implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.VAR'
+c include 'include_unres/COMMON.VAR'
include 'COMMON.INTERACT'
include 'COMMON.LOCAL'
include 'COMMON.NAMES'
call reada(controlcard,'SCALSCP',scalscp,1.0d0)
call reada(controlcard,'CUTOFF',cutoff_corr,7.0d0)
call reada(controlcard,'DELT_CORR',delt_corr,0.5d0)
+C Bartek
+ call reada(controlcard,'WDFAD',wdfa_dist,0.0d0)
+ call reada(controlcard,'WDFAT',wdfa_tor,0.0d0)
+ call reada(controlcard,'WDFAN',wdfa_nei,0.0d0)
+ call reada(controlcard,'WDFAB',wdfa_beta,0.0d0)
+ write (iout,*) "wdfa_dist",wdfa_dist," wdfa_tor",wdfa_tor,
+ & " wdfa_nei",wdfa_nei," wdfa_beta",wdfa_beta
r0_corr=cutoff_corr-delt_corr
call readi(controlcard,"NRES",nres,0)
iscode=index(controlcard,"ONE_LETTER")
do i=1,nres
itype(i)=rescode(i,sequence(i),iscode)
enddo
+ if (itype(2).eq.10.and.itype(1).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the first full residue, initial dummy deleted"
+ do i=1,nres
+ itype(i)=itype(i+1)
+ enddo
+ nres=nres-1
+ endif
+ if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the last full residue, terminal dummy deleted"
+ nres=nres-1
+ endif
write (iout,*) "Numeric code:"
write (iout,'(20i4)') (itype(i),i=1,nres)
do i=1,nres-1
if (itype(1).eq.21) nnt=2
if (itype(nres).eq.21) nct=nct-1
write(iout,*) 'NNT=',NNT,' NCT=',NCT
+
+C Juyong:READ init_vars
+C Initialize variables!
+C Juyong:READ read_info
+C READ fragment information!!
+C both routines should be in dfa.F file!!
+
+ if (.not. (wdfa_dist.eq.0.0 .and. wdfa_tor.eq.0.0 .and.
+ & wdfa_nei.eq.0.0 .and. wdfa_beta.eq.0.0)) then
+ write (iout,*) "Calling init_dfa_vars"
+ call flush(iout)
+ call init_dfa_vars
+ write (iout,*) 'init_dfa_vars finished!'
+ call flush(iout)
+ call read_dfa_info
+ write (iout,*) 'read_dfa_info finished!'
+ call flush(iout)
+ endif
+
c Read distance restraints
if (constr_dist.gt.0) then
if (refstr) call read_ref_structure(*11)
call hpb_partition
endif
+ if (constr_homology.gt.0) then
+c write (iout,*) "About to call read_constr_homology"
+c call flush(iout)
+ call read_constr_homology
+c write (iout,*) "Exit read_constr_homology"
+c call flush(iout)
+ if (indpdb.gt.0 .or. pdbref) then
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=crefjlee(j,i)
+ cref(j,i)=crefjlee(j,i)
+ enddo
+ enddo
+ endif
+#ifdef DEBUG
+ write (iout,*) "Array C"
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(c(j,i),j=1,3),
+ & (c(j,i+nres),j=1,3)
+ enddo
+ write (iout,*) "Array Cref"
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(cref(j,i),j=1,3),
+ & (cref(j,i+nres),j=1,3)
+ enddo
+#endif
+#ifdef DEBUG
+ call int_from_cart1(.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ write (iout,*) i," phiref",phiref(i)," thetaref",thetaref(i)
+ enddo
+ do i=1,nres-1
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
+ enddo
+ enddo
+ do i=2,nres-1
+ do j=1,3
+ dc(j,i+nres)=c(j,i+nres)-c(j,i)
+ dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
+ enddo
+ enddo
+#endif
+ else
+ homol_nset=0
+ endif
+
+
call setup_var
call init_int_table
if (ns.gt.0) then
enddo
endif
endif
+ if (ns.gt.0.and.dyn_ss) then
+C /06/28/2013 Adasko:ns is number of Cysteins bonded also called half of
+C the bond
+ do i=nss+1,nhpb
+C /06/28/2013 Adasko: nss number of full SS bonds
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+C /06/28/2013 Adasko: dyn_ss_mask which Cysteins can form disulfidebond
+c write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU"
+ enddo
+ endif
return
end
c------------------------------------------------------------------------------
integer ifrag_(2,100),ipair_(2,100)
double precision wfrag_(100),wpair_(100)
character*500 controlcard
-c write (iout,*) "Calling read_dist_constr"
+ logical normalize,next
+ integer restr_type
+ double precision xlink(4,0:4) /
+c a b c sigma
+ & 0.0d0,0.0d0,0.0d0,0.0d0, ! default, no xlink potential
+ & 0.00305218d0,9.46638d0,4.68901d0,4.74347d0, ! ZL
+ & 0.00214928d0,12.7517d0,0.00375009d0,6.13477d0, ! ADH
+ & 0.00184547d0,11.2678d0,0.00140292d0,7.00868d0, ! PDH
+ & 0.000161786d0,6.29273d0,4.40993d0,7.13956d0 / ! DSS
+ write (iout,*) "Calling read_dist_constr"
c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
c call flush(iout)
+ next=.true.
