include 'COMMON.CONTROL'
include 'COMMON.SBRIDGE'
include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
logical file_exist
C Read force-field parameters except weights
call parmread
#ifdef MPI
if (.not. out1file .or. me.eq.king) then
#endif
- if (nhpb.gt.nss)
- &write (iout,'(a,i5,a)') "The following",nhpb-nss,
- & " distance constraints have been imposed"
- do i=nss+1,nhpb
- write (iout,'(3i6,i2,3f10.5)') i-nss,ihpb(i),jhpb(i),
- & ibecarb(i),dhpb(i),dhpb1(i),forcon(i)
- enddo
+ 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
#ifdef MPI
endif
#endif
read_cart=index(controlcard,'READ_CART').gt.0
call readi(controlcard,'CONSTR_DIST',constr_dist,0)
call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
+ read_homol_frag = index(controlcard,"READ_HOMOL_FRAG").gt.0
call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
sideadd=(index(controlcard,'SIDEADD').gt.0)
energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
outpdb=(index(controlcard,'PDBOUT').gt.0)
+ outx=(index(controlcard,'XOUT').gt.0)
outmol2=(index(controlcard,'MOL2OUT').gt.0)
pdbref=(index(controlcard,'PDBREF').gt.0)
refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
modecalc=1
refstr=.true.
endif
+ call reada(controlcard,"CHECKGRAD_INC",checkgrad_inc,1.0d-4)
if (index(controlcard,'CHECKGRAD').gt.0) then
modecalc=5
if (index(controlcard,'CART').gt.0) then
large = index(controlcard,"LARGE").gt.0
print_compon = index(controlcard,"PRINT_COMPON").gt.0
rattle = index(controlcard,"RATTLE").gt.0
+ preminim = index(controlcard,"PREMINIM").gt.0
+ if (preminim) then
+ dccart=(index(controlcard,'CART').gt.0)
+ call read_minim
+ endif
c if performing umbrella sampling, fragments constrained are read from the fragment file
nset=0
if(usampl) then
write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
if (rattle) write (iout,'(a60)')
& "Rattle algorithm used to constrain the virtual bonds"
+ if (preminim .or. iranconf.gt.0) then
+ write (iout,'(a60)')
+ & "Initial structure will be energy-minimized"
+ endif
endif
reset_fricmat=1000
if (lang.gt.0) then
common /pizda/ itype_pdb
logical seq_comp,fail
double precision energia(0:n_ene)
+
integer ilen
external ilen
C
34 continue
c print *,'Begin reading pdb data'
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
c print *,'Finished reading pdb data'
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3,a,i3)')'nsup=',nsup,
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
+
C Assign initial virtual bond lengths
do i=2,nres
vbld(i)=vbl
C READ fragment information!!
C both routines should be in dfa.F file!!
+#ifdef DFA
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
call init_dfa_vars
call read_dfa_info
print*, 'read_dfa_info finished!'
endif
+#endif
C
if (pdbref) then
if(me.eq.king.or..not.out1file)
if (constr_homology.gt.0) then
call read_constr_homology
+ 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
+ call int_from_cart1(.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(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
else
homol_nset=0
endif
if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
& write (iout,'(a)') 'Initial geometry will be read in.'
