void set_res_morph_params(DICT_WORD res_name_dict[],int num_res_name_dict,
char fun_key[],char file_name[],NAME res_typ[],
int natm_jres_jmol_typ[],int jmol_typ,
int jres,int jres_off,
int ires_typ_jres_jmol_typ[])
/*==========================================================================*/
{
int i,index,index2;
/*=======================================================================*/
/* I) Check for missing key words*/
for(i=1;i<=1;i++){
if(res_name_dict[i].iuset==0 && res_name_dict[i].key_type==1){
keyword_miss(res_name_dict,file_name,fun_key,i);}
} /*endfor*/
/*======================================================================*/
/* II) Set the keywords */
/*-------------------------------------------------------------------------*/
/* 1) \residue_name{} */
index = 1;
index2 = ires_typ_jres_jmol_typ[(jres+jres_off)];
if(strcasecmp(res_typ[index2],res_name_dict[1].keyarg)!=0){
keyarg_barf(res_name_dict,file_name,fun_key,index);}
/*---------------------------------------------------------------------*/
} /*end routine*/
void set_mol_name_params(DICT_WORD mol_name_dict[],int num_mol_name_dict,
char fun_key[],char filename[],NAME mol_typ[],
int natm_1mol_jmol_typ[],int jmol_typ,int nres_expt)
/*==========================================================================*/
{
int num,i,index;
/*=======================================================================*/
/* I) Check for missing key words*/
for(i=1;i<=num_mol_name_dict;i++){
if(mol_name_dict[i].iuset==0 && mol_name_dict[i].key_type==1){
keyword_miss(mol_name_dict,filename,fun_key,i);}
} /*endfor*/
/*======================================================================*/
/* II) Set the keywords */
/*-------------------------------------------------------------------------*/
/* 1) \mol_name{} */
index = 1;
if(strcasecmp(mol_typ[jmol_typ],mol_name_dict[1].keyarg)!=0){
keyarg_barf(mol_name_dict,filename,fun_key,index);}
/*-------------------------------------------------------------------------*/
/* 2) \nresidue{} */
sscanf(mol_name_dict[2].keyarg,"%d",&num);
index = 2;
if(num < 0){
keyarg_barf(mol_name_dict,filename,fun_key,index);
}
if(num != nres_expt){
printf("@@@@@@@@@@@@@@@@@@@@_ERROR_@@@@@@@@@@@@@@@@@@@@\n");
printf("Number of residue's specified %d not equal to number expected %d\n",
num,nres_expt);
printf("in file %s\n",filename);
printf("@@@@@@@@@@@@@@@@@@@@_ERROR_@@@@@@@@@@@@@@@@@@@@\n");
fflush(stdout);
exit(1);
}
/*-------------------------------------------------------------------------*/
/* 3) \natom{} */
sscanf(mol_name_dict[3].keyarg,"%d",&num);
index = 3;
if(num<0){
keyarg_barf(mol_name_dict,filename,fun_key,index);
}
natm_1mol_jmol_typ[jmol_typ] = num;
/*---------------------------------------------------------------------*/
} /*end routine*/
void set_surf_params(char *molsetname, char *fun_key,
DICT_WORD surface_dict[],int num_surface_dict,
MDSURFACE *mdsurface)
/*==========================================================================*/
{ /* Begin routine */
/*==========================================================================*/
int i,index;
double real_key_arg;
/*==========================================================================*/
/* I) Check for missing key words*/
for(i=1;i<num_surface_dict;i++){
if(surface_dict[i].iuset==0 && surface_dict[i].key_type==1){
keyword_miss(surface_dict,molsetname,fun_key,i);
}/*endif*/
}/*endfor*/
/*==========================================================================*/
/* II) Fill the surface structure */
/*------------------------------------------------------------------------*/
/* 1)\surface_type{} */
strcpy(mdsurface->surface_type,surface_dict[1].keyarg);
/*------------------------------------------------------------------------*/
/* 2)\surface_height{} */
sscanf(surface_dict[2].keyarg,"%lg",&real_key_arg);
mdsurface->surface_height = real_key_arg;
/*------------------------------------------------------------------------*/
/* 3)\num_spline_pts{} */
sscanf(surface_dict[3].keyarg,"%lg",&real_key_arg);
mdsurface->nsplin_surf = (int) real_key_arg;
index = 3;
if(real_key_arg<=0.0){
keyarg_barf(surface_dict,molsetname,fun_key,index);
}/*endif*/
/*------------------------------------------------------------------------*/
/* 4)\healing_length{} */
sscanf(surface_dict[4].keyarg,"%lg",&real_key_arg);
mdsurface->zheal = real_key_arg;
index = 4;
if(real_key_arg<=0.0){
keyarg_barf(surface_dict,molsetname,fun_key,index);
}/*endif*/
/*------------------------------------------------------------------------*/
/*==========================================================================*/
}/*end routine*/
/*==========================================================================*/
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*/
void set_bend_params(DICT_WORD intra_dict[],int num_intra_dict,
char *fun_key,char *file_name,int jmol_typ,
CLATOMS_INFO *clatoms_info,ATOMMAPS *atommaps,
BEND *bend,NULL_INTER_PARSE *null_inter_parse,
BUILD_INTRA *build_intra, int iresidue, int ires_off)
/*==========================================================================*/
{
int num,index,ifound,igo;
int itype1,itype2,itype3;
int iatm_ind1,iatm_ind2,iatm_ind3;
int imask1,imask2,imask3;
int i,itype;
/*========================================================================*/
/* I) Check for missing key words*/
for(i=1;i<=3;i++){
if(intra_dict[i].iuset==0 && intra_dict[i].key_type==1){
keyword_miss(intra_dict,file_name,fun_key,i);
}
} /*endfor*/
/*=======================================================================*/
/* II) Fill the dictionary with words */
/*-----------------------------------------------------------------------*/
/* 1) \atom1{} */
index = 1;
sscanf(intra_dict[1].keyarg,"%d",&num);
iatm_ind1 = num;
if(iatm_ind1>build_intra->natmind_1res_now||iatm_ind1<0){
keyarg_barf(intra_dict,file_name,fun_key,index);
}
imask1 = build_intra->mask_atm[iatm_ind1];