+
+ DO WHILE (next)
+
call card_concat(controlcard,.true.)
+ next = index(controlcard,"NEXT").gt.0
+ call readi(controlcard,"RESTR_TYPE",restr_type,constr_dist)
+ write (iout,*) "restr_type",restr_type
+ call readi(controlcard,"NFRAG",nfrag_,0)
call readi(controlcard,"NFRAG",nfrag_,0)
call readi(controlcard,"NPAIR",npair_,0)
call readi(controlcard,"NDIST",ndist_,0)
call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
+ if (restr_type.eq.10)
+ & call reada(controlcard,'WBOLTZD',wboltzd,0.591d0)
call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
- write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
- write (iout,*) "IFRAG"
- do i=1,nfrag_
- write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
- enddo
- write (iout,*) "IPAIR"
- do i=1,npair_
- write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
- enddo
- call flush(iout)
- if (.not.refstr .and. nfrag_.gt.0) then
+ normalize = index(controlcard,"NORMALIZE").gt.0
+ write (iout,*) "WBOLTZD",wboltzd
+c write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
+c write (iout,*) "IFRAG"
+c do i=1,nfrag_
+c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
+c enddo
+c write (iout,*) "IPAIR"
+c do i=1,npair_
+c write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
+c enddo
+ if (nfrag_.gt.0) then
+ nres0=nres
+ read(inp,'(a)') pdbfile
write (iout,*)
- & "ERROR: no reference structure to compute distance restraints"
- write (iout,*)
- & "Restraints must be specified explicitly (NDIST=number)"
- stop
+ & "Distance restraints will be constructed from structure ",pdbfile
+ open(ipdbin,file=pdbfile,status='old',err=11)
+ call readpdb(.true.)
+ nres=nres0
+ close(ipdbin)
endif
- if (nfrag_.lt.2 .and. npair_.gt.0) then
- write (iout,*) "ERROR: Less than 2 fragments specified",
- & " but distance restraints between pairs requested"
- stop
- endif
- call flush(iout)
do i=1,nfrag_
if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
if (ifrag_(2,i).gt.nstart_sup+nsup-1)
& ifrag_(2,i)=nstart_sup+nsup-1
c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
- call flush(iout)
- if (wfrag_(i).gt.0.0d0) then
+c call flush(iout)
+ if (wfrag_(i).eq.0.0d0) cycle
do j=ifrag_(1,i),ifrag_(2,i)-1
do k=j+1,ifrag_(2,i)
- write (iout,*) "j",j," k",k
+c write (iout,*) "j",j," k",k
ddjk=dist(j,k)
- if (constr_dist.eq.1) then
- nhpb=nhpb+1
- ihpb(nhpb)=j
- jhpb(nhpb)=k
+ if (restr_type.eq.1) then
+ nhpb=nhpb+1
+ irestr_type(nhpb)=1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
dhpb(nhpb)=ddjk
- forcon(nhpb)=wfrag_(i)
+ forcon(nhpb)=wfrag_(i)
else if (constr_dist.eq.2) then
if (ddjk.le.dist_cut) then
nhpb=nhpb+1
+ irestr_type(nhpb)=1
ihpb(nhpb)=j
jhpb(nhpb)=k
dhpb(nhpb)=ddjk
forcon(nhpb)=wfrag_(i)
endif
- else
+ else if (restr_type.eq.3) then
nhpb=nhpb+1
+ irestr_type(nhpb)=1
ihpb(nhpb)=j
jhpb(nhpb)=k
dhpb(nhpb)=ddjk
forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
endif
- write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
+ write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.restr ",
& nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
