--- /dev/null
+ module conform_compar
+!-----------------------------------------------------------------------------
+ use names
+ use io_units
+ use geometry_data, only:nres
+ use math, only:pinorm
+ use geometry, only:dist
+ use regularize_, only:fitsq
+!
+ use wham_data
+#ifndef CLUSTER
+ use w_compar_data
+#endif
+#ifdef MPI
+ use MPI_data
+! include "COMMON.MPI"
+#endif
+ implicit none
+!-----------------------------------------------------------------------------
+!
+!
+!-----------------------------------------------------------------------------
+ contains
+#ifndef CLUSTER
+!-----------------------------------------------------------------------------
+! conf_compar.F
+!-----------------------------------------------------------------------------
+ subroutine conf_compar(jcon,lprn,print_class)
+! implicit real*8 (a-h,o-z)
+ use energy_data, only:icont,ncont,nnt,nct,maxcont!,&
+! nsccont_frag_ref,isccont_frag_ref
+#ifdef MPI
+ include "mpif.h"
+#endif
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'DIMENSIONS.FREE'
+! include 'COMMON.CONTROL'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.VAR'
+! include 'COMMON.PEPTCONT'
+! include 'COMMON.CONTACTS1'
+! include 'COMMON.HEADER'
+! include 'COMMON.FREE'
+! include 'COMMON.ENERGIES'
+!#ifdef MPI
+! include 'COMMON.MPI'
+!#endif
+! integer ilen
+! external ilen
+ logical :: lprn,print_class
+ integer :: ncont_frag(mmaxfrag),&
+ icont_frag(2,maxcont,mmaxfrag),ncontsc,&
+ icontsc(1,maxcont),nsccont_frag(mmaxfrag),&
+ isccont_frag(2,maxcont,mmaxfrag)
+ integer :: isecstr(nres)
+ integer :: itemp(maxfrag)
+ character(len=4) :: liczba
+ real(kind=8) :: Epot,rms
+ integer :: jcon,i,j,ind,ncnat,nsec_match,ishift,ishif1,ishif2,&
+ nc_match,ncon_match,iclass_rms,ishifft_rms,ishiff,ishif
+ integer :: k,kk,iclass_con,iscor,ik,ishifft_con,idig,iex,im
+! print *,"Enter conf_compar",jcon
+ call angnorm12(rmsang)
+! Level 1: check secondary and supersecondary structure
+ call elecont(lprn,ncont,icont,nnt,nct)
+ if (lprn) then
+ write (iout,*) "elecont finished"
+ call flush(iout)
+ endif
+ call secondary2(lprn,.false.,ncont,icont,isecstr)
+ if (lprn) then
+ write (iout,*) "secondary2 finished"
+ call flush(iout)
+ endif
+ call contact(lprn,ncontsc,icontsc,nnt,nct)
+ if (lprn) then
+ write(iout,*) "Assigning electrostatic contacts"
+ call flush(iout)
+ endif
+ call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,&
+ icont_frag)
+ if (lprn) then
+ write(iout,*) "Assigning sidechain contacts"
+ call flush(iout)
+ endif
+ call contacts_between_fragments(lprn,3,ncontsc,icontsc,&
+ nsccont_frag,isccont_frag)
+ if (lprn) then
+ write(iout,*) "--> After contacts_between_fragments"
+ call flush(iout)
+ endif
+ do i=1,nlevel
+ do j=1,isnfrag(nlevel+1)
+ iclass(j,i)=0
+ enddo
+ enddo
+ do j=1,nfrag(1)
+ ind = icant(j,j)
+ if (lprn) then
+ write (iout,'(80(1h=))')
+ write (iout,*) "Level",1," fragment",j
+ write (iout,'(80(1h=))')
+ endif
+ call flush(iout)
+ rmsfrag(j,1)=rmscalc(0,1,j,jcon,lprn)
+! Compare electrostatic contacts in the current conf with that in the native
+! structure.