if(imask1>0)iatm_ind1 = build_intra->index_atm[iatm_ind1];
/*------------------------------------------------------------------------*/
/* 2) \atom2{} */
index = 2;
sscanf(intra_dict[2].keyarg,"%d",&num);
iatm_ind2 = num;
if(iatm_ind2>build_intra->natmind_1res_now||iatm_ind2<0){
keyarg_barf(intra_dict,file_name,fun_key,index);
}
imask2 = build_intra->mask_atm[iatm_ind2];
if(imask2>0)iatm_ind2 = build_intra->index_atm[iatm_ind2];
/*-----------------------------------------------------------------------*/
/* 3) \atom3{} */
index = 3;
sscanf(intra_dict[3].keyarg,"%d",&num);
iatm_ind3 = num;
if(iatm_ind3>build_intra->natmind_1res_now||iatm_ind3<0){
keyarg_barf(intra_dict,file_name,fun_key,index);}
imask3 = build_intra->mask_atm[iatm_ind3];
if(imask3>0)iatm_ind3 = build_intra->index_atm[iatm_ind3];
/*-----------------------------------------------------------------------*/
/* 5) \modifier{} */
index = 5;
ifound = 0;
if(strcasecmp(intra_dict[5].keyarg,"on")==0) {ifound = 1;}
if(strcasecmp(intra_dict[5].keyarg,"con")==0){ifound = 2;}
if(strcasecmp(intra_dict[5].keyarg,"off")==0){ifound = 3;}
if(ifound==0){
keyarg_barf(intra_dict,file_name,fun_key,index);
}
if(ifound == 2 && clatoms_info->pi_beads>1){
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
printf("Constraints not implemented under \n");
printf(" path integral dynamics. \n");
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
fflush(stdout);
exit(1);
}/*endif*/
/*-----------------------------------------------------------------------*/
/* 6) bend type */
igo = imask1*imask2*imask3;
if(igo==1){
itype1 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind1)];
itype2 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind2)];
itype3 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind3)];
strcpy(build_intra->cbend_typ_now->atm1,atommaps->atm_typ[itype1]);
strcpy(build_intra->cbend_typ_now->atm2,atommaps->atm_typ[itype2]);
strcpy(build_intra->cbend_typ_now->atm3,atommaps->atm_typ[itype3]);
strcpy(build_intra->cbend_typ_now->label,intra_dict[6].keyarg);
}/*endif*/
/*=======================================================================*/
/* III) Spread Power bends */
if(ifound==1&&igo==1){
/* A) Add more space */
if(bend->npow > build_intra->nbend_pow_max){
build_intra->nbend_pow_max += NMEM_MIN;
bend->j1_pow =(int*)crealloc(&(bend->j1_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bend->j2_pow =(int*)crealloc(&(bend->j2_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bend->j3_pow =(int*)crealloc(&(bend->j3_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bend->jtyp_pow=(int*)crealloc(&(bend->jtyp_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
}/*endif*/
/*--------------------------------------------------------------------*/
/* C) Check type */
itype = bend->ntyp_pow+1;
for(i=1;i<=bend->ntyp_pow;i++){
if((strcasecmp(build_intra->cbend_typ_pow[i].atm1,
build_intra->cbend_typ_now->atm1)==0)
&&(strcasecmp(build_intra->cbend_typ_pow[i].atm2,
build_intra->cbend_typ_now->atm2)==0)
&&(strcasecmp(build_intra->cbend_typ_pow[i].atm3,
build_intra->cbend_typ_now->atm3)==0)
&&(strcasecmp(build_intra->cbend_typ_pow[i].label,
build_intra->cbend_typ_now->label)==0)) {itype=i;}
if((strcasecmp(build_intra->cbend_typ_pow[i].atm1,
build_intra->cbend_typ_now->atm3)==0)
&&(strcasecmp(build_intra->cbend_typ_pow[i].atm2,
build_intra->cbend_typ_now->atm2)==0)
&&(strcasecmp(build_intra->cbend_typ_pow[i].atm3,
build_intra->cbend_typ_now->atm1)==0)
&&(strcasecmp(build_intra->cbend_typ_pow[i].label,
build_intra->cbend_typ_now->label)==0)) {itype=i;}
} /*endfor*/
/*---------------------------------------------------------------------*/
/* D) Add space */
if(itype>build_intra->nbend_typ_pow_max){
build_intra->nbend_typ_pow_max += NMEM_MIN;
build_intra->cbend_typ_pow =
(CBEND *) crealloc(&build_intra->cbend_typ_pow[1],
build_intra->nbend_typ_pow_max*sizeof(CBEND))-1;
}/*endif*/
/*----------------------------------------------------------------------*/
/* E) Add a type */
if(itype==bend->ntyp_pow+1){
bend->ntyp_pow++;
strcpy(build_intra->cbend_typ_pow[itype].atm1,
build_intra->cbend_typ_now->atm1);
strcpy(build_intra->cbend_typ_pow[itype].atm2,
build_intra->cbend_typ_now->atm2);
strcpy(build_intra->cbend_typ_pow[itype].atm3,
build_intra->cbend_typ_now->atm3);
strcpy(build_intra->cbend_typ_pow[itype].label,
build_intra->cbend_typ_now->label);
}/*endif*/
/*---------------------------------------------------------------------*/
/* B) Spread */
bend->npow += 1;
bend->j1_pow[bend->npow] = iatm_ind1 + clatoms_info->natm_tot;
bend->j2_pow[bend->npow] = iatm_ind2 + clatoms_info->natm_tot;
bend->j3_pow[bend->npow] = iatm_ind3 + clatoms_info->natm_tot;
bend->jtyp_pow[bend->npow] = itype;
}/*endif*/
/*=======================================================================*/
/* IV) Spread Con bends */
if(ifound==2&&igo==1){
ires_off = atommaps->jres_jmol_typ_strt[jmol_typ]-1;
atommaps->nfree_jres_jmol_typ[ires_off+iresidue] -= 1;
atommaps->icons_jres_jmol_typ[ires_off+iresidue] = 1;
/*---------------------------------------------------------------------*/
/* A) Add more space */
if(bend->ncon+1 > build_intra->nbend_con_max){
build_intra->nbend_con_max += NMEM_MIN;
bend->j1_con = (int *)crealloc(&(bend->j1_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
bend->j2_con = (int *)crealloc(&(bend->j2_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
bend->jtyp_con=(int *)crealloc(&(bend->jtyp_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
}/*endif*/
/*---------------------------------------------------------------------*/
/* C) Check type */
itype = (bend->ntyp_con)+1;
for(i=1;i<=bend->ntyp_con;i++){
if((strcasecmp(build_intra->cbend_typ_con[i].atm1,
build_intra->cbend_typ_now->atm1)==0)
&&(strcasecmp(build_intra->cbend_typ_con[i].atm2,
build_intra->cbend_typ_now->atm2)==0)