enddo
enddo
- endif
enddo
do i=1,npair_
- if (wpair_(i).gt.0.0d0) then
+ if (wpair_(i).eq.0.0d0) cycle
ii = ipair_(1,i)
jj = ipair_(2,i)
if (ii.gt.jj) then
endif
do j=ifrag_(1,ii),ifrag_(2,ii)
do k=ifrag_(1,jj),ifrag_(2,jj)
- nhpb=nhpb+1
- ihpb(nhpb)=j
- jhpb(nhpb)=k
- forcon(nhpb)=wpair_(i)
- dhpb(nhpb)=dist(j,k)
- write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
+ if (restr_type.eq.1) then
+ nhpb=nhpb+1
+ irestr_type(nhpb)=1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
+ dhpb(nhpb)=ddjk
+ forcon(nhpb)=wfrag_(i)
+ else if (constr_dist.eq.2) then
+ if (ddjk.le.dist_cut) then
+ nhpb=nhpb+1
+ irestr_type(nhpb)=1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
+ dhpb(nhpb)=ddjk
+ forcon(nhpb)=wfrag_(i)
+ endif
+ else if (restr_type.eq.3) then
+ nhpb=nhpb+1
+ irestr_type(nhpb)=1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
+ dhpb(nhpb)=ddjk
+ forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
+ endif
+ write (iout,'(a,3i5,f8.2,f10.1)') "+dist.restr ",
& nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
enddo
enddo
- endif
enddo
+
+c print *,ndist_
+ write (iout,*) "Distance restraints as read from input"
do i=1,ndist_
- read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
- & ibecarb(i),forcon(nhpb+1)
- if (forcon(nhpb+1).gt.0.0d0) then
+ if (restr_type.eq.11) then
+ read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(nhpb+1),
+ & dhpb1(nhpb+1),ibecarb(i),forcon(nhpb+1),fordepth(nhpb+1)
+c fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1)
+ if (forcon(nhpb+1).le.0.0d0.or.fordepth(nhpb+1).le.0.0d0)cycle
+ nhpb=nhpb+1
+ irestr_type(nhpb)=11
+ write (iout,'(a,4i5,2f8.2,2f10.5,i5)') "+dist.restr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb),
+ & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),irestr_type(nhpb)
+ if (ibecarb(nhpb).gt.0) then
+ ihpb(nhpb)=ihpb(nhpb)+nres
+ jhpb(nhpb)=jhpb(nhpb)+nres
+ endif
+ else if (constr_dist.eq.10) then
+c Cross-lonk Markov-like potential
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,"ILINK",ihpb(nhpb+1),0)
+ call readi(controlcard,"JLINK",jhpb(nhpb+1),0)
+ ibecarb(nhpb+1)=0
+ if (index(controlcard,"BETA").gt.0) ibecarb(nhpb+1)=1
+ if (ihpb(nhpb+1).eq.0 .or. jhpb(nhpb+1).eq.0) cycle
+ if (index(controlcard,"ZL").gt.0) then
+ link_type=1
+ else if (index(controlcard,"ADH").gt.0) then
+ link_type=2
+ else if (index(controlcard,"PDH").gt.0) then
+ link_type=3
+ else if (index(controlcard,"DSS").gt.0) then
+ link_type=4
+ else
+ link_type=0
+ endif
+ call reada(controlcard,"AXLINK",dhpb(nhpb+1),
+ & xlink(1,link_type))
+ call reada(controlcard,"BXLINK",dhpb1(nhpb+1),
+ & xlink(2,link_type))
+ call reada(controlcard,"CXLINK",fordepth(nhpb+1),
+ & xlink(3,link_type))
+ call reada(controlcard,"SIGMA",forcon(nhpb+1),
+ & xlink(4,link_type))
+ call reada(controlcard,"SCORE",xlscore(nhpb+1),1.0d0)
+c read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),ibecarb(nhpb+1),
+c & dhpb(nhpb+1),dhpb1(nhpb+1),forcon(nhpb+1),fordepth(nhpb+1)
+ if (forcon(nhpb+1).le.0.0d0 .or.