+ if (lprn) write (iout,*) &
+ "Comparing electrostatic contact map and local structure"
+ call flush(iout)
+ ncnat=ncont_frag_ref(ind)
+! write (iout,*) "before match_contact:",nc_fragm(j,1),
+! & nc_req_setf(j,1)
+! call flush(iout)
+ call match_secondary(j,isecstr,nsec_match,lprn)
+ if (lprn) write (iout,*) "Fragment",j," nsec_match",&
+ nsec_match," length",len_frag(j,1)," min_len",&
+ frac_sec*len_frag(j,1)
+ if (nsec_match.lt.frac_sec*len_frag(j,1)) then
+ iclass(j,1)=0
+ if (lprn) write (iout,*) "Fragment",j,&
+ " has incorrect secondary structure"
+ else
+ iclass(j,1)=1
+ if (lprn) write (iout,*) "Fragment",j,&
+ " has correct secondary structure"
+ endif
+ if (ielecont(j,1).gt.0) then
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,&
+ ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
+ ncont_frag(ind),icont_frag(1,1,ind),&
+ j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
+ nc_req_setf(j,1),istruct(j),.true.,lprn)
+ else if (isccont(j,1).gt.0) then
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,&
+ nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
+ nsccont_frag(ind),isccont_frag(1,1,ind),&
+ j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
+ nc_req_setf(j,1),istruct(j),.true.,lprn)
+ else if (iloc(j).gt.0) then
+! write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,&
+ 0,icont_frag_ref(1,1,ind),&
+ ncont_frag(ind),icont_frag(1,1,ind),&
+ j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
+ 0,istruct(j),.true.,lprn)
+! write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
+ else
+ ishif=0
+ nc_match=1
+ endif
+ if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
+ ishif=ishif1
+ qfrag(j,1)=qwolynes(1,j)
+ if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
+ if (lprn) write (iout,*) "ishift",ishif," nc_match",nc_match
+! write (iout,*) "j",j," ishif",ishif," rms",rmsfrag(j,1)
+ if (irms(j,1).gt.0) then
+ if (rmsfrag(j,1).le.rmscutfrag(1,j,1)) then
+ iclass_rms=2
+ ishifft_rms=0
+ else
+ ishiff=0
+ rms=1.0d2
+ iclass_rms=0
+ do while (rms.gt.rmscutfrag(1,j,1) .and. &
+ ishiff.lt.n_shift(1,j,1))
+ ishiff=ishiff+1
+ rms=rmscalc(-ishiff,1,j,jcon,lprn)
+! write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
+! & " rms",rms," rmscut",rmscutfrag(1,j,1)
+ if (lprn) write (iout,*) "rms",rmsfrag(j,1)
+ if (rms.gt.rmscutfrag(1,j,1)) then
+ rms=rmscalc(ishiff,1,j,jcon,lprn)
+! write (iout,*) "jcon,1,j,ishiff",jcon,1,j,ishiff,
+! & " rms",rms
+ endif
+ if (lprn) write (iout,*) "rms",rmsfrag(j,1)
+ enddo
+! write (iout,*) "After loop: rms",rms,
+! & " rmscut",rmscutfrag(1,j,1)
+! write (iout,*) "iclass_rms",iclass_rms
+ if (rms.le.rmscutfrag(1,j,1)) then
+ ishifft_rms=ishiff
+ rmsfrag(j,1)=rms
+ iclass_rms=1
+ endif
+! write (iout,*) "iclass_rms",iclass_rms
+ endif
+! write (iout,*) "ishif",ishif
+ if (iabs(ishifft_rms).gt.iabs(ishif)) ishif=ishifft_rms
+ else
+ iclass_rms=1
+ endif
+! write (iout,*) "ishif",ishif," iclass",iclass(j,1),
+! & " iclass_rms",iclass_rms
+ if (nc_match.gt.0 .and. iclass_rms.gt.0) then
+ if (ishif.eq.0) then
+ iclass(j,1)=iclass(j,1)+6
+ else
+ iclass(j,1)=iclass(j,1)+2
+ endif
+ endif
+ ncont_nat(1,j,1)=nc_match
+ ncont_nat(2,j,1)=ncon_match
+ ishifft(j,1)=ishif
+! write (iout,*) "iclass",iclass(j,1)
+ enddo
+! Next levels: Check arrangements of elementary fragments.