if (read_cart) then
+ read (inp,*) time,potE,uconst,t_bath,
+ & nss,(ihpb(j),jhpb(j),j=1,nss), nn, (qfrag(i),i=1,nn)
read(inp,'(8f10.5)',end=36,err=36)
& ((c(l,k),l=1,3),k=1,nres),
& ((c(l,k+nres),l=1,3),k=nnt,nct)
enddo
endif
enddo
- return
+c return
else
call read_angles(inp,*36)
endif
if (nthread.gt.0) then
call read_threadbase
endif
+ write (iout,*) "READRTNS: Calling setup_var"
+ call flush(iout)
call setup_var
if (me.eq.king .or. .not. out1file)
& call intout
& //'.pdb'
mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//
& liczba(:ilen(liczba))//'.mol2'
+ cartname=prefix(:lenpre)//'_'//pot(:lenpot)//
+ & liczba(:ilen(liczba))//'.x'
statname=prefix(:lenpre)//'_'//pot(:lenpot)//
& liczba(:ilen(liczba))//'.stat'
if (lentmp.gt.0)
intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
+ cartname=prefix(:lenpre)//'_'//pot(:lenpot)//'.x'
statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
if (lentmp.gt.0)
& call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
include 'COMMON.IOUNITS'
include 'COMMON.MD'
include 'COMMON.CONTROL'
+ integer iset1
read(inp,*) nset,nfrag,npair,nfrag_back
if(me.eq.king.or..not.out1file)
& write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
& " nfrag_back",nfrag_back
- do iset=1,nset
- read(inp,*) mset(iset)
+ do iset1=1,nset
+ read(inp,*) mset(iset1)
do i=1,nfrag
- read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
- & qinfrag(i,iset)
+ read(inp,*) wfrag(i,iset1),ifrag(1,i,iset1),ifrag(2,i,iset1),
+ & qinfrag(i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
- & ifrag(2,i,iset), qinfrag(i,iset)
+ & write(iout,*) "R ",i,wfrag(i,iset1),ifrag(1,i,iset1),
+ & ifrag(2,i,iset1), qinfrag(i,iset1)
enddo
do i=1,npair
- read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
- & qinpair(i,iset)
+ read(inp,*) wpair(i,iset1),ipair(1,i,iset1),ipair(2,i,iset1),
+ & qinpair(i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
- & ipair(2,i,iset), qinpair(i,iset)
+ & write(iout,*) "R ",i,wpair(i,iset1),ipair(1,i,iset1),
+ & ipair(2,i,iset1), qinpair(i,iset1)
enddo
do i=1,nfrag_back
- read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
- & wfrag_back(3,i,iset),
- & ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+ read(inp,*) wfrag_back(1,i,iset1),wfrag_back(2,i,iset1),
+ & wfrag_back(3,i,iset1),
+ & ifrag_back(1,i,iset1),ifrag_back(2,i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
- & wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+ & write(iout,*) "A",i,wfrag_back(1,i,iset1),
+ & wfrag_back(2,i,iset1),
+ & wfrag_back(3,i,iset1),ifrag_back(1,i,iset1),
+ & ifrag_back(2,i,iset1)
enddo
enddo
return
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
+c print *, "WCHODZE"
+ 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)
+ 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)
+ 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 do i=1,npair_
c write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
c enddo
- if (.not.refstr .and. nfrag.gt.0) then
- write (iout,*)
- & "ERROR: no reference structure to compute distance restraints"
- write (iout,*)
- & "Restraints must be specified explicitly (NDIST=number)"
- stop
- 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)
+ if (nfrag_.gt.0) write (iout,*)
+ & "Distance restraints as generated from reference structure"
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)
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
endif
#ifdef MPI
if (.not.out1file .or. me.eq.king)
- & 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)
#else
- 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)
#endif
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)
+ 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
#ifdef MPI
if (.not.out1file .or. me.eq.king)
- & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
+ & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.restr ",
& nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
#else
- write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
+ write (iout,'(a,3i5,f8.2,f10.1)') "+dist.restr ",
& nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
#endif
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
+#ifdef MPI
+ if (.not.out1file .or. me.eq.king)
+ & 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)
+#else
+ 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)
+#endif
+ 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)
+ 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
+#ifdef MPI
+ if (.not.out1file .or. me.eq.king)
+ & 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
+ 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)
+#endif
+ 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
- enddo
#ifdef MPI
- if (.not.out1file .or. me.eq.king) then
+ if (.not.out1file .or. me.eq.king)
+ & write (iout,'(a,4i5,f8.2,f10.1)') "+dist.restr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(i),dhpb(nhpb),forcon(nhpb)
+#else
+ write (iout,'(a,4i5,f8.2,f10.1)') "+dist.restr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(i),dhpb(nhpb),forcon(nhpb)
#endif
- 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)
+ 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
- call flush(iout)
-#ifdef MPI
+
+ 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
-#endif
return
end
c-------------------------------------------------------------------------------
include 'COMMON.MD'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
c
c For new homol impl
c
character*2 kic2
character*24 model_ki_dist, model_ki_angle
character*500 controlcard
- integer ki, i, j, k, l
+ integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
logical lprn /.true./
+ integer ilen
+ external ilen
+ logical liiflag
c
c FP - Nov. 2014 Temporary specifications for new vars
c
- double precision rescore_tmp,x12,y12,z12
+ 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 pdbfile,tpl_k_rescore
c -----------------------------------------------------------------
c Reading multiple PDB ref structures and calculation of retraints
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)
+ start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0)
+ if(.not.read2sigma.and.start_from_model) then
+ write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA'
+ start_from_model=.false.
