,fun_key,nline,
                    nkey,*nfun_key,molsetname);
       break;
      case 9:
       put_word_dict(word,dict_mol->surface_dict,
                    dict_mol->num_surface_dict,fun_key,nline,
                    nkey,*nfun_key,molsetname);
       break;
      } /* end switch dictionary fills*/
    } /* endwhile fetching keywords and keyargs*/
  
/*=====================================================================*/
/* III) Assign the key args of the key words to the appropriate        */
/*      program variables                                              */

    ifound[num]=1;
    switch(num){
    case 1:
      set_mol_params(filename_parse,fun_key,dict_mol->mol_dict,
                   dict_mol->num_mol_dict,
                   class_parse,atommaps,mol_ind_chk,pi_beads);
      break;

    case 2:
      set_wave_params(molsetname,fun_key,
                    dict_mol->wave_dict,dict_mol->num_wave_dict,
                    cpopts,cpcoeffs_info,cp_parse);
      break;
      
    case 3:
      set_bond_free_params(molsetname,fun_key,
                        dict_mol->bond_free_dict,
                        dict_mol->num_bond_free_dict,
                        &(bonded->bond_free),free_parse,
                        atommaps->nmol_typ);
      break;
    case 4:
      set_bend_free_params(molsetname,fun_key,
                        dict_mol->bend_free_dict,
                        dict_mol->num_bend_free_dict,
                        &(bonded->bend_free),free_parse,
                        atommaps->nmol_typ);
      break;
      
    case 5:
      set_tors_free_params(molsetname,fun_key,
                        dict_mol->tors_free_dict,
                        dict_mol->num_tors_free_dict,
                        &(bonded->tors_free),free_parse,
                        atommaps->nmol_typ);
      break;
    case 6:
      set_def_base_params(filename_parse,dict_mol->def_base_dict,
                       dict_mol->num_def_base_dict);
      break;
    case 7:
      set_user_base_params(filename_parse,dict_mol->user_base_dict,
                        dict_mol->num_user_base_dict);
      break;
    case 8:
      set_rbar_free_params(molsetname,fun_key,
                        dict_mol->rbar_free_dict,
                        dict_mol->num_rbar_free_dict,
                        &(bonded->rbar_sig_free),free_parse,
                        atommaps->nmol_typ);
      break;
    case 9:
      set_surf_params(molsetname,fun_key,
                      dict_mol->surface_dict,
                      dict_mol->num_surface_dict,
                      surface); 
      break;
    } /* end switch assigning dict stuff to variables */

  } /*endwhile getting functional keywords data*/

/*=====================================================================*/
/* IV) Make sure everything that is required has been found            */ 
/*     if it hasn't either die or define defaults                      */ 

  if(ifound[1]==0){
    printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
    printf("  Required functional keyword %s not found     \n",
              dict_mol->fun_dict[1].keyword);
    printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
    fflush(stdout);
    exit(1);
  }/*endif*/
  if(ifound[6]==0){
    set_def_base_params(filename_parse,dict_mol->def_base_dict,
                     dict_mol->num_def_base_dict);
  }/*endif*/
  if(ifound[7]==0){
    set_user_base_params(filename_parse,dict_mol->user_base_dict,
                      dict_mol->num_user_base_dict);
  }/*endif*/
  
/*=======================================================================*/
/* IV) Check  indices                                                    */

  for(i = 1;i<=nmol_typ;i++){
    if(mol_ind_chk[i]!=1){
      printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@  \n");
      printf("Molecule number %d specified %d times in file %s \n",
              i,mol_ind_chk[i],molsetname);
      printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@  \n");
      fflush(stdout);
      exit(1);
    }/*endif*/
  } /*endfor*/

/*=======================================================================*/
/* V) Check  free energy indices                                         */

  ierr = 0;

  if(bond_free_num>0){
    for(i=1;i<=2;i++){
      if(imol_bond_free[i]>nmol_jmol_typ[imoltyp_bond_free[i]]){ierr=i;}
      if(ires_bond_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_bond_free[i]],1))
                                                               {ierr=i;}
    }/*endfor*/
  }/*endif*/

  if(bend_free_num>0){
    for(i=1;i<=3;i++){
      if(imol_bend_free[i]>nmol_jmol_typ[imoltyp_bend_free[i]]){ierr=i;}
      if(ires_bend_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_bend_free[i]],1))
                                                               {ierr=i;}
    }/*endfor*/
  }/*endif*/

  if(tors_free_num>0){tors_free_num=bonded->tors_free.num;}
  if(tors_free_num==1){
    for(i=1;i<=4;i++){
      if(imol_tors_free[i]>nmol_jmol_typ[imoltyp_tors_free[i]]){ierr=i;}
      if(ires_tors_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_tors_free[i]],1))
                                                               {ierr=i;}
    }/*endfor*/
  }/*endif*/
  if(tors_free_num==2){
    for(i=1;i<=8;i++){
      if(imol_tors_free[i]>nmol_jmol_typ[imoltyp_tors_free[i]]){ierr=i;}
      if(ires_tors_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_tors_free[i]],1))
                                                               {ierr=i;}
    }/*endfor*/
  }/*endif*/

  if(rbar_sig_free_iopt>0){

    imoltyp_rbar1_free = free_parse->imoltyp_rbar1_free;
    imoltyp_rbar2_free = free_parse->imoltyp_rbar2_free;
    imol_rbar1_free    = free_parse->imol_rbar1_free;
    imol_rbar2_free    = free_parse->imol_rbar2_free;
    ires_rbar1_free    = free_parse->ires_rbar1_free;
    ires_rbar2_free    = free_parse->ires_rbar2_free;
    nbar_bond          = free_parse->nbar_bond;

    for(i=1;i<=nbar_bond;i++){
     if(imol_rbar1_free[i]>nmol_jmol_typ[imoltyp_rbar1_free[i]]){ierr=1;}
     if(imol_rbar2_free[i]>nmol_jmol_typ[imoltyp_rbar2_free[i]]){ierr=2;}
     if(ires_rbar1_free[i]>
              MAX(nres_1mol_jmol_typ[imoltyp_rbar1_free[i]],1)){ierr=1;}
     if(ires_rbar2_free[i]>
              MAX(nres_1mol_jmol_typ[imoltyp_rbar2_free[i]],1)){ierr=2;}
    }/*endfor*/
  }/*endif*/

  if(ierr>0){
      printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
      printf("Error specifing the %dth atom in a free energy def \n",ierr);
      printf("in set up file %s \n",molsetname);
      printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
      fflush(stdout);
      exit(1);
  }/*endif*/ 

/*=======================================================================*/
/* VI) Free memory                                                       */

  cfree(&mol_ind_chk[1]);
  cfree(&ifound[1]);

/*-----------------------------------------------------------------------*/
   }/*end routine*/