&&(strcasecmp(build_intra->cbend_typ_con[i].atm3,
build_intra->cbend_typ_now->atm3)==0)
&&(strcasecmp(build_intra->cbend_typ_con[i].label,
build_intra->cbend_typ_now->label)==0)) {itype=i;}
if((strcasecmp(build_intra->cbend_typ_con[i].atm1,
build_intra->cbend_typ_now->atm3)==0)
&&(strcasecmp(build_intra->cbend_typ_con[i].atm2,
build_intra->cbend_typ_now->atm2)==0)
&&(strcasecmp(build_intra->cbend_typ_con[i].atm3,
build_intra->cbend_typ_now->atm1)==0)
&&(strcasecmp(build_intra->cbend_typ_con[i].label,
build_intra->cbend_typ_now->label)==0)) {itype=i;}
}/*endfor*/
/*--------------------------------------------------------------------*/
/* D) Add space */
if(itype>build_intra->nbend_typ_con_max){
build_intra->nbend_typ_con_max += NMEM_MIN;
build_intra->cbend_typ_con = (CBEND *)
crealloc(&(build_intra->cbend_typ_con[1]),
build_intra->nbend_typ_con_max*sizeof(CBEND))-1;
}/*endif*/
/*---------------------------------------------------------------------*/
/* E) Add a type */
if(itype==(bend->ntyp_con)+1){
bend->ntyp_con+=1;
strcpy(build_intra->cbend_typ_con[itype].atm1,
build_intra->cbend_typ_now->atm1);
strcpy(build_intra->cbend_typ_con[itype].atm2,
build_intra->cbend_typ_now->atm2);
strcpy(build_intra->cbend_typ_con[itype].atm3,
build_intra->cbend_typ_now->atm3);
strcpy(build_intra->cbend_typ_con[itype].label,
build_intra->cbend_typ_now->label);
}/*endif*/
/*---------------------------------------------------------------------*/
/* B) Assign */
bend->ncon += 1;
bend->j1_con[bend->ncon] = iatm_ind1 + clatoms_info->natm_tot;
bend->j2_con[bend->ncon] = iatm_ind2 + clatoms_info->natm_tot;
bend->j3_con[bend->ncon] = iatm_ind3 + clatoms_info->natm_tot;
bend->jtyp_con[bend->ncon] = itype;
/*---------------------------------------------------------------------*/
/* F) Error */
if((atommaps->ighost_flag[bend->j1_con[bend->ncon]]!=0)||
(atommaps->ighost_flag[bend->j2_con[bend->ncon]]!=0)||
(atommaps->ighost_flag[bend->j3_con[bend->ncon]]!=0)){
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
printf("Ghost atoms are not permitted in constrained bends\n");
printf("in molecule index %d in residue index %d in file %s\n",
jmol_typ,iresidue,file_name);
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
fflush(stdout);
exit(1);
}/*endif*/
}/*endif*/
/*=======================================================================*/
/* V) Spread nul bends */
if(ifound==3&&igo==1){
/*---------------------------------------------------------------------*/
/* A) Add more space */
if(null_inter_parse->nbend_nul+1 > build_intra->nbend_nul_max){
build_intra->nbend_nul_max += NMEM_MIN;
null_inter_parse->jbend1_nul =
(int *) crealloc(&(null_inter_parse->jbend1_nul)[1],
build_intra->nbend_nul_max*sizeof(int))-1;
null_inter_parse->jbend2_nul =
(int *) crealloc(&(null_inter_parse->jbend2_nul)[1],
build_intra->nbend_nul_max*sizeof(int))-1;
null_inter_parse->jbend3_nul =
(int *) crealloc(&(null_inter_parse->jbend3_nul)[1],
build_intra->nbend_nul_max*sizeof(int))-1;
} /*endif*/
/*---------------------------------------------------------------------*/
/* B) Spread */
null_inter_parse->nbend_nul += 1;
(null_inter_parse->jbend1_nul)[(null_inter_parse->nbend_nul)] =
iatm_ind1 + clatoms_info->natm_tot;
(null_inter_parse->jbend2_nul)[(null_inter_parse->nbend_nul)] =
iatm_ind2 + clatoms_info->natm_tot;
(null_inter_parse->jbend3_nul)[(null_inter_parse->nbend_nul)] =
iatm_ind3 + clatoms_info->natm_tot;
}/*endif*/
/*----------------------------------------------------------------------*/
}/*end routine*/
void set_atm_params(DICT_WORD atm_dict[],int num_atm_dict,
char fun_key[],char filename[],
int jmol_typ,int jres, int jres_off,
CPATOM_MAPS *cpatom_maps,MDATOM_MAPS *atommaps,
BUILD_INTRA *build_intra,MDCLATOMS_INFO *clatoms_info,
MDGHOST_ATOMS *ghost_atoms,MDCONSTRNT *mdconstrnt)
/*=======================================================================*/
{/*begin routine*/
/*=======================================================================*/
/* Local Variables */
NAME site;
int i,iii,num,num2,num3,num4,iatm_ind,imask,index,num1;
int itype,iatm_ind_sm,ifound;
double dnum;
/*=======================================================================*/
/* I) Check for missing key words */
for(i=1;i<=num_atm_dict;i++){
if(atm_dict[i].iuset==0 && atm_dict[i].key_type==1){
keyword_miss(atm_dict,filename,fun_key,i);}
}/*endfor*/
/*=======================================================================*/
/* II) Get atm index */
sscanf(atm_dict[2].keyarg,"%d",&iatm_ind);
index = 2;
if(iatm_ind>build_intra->natmind_1res_now||iatm_ind<0){
keyarg_barf(atm_dict,filename,fun_key,index);}
imask = build_intra->mask_atm[iatm_ind];
/*=======================================================================*/
/*=======================================================================*/
if(imask>0){
/*=======================================================================*/
/* III) Get rejiggered atm index */
/*-----------------------------------------------------------------------*/
iatm_ind = (build_intra->index_atm)[iatm_ind];
if(iatm_ind>build_intra->natm_1res_now||iatm_ind<0){
keyarg_barf(atm_dict,filename,fun_key,index);}
build_intra->iatm_ind_chk[iatm_ind]++;
iatm_ind_sm = iatm_ind;
iatm_ind = iatm_ind + clatoms_info->natm_tot;
/*=======================================================================*/
/* IV) Fill the dictionary with words */
/*-----------------------------------------------------------------------*/
/* 3) \mass{} */
sscanf(atm_dict[3].keyarg,"%lg",&dnum);
index = 3;
if(dnum<=0.0){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
clatoms_info->mass[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 4) \charge{} */
sscanf(atm_dict[4].keyarg,"%lg",&dnum);
clatoms_info->q[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 5) \alpha_pol{} */
sscanf(atm_dict[5].keyarg,"%lg",&dnum);
index = 5;
if(dnum<0.0){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