+ endif
+ if(start_from_model) write(iout,*) 'START_FROM_MODELS is ON'
+ if(start_from_model .and. rest) then
+ write(iout,*) 'START_FROM_MODELS is OFF'
+ write(iout,*) 'remove restart keyword from input'
+ endif
if (homol_nset.gt.1)then
call card_concat(controlcard)
- read(controlcard,*) (waga_dist1(i),i=1,homol_nset)
- call card_concat(controlcard)
- read(controlcard,*) (waga_angle1(i),i=1,homol_nset)
- write(iout,*) "iset distance_weight angle_weight"
- do i=1,homol_nset
- write(iout,*) i,waga_dist1(i),waga_angle1(i)
- enddo
+ 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 "
+ do i=1,homol_nset
+ write(iout,*) i,waga_homology(i)
+ enddo
+ endif
iset=mod(kolor,homol_nset)+1
else
iset=1
-c call reada(controlcard,"HOMOL_DIST",waga_dist(1),1.0d0)
-c call reada(controlcard,"HOMOL_ANGLE",waga_angle(1),1.0d0)
+ waga_homology(1)=1.0
endif
- write (iout,*) "nnt",nnt," nct",nct
- call flush(iout)
+cd write (iout,*) "nnt",nnt," nct",nct
+cd call flush(iout)
lim_odl=0
lim_dih=0
c
-c New
+ write(iout,*) 'nnt=',nnt,'nct=',nct
c
- lim_theta=0
- lim_xx=0
-c
-c Reading HM global scores (prob not required)
-c
-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
-
-c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+ do i = nnt,nct
+ do k=1,constr_homology
+ idomain(k,i)=0
+ enddo
+ enddo
+
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ ii_in_use(ii)=0
+ enddo
+ enddo
+
+ if (read_homol_frag) then
+ call read_klapaucjusz
+ else
+
do k=1,constr_homology
read(inp,'(a)') pdbfile
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)') 'Error opening PDB file.'
+ 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
stop
34 continue
c print *,'Begin reading pdb data'
write(kic2,'(bz,i2.2)') k
tpl_k_rescore="template"//kic2//".sco"
-c tpl_k_sigma_odl="template"//kic2//".sigma_odl"
-c tpl_k_sigma_dih="template"//kic2//".sigma_dih"
-c tpl_k_sigma_theta="template"//kic2//".sigma_theta"
-c tpl_k_sigma_d="template"//kic2//".sigma_d"
- call readpdb
+ unres_pdb=.false.
+ if (read2sigma) then
+ call readpdb_template(k)
+ else
+ call readpdb
+ endif
c
c Distance restraints
c
c
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
open (ientin,file=tpl_k_rescore,status='old')
- do irec=1,maxdim ! loop for reading res sim
- if (irec.eq.1) then
- rescore(k,irec)=0.0d0
- goto 1301
- endif
- read (ientin,*,end=1401) rescore_tmp
+ 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
+ rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
- 1301 continue
+ endif
enddo
1401 continue
- close (ientin)
-c open (ientin,file=tpl_k_sigma_odl,status='old')
-c do irec=1,maxdim ! loop for reading sigma_odl
-c read (ientin,*,end=1401) i, j,
-c & sigma_odl_temp(i+nnt-1,j+nnt-1,k) ! new variable (?)
-c sigma_odl_temp(j+nnt-1,i+nnt-1,k)= ! which purpose?
-c & sigma_odl_temp(i+nnt-1,j+nnt-1,k)
-c enddo
-c 1401 continue
-c close (ientin)
- if (waga_dist.gt.0.0d0) then
+ close (ientin)
+ if (waga_dist.ne.0.0d0) then
ii=0
- do i = nnt,nct-2 ! right? without parallel.
- do j=i+2,nct ! right?
