min_var=(index(controlcard,'MINVAR').gt.0)
plot_tree=(index(controlcard,'PLOT_TREE').gt.0)
punch_dist=(index(controlcard,'PUNCH_DIST').gt.0)
- call readi(controlcard,'NCUT',ncut,1)
+ call readi(controlcard,'NCUT',ncut,0)
+ call readi(controlcard,'NCLUST',nclust,5)
call readi(controlcard,'NSTART',nstart,0)
call readi(controlcard,'NEND',nend,0)
call reada(controlcard,'ECUT',ecut,10.0d0)
lgrp=(index(controlcard,'LGRP').gt.0)
caonly=(index(controlcard,'CA_ONLY').gt.0)
print_dist=(index(controlcard,'PRINT_DIST').gt.0)
- call multreada(controlcard,'CUTOFF',rcutoff,ncut,-1.0d0)
+ if (ncut.gt.0)
+ & call multreada(controlcard,'CUTOFF',rcutoff,ncut,-1.0d0)
call readi(controlcard,'IOPT',iopt,2)
lside = index(controlcard,"SIDE").gt.0
efree = index(controlcard,"EFREE").gt.0
call readi(controlcard,'CONSTR_DIST',constr_dist,0)
write (iout,*) "with_dihed_constr ",with_dihed_constr,
& " CONSTR_DIST",constr_dist
+<<<<<<< HEAD
+=======
+
+ call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
+ write (iout,*) "with_homology_constr ",with_dihed_constr,
+ & " CONSTR_HOMOLOGY",constr_homology
+ print_homology_restraints=
+ & index(controlcard,"PRINT_HOMOLOGY_RESTRAINTS").gt.0
+ print_contact_map=index(controlcard,"PRINT_CONTACT_MAP").gt.0
+ print_homology_models=
+ & index(controlcard,"PRINT_HOMOLOGY_MODELS").gt.0
+
+#ifdef AIX
+ call flush_(iout)
+#else
+>>>>>>> 3d6f9e7... Adam's changes to wham and cluster following previous commit
call flush(iout)
if (min_var) iopt=1
return
do i=1,nres
itype(i)=rescode(i,sequence(i),iscode)
enddo
+ if (itype(2).eq.10) 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).eq.10) then
+ write (iout,*)
+ & "Glycine is the last full residue, terminal dummy deleted"
+ nres=nres-1
+ endif
print *,nres
print '(20i4)',(itype(i),i=1,nres)
if (nend.gt.nct .or. nend.eq.0) nend=nct
write (iout,*) "nstart",nstart," nend",nend
nres0=nres
+<<<<<<< HEAD
+=======
+
+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
+#ifdef DEBUG
+ write (iout,*) "Calling init_dfa_vars"
+#ifdef AIX
+ call flush_(iout)
+#else
+ call flush(iout)
+#endif
+#endif
+ call init_dfa_vars
+#ifdef DEBUG
+ write (iout,*) 'init_dfa_vars finished!'
+#ifdef AIX
+ call flush_(iout)
+#else
+ call flush(iout)
+#endif
+#endif
+ call read_dfa_info
+#ifdef DEBUG
+ write (iout,*) 'read_dfa_info finished!'
+#ifdef AIX
+ call flush_(iout)
+#else
+ call flush(iout)
+#endif
+#endif
+ endif
+
+ if (constr_homology.gt.0) then
+ call read_constr_homology(print_homology_restraints)
+ endif
+
+>>>>>>> 3d6f9e7... Adam's changes to wham and cluster following previous commit
c if (pdbref) then
c read(inp,'(a)') pdbfile
c write (iout,'(2a)') 'PDB data will be read from file ',pdbfile
enddo
enddo
endif
- call contact(.true.,ncont_ref,icont_ref)
+ call contact(print_contact_map,ncont_ref,icont_ref)
endif
c Read distance restraints
if (constr_dist.gt.0) then
call flush(iout)
return
end
+<<<<<<< HEAD
+=======
+
+c====-------------------------------------------------------------------
+ subroutine read_constr_homology(lprn)
+
+ include 'DIMENSIONS'
+#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.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
+ logical lprn
+ logical unres_pdb
+c
+c FP - Nov. 2014 Temporary specifications for new vars
+c
+ double precision rescore_tmp,x12,y12,z12
+ double precision, dimension (max_template,maxres) :: rescore
+ 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
+#ifdef DEBUG
+ write (iout,*) "BEGIN READ HOMOLOGY INFO"
+#ifdef AIX
+ call flush_(iout)
+#else
+ call flush(iout)
+#endif
+#endif
+ call card_concat(controlcard)
+ 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 readi(controlcard,"HOMOL_NSET",homol_nset,1)
+ if (homol_nset.gt.1)then
+ call readi(controlcard,"ISET",iset,1)
+ call card_concat(controlcard)
+ read(controlcard,*) (waga_homology(i),i=1,homol_nset)
+ else
+ iset=1
+ waga_homology(1)=1.0
+ endif
+c
+#ifdef DEBUG
+ write(iout,*) "read_constr_homology iset",iset
+ write(iout,*) "waga_homology(",iset,")",waga_homology(iset)
+#ifdef AIX
+ call flush_(iout)
+#else
+ call flush(iout)
+#endif
+#endif
+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
+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
+
+ write (iout,*) "CONSTR_HOMOLOGY",constr_homology
+ do k=1,constr_homology
+
+ read(inp,'(a)') pdbfile
+c write (iout,*) "k ",k," pdbfile ",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))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a)') 'Error opening PDB file.'
+ 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"
+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"
+
+ 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
+ write (iout,*) "READ HOMOLOGY INFO"
+ write (iout,*) "read_constr_homology x: after reading pdb file"
+ write (iout,*) "waga_homology(",iset,")",waga_homology(iset)
+ write (iout,*) "waga_dist",waga_dist
+ write (iout,*) "waga_angle",waga_angle
+ write (iout,*) "waga_theta",waga_theta
+ write (iout,*) "waga_d",waga_d
+ write (iout,*) "dist_cut",dist_cut
+#endif
+#ifdef AIX
+ call flush_(iout)
+#else
+ call flush(iout)
+#endif
+
+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')
+ 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
+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)
+ 1301 continue
+ 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.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
+ ii=ii+1
+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
+#ifdef OLDSIGMA
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
+#else
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+#endif
+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)
+ 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
+ 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 ! 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.
+ 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) ! right expression ?
+c
+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))
+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
+ 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.
+ 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))
+
+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
+
+ 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
+ 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?
+ 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 ?
+ 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.ne.0.0d0) lim_odl=ii
+ 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,'(3i5,10(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),
+ & 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),
+ & 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,
+ & (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
+
+
+>>>>>>> 3d6f9e7... Adam's changes to wham and cluster following previous commit
projects / unres.git / blobdiff