clatoms_info->alp_pol[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 6) \b_neut{} */
sscanf(atm_dict[6].keyarg,"%lg",&dnum);
clatoms_info->b_neut[iatm_ind] = dnum;
/*--------------------------------------------------------------------*/
/* 7) \valence{} */
sscanf(atm_dict[7].keyarg,"%d",&num);
build_intra->bond_site[iatm_ind_sm].valence = num;
index = 7;
if(num<0||num>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);}
/*--------------------------------------------------------------------*/
/* 8) \improper_def{} */
strcpy(build_intra->strip1,atm_dict[8].keyarg);
parse_improp(build_intra->strip1,build_intra->strip2,&num1,&num2,&num3,
&num4);
build_intra->bond_site[iatm_ind_sm].improper_ind[1]=num1+1;
build_intra->bond_site[iatm_ind_sm].improper_ind[2]=num2+1;
build_intra->bond_site[iatm_ind_sm].improper_ind[3]=num3+1;
build_intra->bond_site[iatm_ind_sm].improper_ind[4]=num4+1;
index = 8;
if((num1+num2+num3+num4)!=0&&(num1+num2+num3+num4)!=6){
keyarg_barf(atm_dict,filename,fun_key,index);}
if((num1+num2+num3+num4)==6){
if(num1<0||num1>3||num2<0||num2>3||num3<0||num3>3||num4<0||num4>3||
num1==num2||num1==num3||num2==num3||num1==num4||num2==num4||
num3==num4){
keyarg_barf(atm_dict,filename,fun_key,index);}}
/*--------------------------------------------------------------------*/
/* 9) \bond_site_1{} */
strcpy(build_intra->strip1,atm_dict[9].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[1],site);
build_intra->bond_site[iatm_ind_sm].branch_1[1] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[1] = num3;
index = 9;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
/*--------------------------------------------------------------------*/
/* 10) \bond_site_2{} */
strcpy(build_intra->strip1,atm_dict[10].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[2],site);
build_intra->bond_site[iatm_ind_sm].branch_1[2] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[2] = num3;
index = 10;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);
}
/*---------------------------------------------------------------------*/
/* 11) \bond_site_3{} */
strcpy(build_intra->strip1,atm_dict[11].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[3],site);
build_intra->bond_site[iatm_ind_sm].branch_1[3] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[3] = num3;
index = 11;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);}
/*---------------------------------------------------------------------*/
/* 12) \bond_site_4{} */
strcpy(build_intra->strip1,atm_dict[12].keyarg);
parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[4],site);
build_intra->bond_site[iatm_ind_sm].branch_1[4] = num2;
build_intra->bond_site[iatm_ind_sm].branch_2[4] = num3;
index = 12;
if(strlen(site)==0||num2<-1||num3<-1||num2>MAX_VALENCE||num3>MAX_VALENCE){
keyarg_barf(atm_dict,filename,fun_key,index);}
/*------------------------------------------------------------------------*/
/* 15) \cp_atom{} */
ifound = 0;
if(strcasecmp(atm_dict[15].keyarg,"yes")==0){
ifound=1;cpatom_maps->cp_atm_flag[iatm_ind] = 1;
}
if(strcasecmp(atm_dict[15].keyarg,"no")==0){
ifound=1;cpatom_maps->cp_atm_flag[iatm_ind] = 0;
}
/*--------------------------------------------------------------------*/
/* 13) \cp_valence_up{} */
cpatom_maps->cp_vlnc_up[iatm_ind] = 0;
if(atm_dict[13].iuset==1){
sscanf(atm_dict[13].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_up[iatm_ind] = num;
}/*endif*/
if(atm_dict[13].iuset==0 && cpatom_maps->cp_atm_flag[iatm_ind]==1){
index = 13;
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
/*--------------------------------------------------------------------*/
/* 14) \cp_valence_dn{} */
cpatom_maps->cp_vlnc_dn[iatm_ind] = cpatom_maps->cp_vlnc_up[iatm_ind];
if(atm_dict[14].iuset == 1){
sscanf(atm_dict[14].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_dn[iatm_ind] = num;
}/*endif*/
/*------------------------------------------------------------------------*/
/* 16) /def_ghost1{} */
ghost_atoms->ighost_flag[iatm_ind] = 0;
if(atm_dict[16].iuset!=0){
set_ghost(ghost_atoms,clatoms_info,atommaps,build_intra,
atm_dict,num_atm_dict,
filename,fun_key,iatm_ind);
}/*endif*/
/*------------------------------------------------------------------------*/
/* 17) \label{} */
index = 16+NCOEF_GHOST_MAX;
ifound = 0;
if(strcasecmp(atm_dict[index].keyarg,"standard")==0){
ifound=1;mdconstrnt->atom_label[iatm_ind] = 0;
}
if(strcasecmp(atm_dict[index].keyarg,"backbone")==0){
ifound=1;mdconstrnt->atom_label[iatm_ind] = 1;
}
if(strcasecmp(atm_dict[index].keyarg,"sidechain")==0){
ifound=1;mdconstrnt->atom_label[iatm_ind] = 2;
}
if(ifound==0){
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
/*--------------------------------------------------------------------*/
/* 18+NCOEF_GHOST_MAX) \cp_valence_true_up{} */
cpatom_maps->cp_vlnc_true_up[iatm_ind] = cpatom_maps->cp_vlnc_up[iatm_ind];
if(atm_dict[18+NCOEF_GHOST_MAX].iuset == 1){
sscanf(atm_dict[18+NCOEF_GHOST_MAX].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_true_up[iatm_ind] = num;
if (num>cpatom_maps->cp_vlnc_up[iatm_ind]){
index = 18+NCOEF_GHOST_MAX;
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
}/*endif*/
/*--------------------------------------------------------------------*/
/* 19+NCOEF_GHOST_MAX) \cp_valence_true_dn{} */
cpatom_maps->cp_vlnc_true_dn[iatm_ind] = cpatom_maps->cp_vlnc_true_up[iatm_ind];
if(atm_dict[19+NCOEF_GHOST_MAX].iuset == 1){
sscanf(atm_dict[19+NCOEF_GHOST_MAX].keyarg,"%d",&num);
cpatom_maps->cp_vlnc_true_dn[iatm_ind] = num;
if (num>cpatom_maps->cp_vlnc_dn[iatm_ind]){
index = 19+NCOEF_GHOST_MAX;
keyarg_barf(atm_dict,filename,fun_key,index);
}/*endif*/
}/*endif*/
/*------------------------------------------------------------------------*/
/*====================================================================*/
/* IV) Do up atom types */
itype = atommaps->natm_typ + 1;