+ & (dhpb(nhpb+1).eq.0 .and. dhpb1(nhpb+1).eq.0)) cycle
+ nhpb=nhpb+1
+ irestr_type(nhpb)=10
+ if (ibecarb(nhpb).gt.0) then
+ ihpb(nhpb)=ihpb(nhpb)+nres
+ jhpb(nhpb)=jhpb(nhpb)+nres
+ endif
+ write (iout,'(a,4i5,2f8.2,3f10.5,i5)') "+dist.restr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb),
+ & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),xlscore(nhpb),
+ & irestr_type(nhpb)
+ else
+C print *,"in else"
+ read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(nhpb+1),
+ & dhpb1(nhpb+1),ibecarb(nhpb+1),forcon(nhpb+1)
+ if (forcon(nhpb+1).gt.0.0d0) then
nhpb=nhpb+1
- if (ibecarb(i).gt.0) then
- ihpb(i)=ihpb(i)+nres
- jhpb(i)=jhpb(i)+nres
+ if (dhpb1(nhpb).eq.0.0d0) then
+ irestr_type(nhpb)=1
+ else
+ irestr_type(nhpb)=2
+ endif
+ if (ibecarb(nhpb).gt.0) then
+ ihpb(nhpb)=ihpb(nhpb)+nres
+ jhpb(nhpb)=jhpb(nhpb)+nres
endif
- if (dhpb(nhpb).eq.0.0d0)
+ if (dhpb(nhpb).eq.0.0d0)
& dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
endif
+ write (iout,'(a,4i5,f8.2,f10.1)') "+dist.restr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(i),dhpb(nhpb),forcon(nhpb)
+ endif
+C read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
+C if (forcon(nhpb+1).gt.0.0d0) then
+C nhpb=nhpb+1
+C dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
enddo
- do i=1,nhpb
- write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
- & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
- enddo
+
+ ENDDO ! next
+
+ fordepthmax=0.0d0
+ if (normalize) then
+ do i=nss+1,nhpb
+ if (irestr_type(i).eq.11.and.fordepth(i).gt.fordepthmax)
+ & fordepthmax=fordepth(i)
+ enddo
+ do i=nss+1,nhpb
+ if (irestr_type(i).eq.11) fordepth(i)=fordepth(i)/fordepthmax
+ enddo
+ endif
+ if (nhpb.gt.nss) then
+ write (iout,'(/a,i5,a/4a5,2a8,3a10,a5)')
+ & "The following",nhpb-nss,
+ & " distance restraints have been imposed:",
+ & " Nr"," res1"," res2"," beta"," d1"," d2"," k"," V",
+ & " score"," type"
+ do i=nss+1,nhpb
+ write (iout,'(4i5,2f8.2,3f10.5,i5)')i-nss,ihpb(i),jhpb(i),
+ & ibecarb(i),dhpb(i),dhpb1(i),forcon(i),fordepth(i),xlscore(i),
+ & irestr_type(i)
+ enddo
+ endif
+ write (iout,*)
+ call hpb_partition
call flush(iout)
return
+ 11 write (iout,*)"read_dist_restr: error reading reference structure"
+ stop
+ end
+c====-------------------------------------------------------------------
+ subroutine read_constr_homology
+
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.HOMRESTR'
+c
+c For new homol impl
+c
+ include 'COMMON.VAR'
+c include 'include_unres/COMMON.VAR'
+c
+
+c double precision odl_temp,sigma_odl_temp,waga_theta,waga_d,
+c & dist_cut
+c common /przechowalnia/ odl_temp(maxres,maxres,max_template),
+c & sigma_odl_temp(maxres,maxres,max_template)
+ character*2 kic2
+ character*24 model_ki_dist, model_ki_angle
+ character*500 controlcard
+ integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
+ integer idomain(max_template,maxres)
+ logical lprn /.true./
+ integer ilen
+ external ilen
+ logical unres_pdb,liiflag
+c
+c FP - Nov. 2014 Temporary specifications for new vars
+c
+ double precision rescore_tmp,x12,y12,z12,rescore2_tmp
+ double precision, dimension (max_template,maxres) :: rescore
+ double precision, dimension (max_template,maxres) :: rescore2
+ character*24 tpl_k_rescore
+c -----------------------------------------------------------------
+c Reading multiple PDB ref structures and calculation of retraints
+c not using pre-computed ones stored in files model_ki_{dist,angle}
+c FP (Nov., 2014)
+c -----------------------------------------------------------------
+c
+c
+c Alternative: reading from input
+ call card_concat(controlcard,.true.)