+ do i=2,nlevel
+ do j=1,nfrag(i)
+ if (i .eq. 2) ind = icant(ipiece(1,j,i),ipiece(2,j,i))
+ if (lprn) then
+ write (iout,'(80(1h=))')
+ write (iout,*) "Level",i," fragment",j
+ write (iout,'(80(1h=))')
+ endif
+! If an elementary fragment doesn't exist, don't check higher hierarchy levels.
+ do k=1,npiece(j,i)
+ ik=ipiece(k,j,i)
+ if (iclass(ik,1).eq.0) then
+ iclass(j,i)=0
+ goto 12
+ endif
+ enddo
+ if (i.eq.2 .and. ielecont(j,i).gt.0) then
+ iclass_con=0
+ ishifft_con=0
+ if (lprn) write (iout,*) &
+ "Comparing electrostatic contact map: fragments",&
+ ipiece(1,j,i),ipiece(2,j,i)," ind",ind
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,&
+ ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
+ ncont_frag(ind),icont_frag(1,1,ind),&
+ j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
+ nc_req_setf(j,i),2,.false.,lprn)
+ ishif=ishif1
+ if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
+ if (nc_match.gt.0) then
+ if (ishif.eq.0) then
+ iclass_con=2
+ else
+ iclass_con=1
+ endif
+ endif
+ ncont_nat(1,j,i)=nc_match
+ ncont_nat(2,j,i)=ncon_match
+ ishifft_con=ishif
+ else if (i.eq.2 .and. isccont(j,i).gt.0) then
+ iclass_con=0
+ ishifft_con=0
+ if (lprn) write (iout,*) &
+ "Comparing sidechain contact map: fragments",&
+ ipiece(1,j,i),ipiece(2,j,i)," ind",ind
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,&
+ nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
+ nsccont_frag(ind),isccont_frag(1,1,ind),&
+ j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
+ nc_req_setf(j,i),2,.false.,lprn)
+ ishif=ishif1
+ if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
+ if (nc_match.gt.0) then
+ if (ishif.eq.0) then
+ iclass_con=2
+ else
+ iclass_con=1
+ endif
+ endif
+ ncont_nat(1,j,i)=nc_match
+ ncont_nat(2,j,i)=ncon_match
+ ishifft_con=ishif
+ else if (i.eq.2) then
+ iclass_con=2
+ ishifft_con=0
+ endif
+ if (i.eq.2) qfrag(j,2)=qwolynes(2,j)
+ if (lprn) write (iout,*) &
+ "Comparing rms: fragments",&
+ (ipiece(k,j,i),k=1,npiece(j,i))
+ rmsfrag(j,i)=rmscalc(0,i,j,jcon,lprn)
+ if (irms(j,i).gt.0) then
+ iclass_rms=0
+ ishifft_rms=0
+ if (lprn) write (iout,*) "rms",rmsfrag(j,i)
+! write (iout,*) "i",i," j",j," rmsfrag",rmsfrag(j,i),
+! & " rmscutfrag",rmscutfrag(1,j,i)
+ if (rmsfrag(j,i).le.rmscutfrag(1,j,i)) then
+ iclass_rms=2
+ ishifft_rms=0
+ else
+ ishif=0
+ rms=1.0d2
+ do while (rms.gt.rmscutfrag(1,j,i) .and. &
+ ishif.lt.n_shift(1,j,i))
+ ishif=ishif+1
+ rms=rmscalc(-ishif,i,j,jcon,lprn)
+! print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
+ if (lprn) write (iout,*) "rms",rmsfrag(j,i)
+ if (rms.gt.rmscutfrag(1,j,i)) then
+ rms=rmscalc(ishif,i,j,jcon,lprn)
+! print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
+ endif
+ if (lprn) write (iout,*) "rms",rms
+ enddo
+ if (rms.le.rmscutfrag(1,j,i)) then
+ ishifft_rms=ishif
+ rmsfrag(j,i)=rms
+ iclass_rms=1
+ endif
+ endif
+ endif
+ if (irms(j,i).eq.0 .and. ielecont(j,i).eq.0 .and. &
+ isccont(j,i).eq.0 ) then
+ write (iout,*) "Error: no measure of comparison specified:",&