for(i=1;i<=atommaps->natm_typ;i++){
if(strcasecmp(atm_dict[1].keyarg,atommaps->atm_typ[i])==0)
itype=i;
} /*endfor*/
if(itype>build_intra->natm_typ_max){
build_intra->natm_typ_max+=NMEM_MIN;
atommaps->atm_typ = (NAME *)
crealloc(&(atommaps->atm_typ[1]),
(build_intra->natm_typ_max)*sizeof(NAME),"set_atm_params")-1;
}/*endif*/
if(itype==atommaps->natm_typ+1){
atommaps->natm_typ+=1;
strcpy(atommaps->atm_typ[itype],atm_dict[1].keyarg);
}/*endif*/
/*====================================================================*/
/* V) Do up types */
atommaps->iatm_mol_typ[iatm_ind] = jmol_typ;
atommaps->iatm_mol_num[iatm_ind] = 1;
atommaps->iatm_res_num[iatm_ind] = jres;
atommaps->iatm_atm_typ[iatm_ind] = itype;
atommaps->iatm_res_typ[iatm_ind] =
atommaps->ires_typ_jres_jmol_typ[jres+jres_off];
/*====================================================================*/
/*====================================================================*/
} /*endif (imask>0) */
/*======================================================================*/
} /*end routine*/
void set_onfo_params(DICT_WORD *intra_dict,int num_intra_dict,
char *fun_key,char *file_name,int jmol_typ,
MDCLATOMS_INFO *clatoms_info,MDATOM_MAPS *atommaps,
MDONFO *onfo,NULL_INTER_PARSE *null_inter_parse,
BUILD_INTRA *build_intra, int iresidue, int ires_off)
/*==========================================================================*/
{/*begin routine */
int num,index,ifound,igo;
int itype1,itype2;
int iatm_ind1,iatm_ind2;
int imask1,imask2;
int i,itype;
/*=======================================================================*/
/* I) Check for missing key words*/
for(i=1;i<=2;i++){
if(intra_dict[i].iuset==0 && intra_dict[i].key_type==1){
keyword_miss(intra_dict,file_name,fun_key,i);}
} /*endfor*/
/*=======================================================================*/
/* II) Fill the dictionary with words */
/*-----------------------------------------------------------------------*/
/* 1) \atom1{} */
index = 1;
sscanf(intra_dict[1].keyarg,"%d",&num);
iatm_ind1 = num;
if(iatm_ind1>build_intra->natmind_1res_now||iatm_ind1<0){
keyarg_barf(intra_dict,file_name,fun_key,index);}
imask1 = build_intra->mask_atm[iatm_ind1];
if(imask1>0)iatm_ind1 = build_intra->index_atm[iatm_ind1];
/*------------------------------------------------------------------------*/
/* 2) \atom2{} */
index = 2;
sscanf(intra_dict[2].keyarg,"%d",&num);
iatm_ind2 = num;
if(iatm_ind2>build_intra->natmind_1res_now||iatm_ind2<0){
keyarg_barf(intra_dict,file_name,fun_key,index);}
imask2 = build_intra->mask_atm[iatm_ind2];
if(imask2>0)iatm_ind2 = build_intra->index_atm[iatm_ind2];
/*-----------------------------------------------------------------------*/
/* 5) \modifier{} */
index = 5;
ifound = 0;
if(strcasecmp(intra_dict[5].keyarg,"on")==0) {ifound = 1;}
if(strcasecmp(intra_dict[5].keyarg,"off")==0){ifound = 2;}
if(ifound==0){
keyarg_barf(intra_dict,file_name,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 6) bond type */
igo = imask1*imask2;
if(igo==1){
itype1 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind1)];
itype2 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind2)];
strcpy(build_intra->confo_typ_now->atm1,atommaps->atm_typ[itype1]);
strcpy(build_intra->confo_typ_now->atm2,atommaps->atm_typ[itype2]);
strcpy(build_intra->confo_typ_now->label,intra_dict[6].keyarg);
}/*endif*/
/*======================================================================*/
/* III) Spread onfos */
if(ifound==1&&igo==1){
/*---------------------------------------------------------------------*/
/* A) Add more space */
if(onfo->num+1 > build_intra->nonfo_max){
build_intra->nonfo_max += NMEM_MIN;
onfo->j1 =(int *) crealloc(&(onfo->j1)[1],
build_intra->nonfo_max*sizeof(int),"set_onfo_params")-1;
onfo->j2 =(int *) crealloc(&(onfo->j2)[1],
build_intra->nonfo_max*sizeof(int),"set_onfo_params")-1;
onfo->jtyp =(int *) crealloc(&(onfo->jtyp)[1],
build_intra->nonfo_max*sizeof(int),"set_onfo_params")-1;
}/*endif*/
/*--------------------------------------------------------------------*/
/* C) Check type */
itype = (onfo->ntyp)+1;
for(i=1;i<=onfo->ntyp;i++){
if((strcasecmp(build_intra->confo_typ[i].atm1,
build_intra->confo_typ_now->atm1)==0)
&&(strcasecmp(build_intra->confo_typ[i].atm2,
build_intra->confo_typ_now->atm2)==0)
&&(strcasecmp(build_intra->confo_typ[i].label,
build_intra->confo_typ_now->label)==0)) {itype=i;}
if((strcasecmp(build_intra->confo_typ[i].atm1,
build_intra->confo_typ_now->atm2)==0)
&&(strcasecmp(build_intra->confo_typ[i].atm2,
build_intra->confo_typ_now->atm1)==0)
&&(strcasecmp(build_intra->confo_typ[i].label,
build_intra->confo_typ_now->label)==0)) {itype=i;}
}/*endfor*/
/*---------------------------------------------------------------------*/
/* D) Add space */
if(itype>build_intra->nonfo_typ_max){
build_intra->nonfo_typ_max += NMEM_MIN;
build_intra->confo_typ = (CBOND *)
crealloc(&(build_intra->confo_typ)[1],
build_intra->nonfo_typ_max*sizeof(CBOND),"set_onfo_params")-1;
}/*endif*/
/*---------------------------------------------------------------------*/
/* E) Add a type */
if(itype==(onfo->ntyp)+1){
onfo->ntyp+=1;
strcpy(build_intra->confo_typ[itype].atm1,
build_intra->confo_typ_now->atm1);
strcpy(build_intra->confo_typ[itype].atm2,
build_intra->confo_typ_now->atm2);
strcpy(build_intra->confo_typ[itype].label,
build_intra->confo_typ_now->label);
}/*endif*/
/*---------------------------------------------------------------------*/
/* B) Spread */
onfo->num += 1;
onfo->j1[onfo->num] = iatm_ind1 + clatoms_info->natm_tot;
onfo->j2[onfo->num] = iatm_ind2 + clatoms_info->natm_tot;
onfo->jtyp[onfo->num] = itype;
}/*endif*/
/*======================================================================*/
/* V) Spread nul onfos */
if(ifound==3&&igo==1){
/*--------------------------------------------------------------------*/
/* A) Add more space */