+ call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0)
+ call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0)
+ call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new
+ call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new
+ call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
+ call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
+ call readi(controlcard,"HOMOL_NSET",homol_nset,1)
+ read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
+ call readi(controlcard,"IHSET",ihset,1)
+ if (homol_nset.gt.1)then
+ call card_concat(controlcard,.true.)
+ read(controlcard,*) (waga_homology(i),i=1,homol_nset)
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "iset homology_weight "
+c do i=1,homol_nset
+c write(iout,*) i,waga_homology(i)
+c enddo
+ endif
+ iset=mod(kolor,homol_nset)+1
+ else
+ iset=1
+ waga_homology(1)=1.0
+ endif
+c write(iout,*) "waga_homology(",iset,")",waga_homology(iset)
+
+cd write (iout,*) "nnt",nnt," nct",nct
+cd call flush(iout)
+
+
+ lim_odl=0
+ lim_dih=0
+c
+c New
+c
+ lim_theta=0
+ lim_xx=0
+c
+c Reading HM global scores (prob not required)
+c
+ do i = nnt,nct
+ do k=1,constr_homology
+ idomain(k,i)=0
+ enddo
+ enddo
+c open (4,file="HMscore")
+c do k=1,constr_homology
+c read (4,*,end=521) hmscore_tmp
+c hmscore(k)=hmscore_tmp ! Another transformation can be used
+c write(*,*) "Model", k, ":", hmscore(k)
+c enddo
+c521 continue
+
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ ii_in_use(ii)=0
+ enddo
+ enddo
+c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+
+ if (read_homol_frag) then
+ call read_klapaucjusz
+ else
+
+ do k=1,constr_homology
+
+ read(inp,'(a)') pdbfile
+c Next stament causes error upon compilation (?)
+c if(me.eq.king.or. .not. out1file)
+c write (iout,'(2a)') 'PDB data will be read from file ',
+c & pdbfile(:ilen(pdbfile))
+ write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ stop
+ 34 continue
+c print *,'Begin reading pdb data'
+c
+c Files containing res sim or local scores (former containing sigmas)
+c
+
+ write(kic2,'(bz,i2.2)') k
+
+ tpl_k_rescore="template"//kic2//".sco"
+
+ unres_pdb=.false.
+ call readpdb
+ do i=1,2*nres
+ do j=1,3
+ crefjlee(j,i)=c(j,i)
+ enddo
+ enddo
+#ifdef DEBUG
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
+ & (crefjlee(j,i+nres),j=1,3)
+ enddo
+#endif
+ write (iout,*) "read_constr_homology: after reading pdb file"
+ call flush(iout)
+
+c
+c Distance restraints
+c
+c ... --> odl(k,ii)
+C Copy the coordinates from reference coordinates (?)
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=cref(j,i)
+c write (iout,*) "c(",j,i,") =",c(j,i)
+ enddo
+ enddo
+c
+c From read_dist_constr (commented out 25/11/2014 <-> res sim)
+c
+c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
+ open (ientin,file=tpl_k_rescore,status='old')
+ if (nnt.gt.1) rescore(k,1)=0.0d0
+ do irec=nnt,nct ! loop for reading res sim
+ if (read2sigma) then
+ read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
+ & idomain_tmp
+ i_tmp=i_tmp+nnt-1
+ idomain(k,i_tmp)=idomain_tmp
+ rescore(k,i_tmp)=rescore_tmp
+ rescore2(k,i_tmp)=rescore2_tmp
+ write(iout,'(a7,i5,2f10.5,i5)') "rescore",
+ & i_tmp,rescore2_tmp,rescore_tmp,
+ & idomain_tmp
+ else
+ idomain(k,irec)=1
+ read (ientin,*,end=1401) rescore_tmp
+
+c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
+ rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
+c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
+ endif
+ enddo
+ 1401 continue
+ close (ientin)
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+
+ x12=c(1,i)-c(1,j)
+ y12=c(2,i)-c(2,j)
+ z12=c(3,i)-c(3,j)
+ distal=dsqrt(x12*x12+y12*y12+z12*z12)
+c write (iout,*) k,i,j,distal,dist2_cut
+
+ if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+ & .and. distal.le.dist2_cut ) then
+
+ ii=ii+1
+ ii_in_use(ii)=1
+ l_homo(k,ii)=.true.