+ " level",i," part",j
+ stop
+ endif
+ if (lprn) &
+ write (iout,*) "iclass_con",iclass_con," iclass_rms",iclass_rms
+ if (i.eq.2) then
+ iclass(j,i) = min0(iclass_con,iclass_rms)
+ if (iabs(ishifft_rms).gt.iabs(ishifft_con)) then
+ ishifft(j,i)=ishifft_rms
+ else
+ ishifft(j,i)=ishifft_con
+ endif
+ else if (i.gt.2) then
+ iclass(j,i) = iclass_rms
+ ishifft(j,i)= ishifft_rms
+ endif
+ 12 continue
+ enddo
+ enddo
+ rms_nat=rmsnat(jcon)
+ qnat=qwolynes(0,0)
+! Compute the structural class
+ iscor=0
+ IF (.NOT. BINARY) THEN
+ do i=1,nlevel
+ IF (I.EQ.1) THEN
+ do j=1,nfrag(i)
+ itemp(j)=iclass(j,i)
+ enddo
+ do kk=-1,1
+ do j=1,nfrag(i)
+ idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-kk*nfrag(i)-j
+ iex = 2**idig
+ im=mod(itemp(j),2)
+ itemp(j)=itemp(j)/2
+! write (iout,*) "i",i," j",j," idig",idig," iex",iex,
+! & " iclass",iclass(j,i)," im",im
+ iscor=iscor+im*iex
+ enddo
+ enddo
+ ELSE
+ do j=1,nfrag(i)
+ idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-j
+ iex = 2**idig
+ if (iclass(j,i).gt.0) then
+ im=1
+ else
+ im=0
+ endif
+! write (iout,*) "i",i," j",j," idig",idig," iex",iex,
+! & " iclass",iclass(j,i)," im",im
+ iscor=iscor+im*iex
+ enddo
+ do j=1,nfrag(i)
+ idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-nfrag(i)-j
+ iex = 2**idig
+ if (iclass(j,i).gt.1) then
+ im=1
+ else
+ im=0
+ endif
+! write (iout,*) "i",i," j",j," idig",idig," iex",iex,
+! & " iclass",iclass(j,i)," im",im
+ iscor=iscor+im*iex
+ enddo
+ ENDIF
+ enddo
+ iscore=iscor
+ ENDIF
+ if (print_class) then
+#ifdef MPI
+ write(istat,'(i6,$)') jcon+indstart(me)-1
+ write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
+ -entfac(jcon)
+#else
+ write(istat,'(i6,$)') jcon
+ write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
+ -entfac(jcon)
+#endif
+ write (istat,'(f8.3,2f6.3,$)') &
+ rms_nat,qnat,rmsang/(nres-3)
+ do j=1,nlevel
+ write(istat,'(1x,$,20(i3,$))') &
+ (ncont_nat(1,k,j),k=1,nfrag(j))
+ if (j.lt.3) then
+ write(istat,'(1x,$,20(f5.1,f5.2$))') &
+ (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j))
+ else
+ write(istat,'(1x,$,20(f5.1$))') &
+ (rmsfrag(k,j),k=1,nfrag(j))
+ endif
+ write(istat,'(1x,$,20(i1,$))') &
+ (iclass(k,j),k=1,nfrag(j))
+ enddo
+ if (binary) then
+ write (istat,'(" ",$)')
+ do j=1,nlevel
+ write (istat,'(100(i1,$))')(iclass(k,j),&
+ k=1,nfrag(j))
+ if (j.lt.nlevel) write(iout,'(".",$)')
+ enddo
+ write (istat,*)
+ else
+ write (istat,'(i10)') iscore
+ endif
+ endif
+ RETURN
+ END subroutine conf_compar
+!-----------------------------------------------------------------------------
+! angnorm.f
+!-----------------------------------------------------------------------------
+ subroutine add_angpair(ici,icj,nang_pair,iang_pair)
+
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.CHAIN'
+ integer :: ici,icj,nang_pair,iang_pair(2,nres)
+ integer :: i,ian1,ian2
+! write (iout,*) "add_angpair: ici",ici," icj",icj,
+! & " nang_pair",nang_pair
+ ian1=ici+2
+ if (ian1.lt.4 .or. ian1.gt.nres) return
+ ian2=icj+2
+! write (iout,*) "ian1",ian1," ian2",ian2