if(null_inter_parse->nonfo_nul+1 > build_intra->nonfo_nul_max){
build_intra->nonfo_nul_max += NMEM_MIN;
null_inter_parse->jonfo1_nul =
(int *) crealloc(&(null_inter_parse->jonfo1_nul)[1],
build_intra->nonfo_nul_max*sizeof(int),"set_onfo_params")-1;
null_inter_parse->jonfo2_nul =
(int *) crealloc(&(null_inter_parse->jonfo2_nul)[1],
build_intra->nonfo_nul_max*sizeof(int),"set_onfo_params")-1;
}/*endif*/
/*--------------------------------------------------------------------*/
/* B) Spread */
null_inter_parse->nonfo_nul += 1;
null_inter_parse->jonfo1_nul[null_inter_parse->nonfo_nul]
= iatm_ind1 + clatoms_info->natm_tot;
null_inter_parse->jonfo2_nul[null_inter_parse->nonfo_nul]
= iatm_ind2 + clatoms_info->natm_tot;
}/*endif*/
/*----------------------------------------------------------------------*/
}/*end routine*/
void set_rbar_free_params(char *molsetname,char fun_key[],
DICT_WORD rbar_free_dict[], int num_rbar_free_dict,
RBAR_SIG_FREE *rbar_sig_free,FREE_PARSE *free_parse,
int nmol_typ)
/*========================================================================*/
{ /*begin routine */
/*========================================================================*/
/* Local variables */
int num,i,index;
double dnum;
FILE *fp;
/*========================================================================*/
/* I) Check for missing key words*/
for(i=1; i<num_rbar_free_dict; i++) {
if((rbar_free_dict[i].iuset==0) && (rbar_free_dict[i].key_type==1)) {
keyword_miss(rbar_free_dict,molsetname,fun_key,i);
}/*endif*/
}/*endfor*/
/*=========================================================================*/
/* II) Set the params */
/*-----------------------------------------------------------------------*/
/* 1)\num_bond{} */
sscanf(rbar_free_dict[1].keyarg,"%d",&num);
rbar_sig_free->nfree = num;
free_parse->nbar_bond = num;
index = 1;
if((num <=0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 3)\eq_bar{} */
sscanf(rbar_free_dict[3].keyarg,"%lg",&dnum);
rbar_sig_free->eq_bar = dnum/BOHR;
index = 3;
if((dnum < 0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 4)\fk_bar{} */
sscanf(rbar_free_dict[4].keyarg,"%lg",&dnum);
rbar_sig_free->fk_bar = dnum*BOHR*BOHR/BOLTZ;
index = 4;
if((dnum < 0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 5)\eq_sig{} */
sscanf(rbar_free_dict[5].keyarg,"%lg",&dnum);
rbar_sig_free->eq_sigma = dnum/BOHR;
index = 5;
if((dnum < 0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 6)\fk_sig{} */
sscanf(rbar_free_dict[6].keyarg,"%lg",&dnum);
rbar_sig_free->fk_sigma = dnum*BOHR*BOHR/BOLTZ;
index = 6;
if((dnum < 0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 7)\rmin_hist{} */
sscanf(rbar_free_dict[7].keyarg,"%lg",&dnum);
rbar_sig_free->rmin = dnum/BOHR;
index = 7;
if((dnum < 0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 8)\rmax_hist{} */
sscanf(rbar_free_dict[8].keyarg,"%lg",&dnum);
rbar_sig_free->rmax = dnum/BOHR;
index = 8;
if((dnum < 0)|| (dnum< rbar_sig_free->rmin)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 9)\num_rbar_hist{} */
sscanf(rbar_free_dict[9].keyarg,"%d",&num);
rbar_sig_free->nhist_bar = num;
index = 9;
if((num <=0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 10)\smin_hist{} */
sscanf(rbar_free_dict[10].keyarg,"%lg",&dnum);
rbar_sig_free->smin = dnum/BOHR;
index = 10;
if((dnum < 0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 11)\smax_hist{} */
sscanf(rbar_free_dict[11].keyarg,"%lg",&dnum);
rbar_sig_free->smax = dnum/BOHR;
index = 11;
if((dnum < 0)|| (dnum< rbar_sig_free->smin)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 12)\num_sig_hist{} */
sscanf(rbar_free_dict[12].keyarg,"%d",&num);
rbar_sig_free->nhist_sig = num;
index = 12;
if((num <=0)) {
keyarg_barf(rbar_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 13)\hist_file{} */
strcpy(rbar_sig_free->file,rbar_free_dict[13].keyarg);
/*-----------------------------------------------------------------------*/
/*=========================================================================*/
/* III) Use the data and malloc */
rbar_sig_free->del_bar = ((rbar_sig_free->rmax)- (rbar_sig_free->rmin))/
((double)(rbar_sig_free->nhist_bar));
rbar_sig_free->del_sig = ((rbar_sig_free->smax)- (rbar_sig_free->smin))/
((double)(rbar_sig_free->nhist_sig));
num = rbar_sig_free->nfree;
rbar_sig_free->rnfree = (double) num;
free_parse->imoltyp_rbar1_free = (int *)cmalloc(num*sizeof(int))-1;
free_parse->imoltyp_rbar2_free = (int *)cmalloc(num*sizeof(int))-1;
free_parse->imol_rbar1_free = (int *)cmalloc(num*sizeof(int))-1;
free_parse->imol_rbar2_free = (int *)cmalloc(num*sizeof(int))-1;
free_parse->ires_rbar1_free = (int *)cmalloc(num*sizeof(int))-1;
free_parse->ires_rbar2_free = (int *)cmalloc(num*sizeof(int))-1;
free_parse->iatm_rbar1_free = (int *)cmalloc(num*sizeof(int))-1;
free_parse->iatm_rbar2_free = (int *)cmalloc(num*sizeof(int))-1;
/*=========================================================================*/
/* IV) Read in the indicies */
fp = cfopen(rbar_free_dict[2].keyarg,"r");
fscanf(fp,"%d",&num);
readtoendofline(fp);
if(num!=rbar_sig_free->nfree) {
printf("To have no errors,\n");
printf("Would be life without meaning,\n");
printf("No struggle, no joy.\n");
printf("Number of free energy bonds %d in file %s,\n",num,
rbar_free_dict[2].keyarg);
printf("does not match the request value %d \n",rbar_sig_free->nfree);
fflush(stdout);
exit(1);
}/*endif*/
for(i=1; i<=num; i++) {
fscanf(fp,"%d %d %d %d",
&(free_parse->imoltyp_rbar1_free[i]),
&(free_parse->imol_rbar1_free[i]),
&(free_parse->ires_rbar1_free[i]),
&(free_parse->iatm_rbar1_free[i]));
readtoendofline(fp);
fscanf(fp,"%d %d %d %d",
&(free_parse->imoltyp_rbar2_free[i]),
&(free_parse->imol_rbar2_free[i]),
&(free_parse->ires_rbar2_free[i]),
&(free_parse->iatm_rbar2_free[i]));
readtoendofline(fp);
}/*endfor*/
fclose(fp);
/*-----------------------------------------------------------------------*/
}/*end routine*/