+
+c write (iout,*) "k",k
+c write (iout,*) "i",i," j",j," constr_homology",
+c & constr_homology
+ ires_homo(ii)=i
+ jres_homo(ii)=j
+ odl(k,ii)=distal
+ if (read2sigma) then
+ sigma_odl(k,ii)=0
+ do ik=i,j
+ sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
+ enddo
+ sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
+ if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
+ & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+ else
+ if (odl(k,ii).le.dist_cut) then
+ sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
+ else
+#ifdef OLDSIGMA
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
+#else
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+#endif
+ endif
+ endif
+ sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
+ else
+ ii=ii+1
+ l_homo(k,ii)=.false.
+ endif
+ enddo
+ enddo
+ lim_odl=ii
+ endif
+c
+c Theta, dihedral and SC retraints
+c
+ if (waga_angle.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_dih,status='old')
+c do irec=1,maxres-3 ! loop for reading sigma_dih
+c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
+c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
+c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_dih(k,i+nnt-1)
+c enddo
+c1402 continue
+c close (ientin)
+ do i = nnt+3,nct
+ if (idomain(k,i).eq.0) then
+ sigma_dih(k,i)=0.0
+ cycle
+ endif
+ dih(k,i)=phiref(i) ! right?
+c read (ientin,*) sigma_dih(k,i) ! original variant
+c write (iout,*) "dih(",k,i,") =",dih(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+c & "rescore(",k,i-1,") =",rescore(k,i-1),
+c & "rescore(",k,i-2,") =",rescore(k,i-2),
+c & "rescore(",k,i-3,") =",rescore(k,i-3)
+
+ sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2)+rescore(k,i-3))/4.0
+c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
+c write (iout,*) "Raw sigmas for dihedral angle restraints"
+c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
+c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
+c Instead of res sim other local measure of b/b str reliability possible
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+
+ if (waga_theta.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_theta,status='old')
+c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
+c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
+c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_theta(k,i+nnt-1)
+c enddo
+c1403 continue
+c close (ientin)
+
+ do i = nnt+2,nct ! right? without parallel.
+c do i = i=1,nres ! alternative for bounds acc to readpdb?
+c do i=ithet_start,ithet_end ! with FG parallel.
+ if (idomain(k,i).eq.0) then
+ sigma_theta(k,i)=0.0
+ cycle
+ endif
+ thetatpl(k,i)=thetaref(i)
+c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+c & "rescore(",k,i-1,") =",rescore(k,i-1),
+c & "rescore(",k,i-2,") =",rescore(k,i-2)
+c read (ientin,*) sigma_theta(k,i) ! 1st variant
+ sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2))/3.0
+c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+
+c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+c rescore(k,i-2) ! right expression ?
+c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
+ enddo
+ endif
+
+ if (waga_d.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_d,status='old')
+c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
+c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
+c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_d(k,i+nnt-1)
+c enddo
+c1404 continue
+
+ do i = nnt,nct ! right? without parallel.
+c do i=2,nres-1 ! alternative for bounds acc to readpdb?
+c do i=loc_start,loc_end ! with FG parallel.
+ if (itype(i).eq.10) cycle
+ if (idomain(k,i).eq.0 ) then
+ sigma_d(k,i)=0.0
+ cycle
+ endif
+ xxtpl(k,i)=xxref(i)
+ yytpl(k,i)=yyref(i)
+ zztpl(k,i)=zzref(i)
+c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
+c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
+c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
+ sigma_d(k,i)=rescore(k,i) ! right expression ?
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+
+c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
+c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
+c read (ientin,*) sigma_d(k,i) ! 1st variant
+ enddo
+ endif
+ enddo
+c
+c remove distance restraints not used in any model from the list
+c shift data in all arrays
+c
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ liiflag=.true.
+ do i=nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ if (ii_in_use(ii).eq.0.and.liiflag) then
+ liiflag=.false.