+ if (ian2.lt.4 .or. ian2.gt.nres) return
+ do i=1,nang_pair
+ if (ian1.eq.iang_pair(1,i) .and. ian2.eq.iang_pair(2,i)) return
+ enddo
+ nang_pair=nang_pair+1
+ iang_pair(1,nang_pair)=ian1
+ iang_pair(2,nang_pair)=ian2
+ return
+ end subroutine add_angpair
+!-------------------------------------------------------------------------
+ subroutine angnorm(jfrag,ishif1,ishif2,diffang_max,angn,fract,lprn)
+
+ use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
+ rad2deg,dwapi
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.VAR'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.GEO'
+ real(kind=8) :: pinorm,deltang
+ logical :: lprn
+ integer :: jfrag,ishif1,ishif2,nn,npart,nn4,nne
+ real(kind=8) :: diffang_max,angn,fract,ff
+ integer :: i,j,nbeg,nend,ll,longest
+ if (lprn) write (iout,'(80(1h*))')
+ angn=0.0d0
+ nn = 0
+ fract = 1.0d0
+ npart = npiece(jfrag,1)
+ nn4 = nstart_sup+3
+ nne = min0(nend_sup,nres)
+ if (lprn) write (iout,*) "nn4",nn4," nne",nne
+ do i=1,npart
+ nbeg = ifrag(1,i,jfrag) + 3 - ishif1
+ if (nbeg.lt.nn4) nbeg=nn4
+ nend = ifrag(2,i,jfrag) + 1 - ishif2
+ if (nend.gt.nne) nend=nne
+ if (nend.ge.nbeg) then
+ nn = nn + nend - nbeg + 1
+ if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
+ " nn",nn," ishift1",ishif1," ishift2",ishif2
+ if (lprn) write (iout,*) "angles"
+ longest=0
+ ll = 0
+ do j=nbeg,nend
+! deltang = pinorm(phi(j)-phi_ref(j+ishif1))
+ deltang=spherang(phi_ref(j+ishif1),theta_ref(j-1+ishif1),&
+ theta_ref(j+ishif1),phi(j),theta(j-1),theta(j))
+ if (dabs(deltang).gt.diffang_max) then
+ if (ll.gt.longest) longest = ll
+ ll = 0
+ else
+ ll=ll+1
+ endif
+ if (ll.gt.longest) longest = ll
+ if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
+ rad2deg*phi_ref(j+ishif1),rad2deg*deltang
+ angn=angn+dabs(deltang)
+ enddo
+ longest=longest+3
+ ff = dfloat(longest)/dfloat(nend - nbeg + 4)
+ if (lprn) write (iout,*)"segment",i," longest fragment within",&
+ diffang_max*rad2deg,":",longest," fraction",ff
+ if (ff.lt.fract) fract = ff
+ endif
+ enddo
+ if (nn.gt.0) then
+ angn = angn/nn
+ else
+ angn = dwapi
+ endif
+ if (lprn) write (iout,*) "nn",nn," norm",rad2deg*angn,&
+ " fract",fract
+ return
+ end subroutine angnorm
+!-------------------------------------------------------------------------
+ subroutine angnorm2(jfrag,ishif1,ishif2,ncont,icont,lprn,&
+ diffang_max,anorm,fract)
+
+ use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
+ rad2deg
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.VAR'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.GEO'
+ integer :: ncont,icont(2,ncont),longest
+ real(kind=8) :: anorm,diffang_max,fract
+ integer :: npiece_c,ifrag_c(2,maxpiece),ishift_c(maxpiece)
+ real(kind=8) :: pinorm
+ logical :: lprn
+ integer :: jfrag,ishif1,ishif2
+ integer :: nn,nn4,nne,npart,i,j,jstart,jend,ic1,ic2,idi,iic
+ integer :: nbeg,nend,ll
+ real(kind=8) :: angn,ishifc,deltang,ff
+
+ if (lprn) write (iout,'(80(1h*))')
+!
+! Determine the segments for which angles will be compared
+!