void set_tors_free_params(char molsetname[],char fun_key[],
DICT_WORD tors_free_dict[], int num_tors_free_dict,
TORS_FREE *tors_free,FREE_PARSE *free_parse,
int nmol_typ)
/*==========================================================================*/
{ /*begin routine*/
/*==========================================================================*/
/* Local variables */
int i,num,index,ntors;
double dnum;
/*==========================================================================*/
/* I) Check for missing key words*/
for(i=1; i<=num_tors_free_dict; i++) {
if(tors_free_dict[i].iuset==0 && tors_free_dict[i].key_type==1) {
keyword_miss(tors_free_dict,molsetname,fun_key,i);
}
} /*endfor*/
/*==========================================================================*/
/* II) Set the params */
/*-----------------------------------------------------------------------*/
/* 39)\ntors{} */
index = 39;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
ntors = num;
tors_free->num = num;
if(num <=0 || num > 2) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
if(ntors>1) {
for(i=22; i<=33; i++) {
if(tors_free_dict[i].iuset==0) {
keyword_miss(tors_free_dict,molsetname,fun_key,i);
}
}/*endfor*/
if(tors_free_dict[38].iuset==0) {
keyword_miss(tors_free_dict,molsetname,fun_key,i);
}/*endif*/
}/*endif*/
/*-----------------------------------------------------------------------*/
/* 1)\atom1.1_moltyp_ind{} */
sscanf(tors_free_dict[1].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[1] = num;
index = 1;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 2)\atom2.1_moltyp_ind{} */
sscanf(tors_free_dict[2].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[2] = num;
index = 2;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 3)\atom3.1_moltyp_ind{} */
sscanf(tors_free_dict[3].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[3] = num;
index = 3;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 4)\atom4.1_moltyp_ind{} */
sscanf(tors_free_dict[4].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[4] = num;
index = 4;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 5)\atom1.1_mol_ind{} */
sscanf(tors_free_dict[5].keyarg,"%d",&num);
free_parse->imol_tors_free[1] = num;
index = 5;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 6)\atom2.1_mol_ind{} */
sscanf(tors_free_dict[6].keyarg,"%d",&num);
free_parse->imol_tors_free[2] = num;
index = 6;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 7)\atom3.1_mol_ind{} */
sscanf(tors_free_dict[7].keyarg,"%d",&num);
free_parse->imol_tors_free[3] = num;
index = 7;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 8)\atom4.1_mol_ind{} */
sscanf(tors_free_dict[8].keyarg,"%d",&num);
free_parse->imol_tors_free[4] = num;
index = 8;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 9)\atom1.1_atm_ind{} */
sscanf(tors_free_dict[9].keyarg,"%d",&num);
free_parse->iatm_tors_free[1] = num;
index = 9;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 10)\atom2.1_atm_ind{} */
sscanf(tors_free_dict[10].keyarg,"%d",&num);
free_parse->iatm_tors_free[2] = num;
index = 10;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 11)\atom3.1_atm_ind{} */
sscanf(tors_free_dict[11].keyarg,"%d",&num);
free_parse->iatm_tors_free[3] = num;
index = 11;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 12)\atom4.1_atm_ind{} */
sscanf(tors_free_dict[12].keyarg,"%d",&num);
free_parse->iatm_tors_free[4] = num;
index = 12;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 13)\eq_1{} */
sscanf(tors_free_dict[13].keyarg,"%lg",&dnum);
tors_free->eq[1] = dnum*M_PI/180.0;
index = 13;
if((dnum <-180.0)||(dnum >180.0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 14)\fk{} */
sscanf(tors_free_dict[14].keyarg,"%lg",&dnum);
tors_free->fk = dnum/BOLTZ;
index = 14;
if((dnum < 0.)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 15)\num_hist{} */
sscanf(tors_free_dict[15].keyarg,"%d",&num);
tors_free->nhist = num;
index = 15;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 16)\power{} */
sscanf(tors_free_dict[16].keyarg,"%d",&num);
tors_free->npow = num;
index = 16;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 17)\hist_file{} */
strcpy(tors_free->file,tors_free_dict[17].keyarg);
/*-----------------------------------------------------------------------*/
/* 18)\atom1.1_residue_ind{} */
sscanf(tors_free_dict[18].keyarg,"%d",&num);
free_parse->ires_tors_free[1] = num;
index = 18;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 19)\atom2.1_iresidue_ind{} */
sscanf(tors_free_dict[19].keyarg,"%d",&num);
free_parse->ires_tors_free[2] = num;
index = 19;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 20)\atom3.1_iresidue_ind{} */
sscanf(tors_free_dict[20].keyarg,"%d",&num);
free_parse->ires_tors_free[3] = num;
index = 20;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 21)\atom4.1_iresidue_ind{} */
sscanf(tors_free_dict[21].keyarg,"%d",&num);
free_parse->ires_tors_free[4] = num;
index = 21;
if(num <=0) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/*-----------------------------------------------------------------------*/
/* 22)\atom1.2_moltyp_ind{} */
index = 22;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[5] = num;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 23)\atom2.2_moltyp_ind{} */
index = 23;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[6] = num;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 24)\atom3.2_moltyp_ind{} */
index = 24;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[7] = num;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 25)\atom4.2_moltyp_ind{} */
index = 25;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imoltyp_tors_free[8] = num;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 26)\atom1.2_mol_ind{} */
index = 26;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imol_tors_free[5] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 27)\atom2.2_mol_ind{} */