+ iistart=ii
+ endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag.or.
+ & .not.liiflag.and.ii.eq.lim_odl) then
+ if (ii.eq.lim_odl) then
+ iishift=ii-iistart+1
+ else
+ iishift=ii-iistart
+ endif
+ liiflag=.true.
+ do ki=iistart,lim_odl-iishift
+ ires_homo(ki)=ires_homo(ki+iishift)
+ jres_homo(ki)=jres_homo(ki+iishift)
+ ii_in_use(ki)=ii_in_use(ki+iishift)
+ do k=1,constr_homology
+ odl(k,ki)=odl(k,ki+iishift)
+ sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
+ l_homo(k,ki)=l_homo(k,ki+iishift)
+ enddo
+ enddo
+ ii=ii-iishift
+ lim_odl=lim_odl-iishift
+ endif
+ enddo
+ enddo
+ endif
+
+ endif ! .not. klapaucjusz
+
+ if (constr_homology.gt.0) call homology_partition
+ if (constr_homology.gt.0) call init_int_table
+cd write (iout,*) "homology_partition: lim_theta= ",lim_theta,
+cd & "lim_xx=",lim_xx
+c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+c
+c Print restraints
+c
+ if (.not.lprn) return
+cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write (iout,*) "Distance restraints from templates"
+ do ii=1,lim_odl
+ write(iout,'(3i5,100(2f8.2,1x,l1,4x))')
+ & ii,ires_homo(ii),jres_homo(ii),
+ & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii),
+ & ki=1,constr_homology)
+ enddo
+ write (iout,*) "Dihedral angle restraints from templates"
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*dih(ki,i),
+ & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
+ enddo
+ write (iout,*) "Virtual-bond angle restraints from templates"
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*thetatpl(ki,i),
+ & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
+ enddo
+ write (iout,*) "SC restraints from templates"
+ do i=nnt,nct
+ write(iout,'(i5,100(4f8.2,4x))') i,
+ & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
+ & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
+ enddo
+ endif
+c -----------------------------------------------------------------
+ return
+ end
+c----------------------------------------------------------------------
+ subroutine read_klapaucjusz
+
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.HOMRESTR'
+ character*256 fragfile
+ integer ninclust(maxclust),inclust(max_template,maxclust),
+ & nresclust(maxclust),iresclust(maxres,maxclust)
+
+ character*2 kic2
+ character*24 model_ki_dist, model_ki_angle
+ character*500 controlcard
+ integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
+ integer idomain(max_template,maxres)
+ logical lprn /.true./
+ integer ilen
+ external ilen
+ logical unres_pdb,liiflag
+c
+c
+ double precision rescore_tmp,x12,y12,z12,rescore2_tmp
+ double precision, dimension (max_template,maxres) :: rescore
+ double precision, dimension (max_template,maxres) :: rescore2
+ character*24 tpl_k_rescore
+
+c
+c For new homol impl
+c
+ include 'COMMON.VAR'
+c
+ double precision chomo(3,maxres2+2,max_template)
+ call getenv("FRAGFILE",fragfile)
+ open(ientin,file=fragfile,status="old",err=10)
+ read(ientin,*) constr_homology,nclust
+ l_homo = .false.
+ sigma_theta=0.0
+ sigma_d=0.0
+ sigma_dih=0.0
+c Read pdb files
+ do k=1,constr_homology
+ read(ientin,'(a)') pdbfile
+ write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ stop
+ 34 continue
+ unres_pdb=.false.
+ call readpdb
+ do i=1,2*nres
+ do j=1,3
+ chomo(j,i,k)=c(j,i)
+ enddo
+ enddo
+ do i=1,nres
+ rescore(k,i)=0.2d0
+ rescore2(k,i)=1.0d0
+ enddo
+ enddo
+c Read clusters
+ do i=1,nclust
+ read(ientin,*) ninclust(i),nresclust(i)
+ read(ientin,*) (inclust(k,i),k=1,ninclust(i))
+ read(ientin,*) (iresclust(k,i),k=1,nresclust(i))
+ enddo
+c
+c Loop over clusters
+c
+ do l=1,nclust
+ do ll = 1,ninclust(l)
+
+ k = inclust(ll,l)
+ do i=1,nres
+ idomain(k,i)=0
+ enddo
+ do i=1,nresclust(l)
+ if (nnt.gt.1) then
+ idomain(k,iresclust(i,l)+1) = 1
+ else
+ idomain(k,iresclust(i,l)) = 1
+ endif
+ enddo
+c
+c Distance restraints
+c
+c ... --> odl(k,ii)
+C Copy the coordinates from reference coordinates (?)