+ nn4 = nstart_sup+3
+ nne = min0(nend_sup,nres)
+ if (lprn) write (iout,*) "nn4",nn4," nne",nne
+ npart=npiece(jfrag,1)
+ npiece_c=0
+ do i=1,npart
+! write (iout,*) "i",i," ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ if (icont(1,ncont).lt.ifrag(1,i,jfrag) .or. &
+ icont(1,1).gt.ifrag(2,i,jfrag)) goto 11
+ jstart=1
+ do while (jstart.lt.ncont .and. &
+ icont(1,jstart).lt.ifrag(1,i,jfrag))
+! write (iout,*) "jstart",jstart," icont",icont(1,jstart),
+! & " ifrag",ifrag(1,i,jfrag)
+ jstart=jstart+1
+ enddo
+! write (iout,*) "jstart",jstart," icont",icont(1,jstart),
+! & " ifrag",ifrag(1,i,jfrag)
+ if (icont(1,jstart).lt.ifrag(1,i,jfrag)) goto 11
+ npiece_c=npiece_c+1
+ ic1=icont(1,jstart)
+ ifrag_c(1,npiece_c)=icont(1,jstart)
+ jend=ncont
+ do while (jend.gt.1 .and. icont(1,jend).gt.ifrag(2,i,jfrag))
+! write (iout,*) "jend",jend," icont",icont(1,jend),
+! & " ifrag",ifrag(2,i,jfrag)
+ jend=jend-1
+ enddo
+! write (iout,*) "jend",jend," icont",icont(1,jend),
+! & " ifrag",ifrag(2,i,jfrag)
+ ic2=icont(1,jend)
+ ifrag_c(2,npiece_c)=icont(1,jend)+1
+ ishift_c(npiece_c)=ishif1
+! write (iout,*) "1: i",i," jstart:",jstart," jend",jend,
+! & " ic1",ic1," ic2",ic2,
+! & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ 11 continue
+ if (ncont.eq.1 .or. icont(2,ncont).gt.icont(2,1)) then
+ idi=1
+ else
+ idi=-1
+ endif
+! write (iout,*) "idi",idi
+ if (idi.eq.1) then
+ if (icont(2,1).gt.ifrag(2,i,jfrag) .or. &
+ icont(2,ncont).lt.ifrag(1,i,jfrag)) goto 12
+ jstart=1
+ do while (jstart.lt.ncont .and. &
+ icont(2,jstart).lt.ifrag(1,i,jfrag))
+! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+! & " ifrag",ifrag(1,i,jfrag)
+ jstart=jstart+1
+ enddo
+! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+! & " ifrag",ifrag(1,i,jfrag)
+ if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
+ npiece_c=npiece_c+1
+ ic1=icont(2,jstart)
+ ifrag_c(2,npiece_c)=icont(2,jstart)+1
+ jend=ncont
+ do while (jend.gt.1 .and. icont(2,jend).gt.ifrag(2,i,jfrag))
+! write (iout,*) "jend",jend," icont",icont(2,jend),
+! & " ifrag",ifrag(2,i,jfrag)
+ jend=jend-1
+ enddo
+! write (iout,*) "jend",jend," icont",icont(2,jend),
+! & " ifrag",ifrag(2,i,jfrag)
+ else if (idi.eq.-1) then
+ if (icont(2,ncont).gt.ifrag(2,i,jfrag) .or. &
+ icont(2,1).lt.ifrag(1,i,jfrag)) goto 12
+ jstart=ncont
+ do while (jstart.gt.ncont .and. &
+ icont(2,jstart).lt.ifrag(1,i,jfrag))
+! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+! & " ifrag",ifrag(1,i,jfrag)
+ jstart=jstart-1
+ enddo
+! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+! & " ifrag",ifrag(1,i,jfrag)
+ if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
+ npiece_c=npiece_c+1
+ ic1=icont(2,jstart)
+ ifrag_c(2,npiece_c)=icont(2,jstart)+1
+ jend=1
+ do while (jend.lt.ncont .and. &
+ icont(2,jend).gt.ifrag(2,i,jfrag))
+! write (iout,*) "jend",jend," icont",icont(2,jend),
+! & " ifrag",ifrag(2,i,jfrag)
+ jend=jend+1
+ enddo
+! write (iout,*) "jend",jend," icont",icont(2,jend),
+! & " ifrag",ifrag(2,i,jfrag)
+ endif
+ ic2=icont(2,jend)
+ if (ic2.lt.ic1) then
+ iic = ic1
+ ic1 = ic2
+ ic2 = iic
+ endif
+! write (iout,*) "2: i",i," ic1",ic1," ic2",ic2,
+! & " jstart:",jstart," jend",jend,
+! & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ ifrag_c(1,npiece_c)=ic1
+ ifrag_c(2,npiece_c)=ic2+1
+ ishift_c(npiece_c)=ishif2
+ 12 continue
+ enddo
+ if (lprn) then
+ write (iout,*) "Before merge: npiece_c",npiece_c
+ do i=1,npiece_c
+ write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
+ enddo
+ endif
+!