index = 27;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imol_tors_free[6] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 28)\atom3.2_mol_ind{} */
index = 28;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imol_tors_free[7] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 29)\atom4.2_mol_ind{} */
index = 29;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->imol_tors_free[8] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 30)\atom1.2_atm_ind{} */
index = 30;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->iatm_tors_free[5] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 31)\atom2.2_atm_ind{} */
index = 31;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->iatm_tors_free[6] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 32)\atom3.2_atm_ind{} */
index = 32;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->iatm_tors_free[7] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 33)\atom4.2_atm_ind{} */
index = 33;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->iatm_tors_free[8] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 34)\atom1.2_residue_ind{} */
index = 34;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->ires_tors_free[5] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 35)\atom2.2_iresidue_ind{} */
index = 35;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->ires_tors_free[6] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 36)\atom3.2_iresidue_ind{} */
index = 36;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->ires_tors_free[7] = num;
if((num <=0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 37)\atom4.2_iresidue_ind{} */
index = 37;
sscanf(tors_free_dict[index].keyarg,"%d",&num);
free_parse->ires_tors_free[8] = num;
if(num <=0) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 38)\eq_2{} */
index = 38;
sscanf(tors_free_dict[index].keyarg,"%lg",&dnum);
tors_free->eq[2] = dnum*M_PI/180.0;
if((dnum <-180.0)||(dnum >180.0)) {
keyarg_barf(tors_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
tors_free->del = (2.0*M_PI)/((double)(tors_free->nhist));
/*-----------------------------------------------------------------------*/
} /*end routine*/
void set_bond_free_params(char *molsetname,char fun_key[],
DICT_WORD bond_free_dict[], int num_bond_free_dict,
BOND_FREE *bond_free,FREE_PARSE *free_parse,
int nmol_typ)
/*========================================================================*/
{ /*begin routine */
/*========================================================================*/
/* Local variables */
int num,i,index;
double dnum;
/*========================================================================*/
/* I) Check for missing key words*/
for(i=1; i<num_bond_free_dict; i++) {
if(bond_free_dict[i].iuset==0 && bond_free_dict[i].key_type==1) {
keyword_miss(bond_free_dict,molsetname,fun_key,i);
}
}/*endfor*/
/*=========================================================================*/
/* II) Set the params */
/*-----------------------------------------------------------------------*/
/* 1)\atom1_moltyp_ind{} */
sscanf(bond_free_dict[1].keyarg,"%d",&num);
free_parse->imoltyp_bond_free[1] = num;
index = 1;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 2)\atom2_moltyp_ind{} */
sscanf(bond_free_dict[2].keyarg,"%d",&num);
free_parse->imoltyp_bond_free[2] = num;
index = 2;
if((num <=0)|| (num>nmol_typ)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 3)\atom1_mol_ind{} */
sscanf(bond_free_dict[3].keyarg,"%d",&num);
free_parse->imol_bond_free[1] = num;
index = 3;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 4)\atom2_mol_ind{} */
sscanf(bond_free_dict[4].keyarg,"%d",&num);
free_parse->imol_bond_free[2] = num;
index = 4;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 5)\atom1_atm_ind{} */
sscanf(bond_free_dict[5].keyarg,"%d",&num);
free_parse->iatm_bond_free[1] = num;
index = 5;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 6)\atom2_atm_ind{} */
sscanf(bond_free_dict[6].keyarg,"%d",&num);
free_parse->iatm_bond_free[2] = num;
index = 6;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 7)\eq{} */
sscanf(bond_free_dict[7].keyarg,"%lg",&dnum);
bond_free->eq = dnum/BOHR;
index = 7;
/*-----------------------------------------------------------------------*/
/* 8)\fk{} */
sscanf(bond_free_dict[8].keyarg,"%lg",&dnum);
bond_free->fk = dnum*BOHR*BOHR/BOLTZ;
index = 8;
if((dnum < 0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 9)\rmin_hist{} */
sscanf(bond_free_dict[9].keyarg,"%lg",&dnum);
bond_free->rmin = dnum/BOHR;
/*-----------------------------------------------------------------------*/
/* 10)\rmax_hist{} */
sscanf(bond_free_dict[10].keyarg,"%lg",&dnum);
bond_free->rmax = dnum/BOHR;
/*-----------------------------------------------------------------------*/
/* 11)\num_hist{} */
sscanf(bond_free_dict[11].keyarg,"%d",&num);
bond_free->nhist = num;
index = 11;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 12)\power{} */
sscanf(bond_free_dict[12].keyarg,"%d",&num);
bond_free->npow = num;
index = 12;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 13)\hist_file{} */
strcpy(bond_free->file,bond_free_dict[13].keyarg);
/*-----------------------------------------------------------------------*/
/* 14)\atom1_residue_ind{} */
sscanf(bond_free_dict[14].keyarg,"%d",&num);
free_parse->ires_bond_free[1] = num;
index = 14;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
/* 15)\atom2_residue_ind{} */
sscanf(bond_free_dict[15].keyarg,"%d",&num);
free_parse->ires_bond_free[2] = num;
index = 15;
if((num <=0)) {
keyarg_barf(bond_free_dict,molsetname,fun_key,index);
}
/*-----------------------------------------------------------------------*/
bond_free->del =((bond_free->rmax)- (bond_free->rmin))/
((double)(bond_free->nhist));
/*-----------------------------------------------------------------------*/
/*end routine*/
}