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=chomo(j,i,k)
+c write (iout,*) "c(",j,i,") =",c(j,i)
+ enddo
+ enddo
+ call int_from_cart(.true.,.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+
+ x12=c(1,i)-c(1,j)
+ y12=c(2,i)-c(2,j)
+ z12=c(3,i)-c(3,j)
+ distal=dsqrt(x12*x12+y12*y12+z12*z12)
+c write (iout,*) k,i,j,distal,dist2_cut
+
+ if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+ & .and. distal.le.dist2_cut ) then
+
+ ii=ii+1
+ ii_in_use(ii)=1
+ l_homo(k,ii)=.true.
+
+c write (iout,*) "k",k
+c write (iout,*) "i",i," j",j," constr_homology",
+c & constr_homology
+ ires_homo(ii)=i
+ jres_homo(ii)=j
+ odl(k,ii)=distal
+ if (read2sigma) then
+ sigma_odl(k,ii)=0
+ do ik=i,j
+ sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
+ enddo
+ sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
+ if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
+ & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+ else
+ if (odl(k,ii).le.dist_cut) then
+ sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
+ else
+#ifdef OLDSIGMA
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
+#else
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+#endif
+ endif
+ endif
+ sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
+ else
+ ii=ii+1
+c l_homo(k,ii)=.false.
+ endif
+ enddo
+ enddo
+ lim_odl=ii
+ endif
+c
+c Theta, dihedral and SC retraints
+c
+ if (waga_angle.gt.0.0d0) then
+ do i = nnt+3,nct
+ if (idomain(k,i).eq.0) then
+c sigma_dih(k,i)=0.0
+ cycle
+ endif
+ dih(k,i)=phiref(i)
+ sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2)+rescore(k,i-3))/4.0
+c write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i),
+c & " sigma_dihed",sigma_dih(k,i)
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+
+ if (waga_theta.gt.0.0d0) then
+ do i = nnt+2,nct
+ if (idomain(k,i).eq.0) then
+c sigma_theta(k,i)=0.0
+ cycle
+ endif
+ thetatpl(k,i)=thetaref(i)
+ sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2))/3.0
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+ enddo
+ endif
+
+ if (waga_d.gt.0.0d0) then
+ do i = nnt,nct
+ if (itype(i).eq.10) cycle
+ if (idomain(k,i).eq.0 ) then
+c sigma_d(k,i)=0.0
+ cycle
+ endif
+ xxtpl(k,i)=xxref(i)
+ yytpl(k,i)=yyref(i)
+ zztpl(k,i)=zzref(i)
+ sigma_d(k,i)=rescore(k,i)
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+ if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1
+ enddo
+ endif
+ enddo ! l
+ enddo ! ll
+c
+c remove distance restraints not used in any model from the list
+c shift data in all arrays
+c
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ liiflag=.true.
+ do i=nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ if (ii_in_use(ii).eq.0.and.liiflag) then
+ liiflag=.false.
+ iistart=ii
+ endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag.or.
+ & .not.liiflag.and.ii.eq.lim_odl) then
+ if (ii.eq.lim_odl) then
+ iishift=ii-iistart+1
+ else
+ iishift=ii-iistart
+ endif
+ liiflag=.true.
+ do ki=iistart,lim_odl-iishift
+ ires_homo(ki)=ires_homo(ki+iishift)
+ jres_homo(ki)=jres_homo(ki+iishift)
+ ii_in_use(ki)=ii_in_use(ki+iishift)
+ do k=1,constr_homology
+ odl(k,ki)=odl(k,ki+iishift)
+ sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
+ l_homo(k,ki)=l_homo(k,ki+iishift)
+ enddo
+ enddo
+ ii=ii-iishift
+ lim_odl=lim_odl-iishift
+ endif
+ enddo
+ enddo
+ endif
+
+ return
+ 10 stop "Error infragment file"
end
+c----------------------------------------------------------------------
projects / unres.git / blobdiff