+! Merge overlapping segments (e.g., avoid splitting helices)
+!
+ i=1
+ do while (i .lt. npiece_c)
+ if (ishift_c(i).eq.ishift_c(i+1) .and. &
+ ifrag_c(2,i).gt.ifrag_c(1,i+1)) then
+ ifrag_c(2,i)=ifrag_c(2,i+1)
+ do j=i+1,npiece_c
+ ishift_c(j)=ishift_c(j+1)
+ ifrag_c(1,j)=ifrag_c(1,j+1)
+ ifrag_c(2,j)=ifrag_c(2,j+1)
+ enddo
+ npiece_c=npiece_c-1
+ else
+ i=i+1
+ endif
+ enddo
+ if (lprn) then
+ write (iout,*) "After merge: npiece_c",npiece_c
+ do i=1,npiece_c
+ write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
+ enddo
+ endif
+!
+! Compare angles
+!
+ angn=0.0d0
+ anorm=0
+ nn = 0
+ fract = 1.0d0
+ npart = npiece_c
+ do i=1,npart
+ ishifc=ishift_c(i)
+ nbeg = ifrag_c(1,i) + 3 - ishifc
+ if (nbeg.lt.nn4) nbeg=nn4
+ nend = ifrag_c(2,i) - ishifc + 1
+ if (nend.gt.nne) nend=nne
+ if (nend.ge.nbeg) then
+ nn = nn + nend - nbeg + 1
+ if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
+ " nn",nn," ishifc",ishifc
+ if (lprn) write (iout,*) "angles"
+ longest=0
+ ll = 0
+ do j=nbeg,nend
+! deltang = pinorm(phi(j)-phi_ref(j+ishifc))
+ deltang=spherang(phi_ref(j+ishifc),theta_ref(j-1+ishifc),&
+ theta_ref(j+ishifc),phi(j),theta(j-1),theta(j))
+ if (dabs(deltang).gt.diffang_max) then
+ if (ll.gt.longest) longest = ll
+ ll = 0
+ else
+ ll=ll+1
+ endif
+ if (ll.gt.longest) longest = ll
+ if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
+ rad2deg*phi_ref(j+ishifc),rad2deg*deltang
+ angn=angn+dabs(deltang)
+ enddo
+ longest=longest+3
+ ff = dfloat(longest)/dfloat(nend - nbeg + 4)
+ if (lprn) write (iout,*)"segment",i," longest fragment within",&
+ diffang_max*rad2deg,":",longest," fraction",ff
+ if (ff.lt.fract) fract = ff
+ endif
+ enddo
+ if (nn.gt.0) anorm = angn/nn
+ if (lprn) write (iout,*) "nn",nn," norm",anorm," fract:",fract
+ return
+ end subroutine angnorm2
+!-------------------------------------------------------------------------
+ real(kind=8) function angnorm1(nang_pair,iang_pair,lprn)
+
+ use geometry_data, only:phi,theta,rad2deg
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.VAR'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.GEO'
+ logical :: lprn
+ integer :: nang_pair,iang_pair(2,nres)
+ real(kind=8) :: pinorm
+ integer :: j,ia1,ia2
+ real(kind=8) :: angn,deltang
+ angn=0.0d0
+ if (lprn) write (iout,'(80(1h*))')
+ if (lprn) write (iout,*) "nang_pair",nang_pair
+ if (lprn) write (iout,*) "angles"
+ do j=1,nang_pair
+ ia1 = iang_pair(1,j)
+ ia2 = iang_pair(2,j)
+! deltang = pinorm(phi(ia1)-phi_ref(ia2))
+ deltang=spherang(phi_ref(ia2),theta_ref(ia2-1),&
+ theta_ref(ia2),phi(ia2),theta(ia2-1),theta(ia2))
+ if (lprn) write (iout,'(3i5,3f10.5)')j,ia1,ia2,rad2deg*phi(ia1),&
+ rad2deg*phi_ref(ia2),rad2deg*deltang
+ angn=angn+dabs(deltang)
+ enddo
+ if (lprn) &
+ write (iout,*)"nang_pair",nang_pair," angn",rad2deg*angn/nang_pair