-c do i = 1,nres ! alternative for bounds as used to set initial values in orig. read_constr_homology
-c do j=i+2,nres ! ibid
-c do i = nnt,nct-2 ! alternative for bounds as used to assign dist restraints in orig. read_constr_homology (s. above)
-c do j=i+2,nct ! ibid
+ 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
-c
-c Attempt to replace dist(i,j) by its definition in ...
-c
- 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)
odl(k,ii)=distal
-c
-c odl(k,ii)=dist(i,j)
-c write (iout,*) "dist(",i,j,") =",dist(i,j)
-c write (iout,*) "distal = ",distal
-c write (iout,*) "odl(",k,ii,") =",odl(k,ii)
-c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
-c & "rescore(",k,j,") =",rescore(k,j)
-c
-c Calculation of sigma from res sim
-c
-c if (odl(k,ii).le.6.0d0) then
-c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)
-c Other functional forms possible depending on odl(k,ii), eg.
-c
- if (odl(k,ii).le.dist_cut) then
- sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) ! other exprs possible
-c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)
- else
- sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
+ 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)
-
-c Following expr replaced by a positive exp argument
-c sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
-c & dexp(-0.5d0*(odl(k,ii)/dist_cut)**2)
-
-c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)*
-c & 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
-c
- sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii)) ! rescore ~ error
-c sigma_odl(k,ii)=sigma_odl(k,ii)*sigma_odl(k,ii)
-c
-c sigma_odl(k,ii)=sigma_odl_temp(i,j,k)* ! new var read from file (?)
-c & sigma_odl_temp(i,j,k) ! not inverse because of use of res. similarity
enddo
-c read (ientin,*) sigma_odl(k,ii) ! 1st variant
enddo
-c lim_odl=ii
-c if (constr_homology.gt.0) call homology_partition
+ lim_odl=ii
endif
c
c Theta, dihedral and SC retraints
c enddo
c1402 continue
c close (ientin)
- do i = nnt+3,nct ! right? without parallel.
-c do i=1,nres ! alternative for bounds acc to readpdb?
-c do i=1,nres-3 ! alternative for bounds as used to set initial values in orig. read_constr_homology
-c do i=idihconstr_start_homo,idihconstr_end_homo ! with FG parallel.
+ 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 & "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) ! right expression ?
-c
+ 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
- sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*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))
c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
- if (i-nnt-2.gt.lim_dih) lim_dih=i-nnt-2 ! right?
-c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! original when readin i from file
enddo
+ lim_dih=nct-nnt-2
endif
if (waga_theta.gt.0.0d0) then
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) ! right expression ?
- sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+ 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)
- if (i-nnt-1.gt.lim_theta) lim_theta=i-nnt-1 ! right?
enddo
endif
c & sigma_d(k,i+nnt-1)
c enddo
c1404 continue
- close (ientin)
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) goto 1 ! right?
+ 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,*) "zztpl(",k,i,") =",zztpl(k,i)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
sigma_d(k,i)=rescore(k,i) ! right expression ?
- sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+ 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
if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
- 1 continue
enddo
endif
- close(ientin)
enddo
- if (waga_dist.gt.0.0d0) lim_odl=ii
+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
- write (iout,*) "homology_partition: lim_theta= ",lim_theta,
- & "lim_xx=",lim_xx
+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
- write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
- write (iout,*) "Distance restraints from templates"
- do ii=1,lim_odl
- write(iout,'(3i5,10(2f16.2,4x))') ii,ires_homo(ii),jres_homo(ii),
- & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),ki=1,constr_homology)
- enddo
- write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
- write (iout,'(i5,10(2f8.2,4x))') i,(rad2deg*dih(ki,i),
+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,lim_theta
- write (iout,'(i5,10(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
+ 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,lim_xx
- write(iout,'(i5,10(4f8.2,4x))') i,
+ 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'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.MD'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ 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
+ logical lprn /.true./
+ integer ilen
+ external ilen
+ logical 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 pdbfile,tpl_k_rescore
+
+c
+c For new homol impl
+c
+ include 'COMMON.VAR'
+c
+ 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_template(k)
+ 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
-c -----------------------------------------------------------------
return
+ 10 stop "Error infragment file"
end
c----------------------------------------------------------------------