+ angnorm1 = angn/nang_pair
+ return
+ end function angnorm1
+!------------------------------------------------------------------------------
+ subroutine angnorm12(diff)
+
+ use geometry_data, only:phi,theta,nstart_sup,nend_sup
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.VAR'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.GEO'
+ real(kind=8) :: pinorm,diff
+ integer :: nn4,nne,j
+ diff=0.0d0
+ nn4 = nstart_sup+3
+ nne = min0(nend_sup,nres)
+! do j=nn4-1,nne
+! diff = diff+rad2deg*dabs(pinorm(theta(j)-theta_ref(j)))
+! enddo
+ do j=nn4,nne
+! diff = diff+rad2deg*dabs(pinorm(phi(j)-phi_ref(j)))
+ diff=diff+spherang(phi_ref(j),theta_ref(j-1),&
+ theta_ref(j),phi(j),theta(j-1),theta(j))
+ enddo
+ return
+ end subroutine angnorm12
+!--------------------------------------------------------------------------------
+ real(kind=8) function spherang(gam1,theta11,theta12,&
+ gam2,theta21,theta22)
+! implicit none
+ use geometry, only:arcos
+ real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,&
+ x1,x2,xmed,f1,f2,fmed
+ real(kind=8) :: tolx=1.0d-4, tolf=1.0d-4
+ real(kind=8) :: sumcos
+!el real(kind=8) :: pinorm,sumangp !arcos,
+ integer :: it,maxit=100
+! Calculate the difference of the angles of two superposed 4-redidue fragments
+!
+! O P
+! \ /
+! O'--C--C
+! \
+! P'
+!
+! The fragment O'-C-C-P' is rotated by angle fi about the C-C axis
+! to achieve the minimum difference between the O'-C-O and P-C-P angles;
+! the sum of these angles is the difference returned by the function.
+!
+! 4/28/04 AL
+! If thetas match, take the difference of gamma and exit.
+ if (dabs(theta11-theta12).lt.tolx &
+ .and. dabs(theta21-theta22).lt.tolx) then
+ spherang=dabs(pinorm(gam2-gam1))
+ return
+ endif
+! If the gammas are the same, take the difference of thetas and exit.
+ x1=0.0d0
+ x2=0.5d0*pinorm(gam2-gam1)
+ if (dabs(x2) .lt. tolx) then
+ spherang=dabs(theta11-theta21)+dabs(theta12-theta22)
+ return
+ else if (x2.lt.0.0d0) then
+ x1=x2
+ x2=0.0d0
+ endif
+! Else apply regula falsi method to compute optimum overlap of the terminal Calphas
+ f1=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x1)
+ f2=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x2)
+ do it=1,maxit
+ xmed=x1-f1*(x2-x1)/(f2-f1)
+ fmed=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,xmed)
+! write (*,*) 'it',it,' xmed ',xmed,' fmed ',fmed
+ if ( (dabs(xmed-x1).lt.tolx .or. dabs(x2-xmed).lt.tolx) &
+ .and. dabs(fmed).lt.tolf ) then
+ x1=xmed
+ f1=fmed
+ goto 10
+ else if ( fmed*f1.lt.0.0d0 ) then
+ x2=xmed
+ f2=fmed
+ else
+ x1=xmed
+ f1=fmed
+ endif
+ enddo
+ 10 continue
+ spherang=arcos(dcos(theta11)*dcos(theta12) &
+ +dsin(theta11)*dsin(theta12)*dcos(x1))+ &
+ arcos(dcos(theta21)*dcos(theta22)+ &
+ dsin(theta21)*dsin(theta22)*dcos(gam2-gam1+x1))
+ return
+ end function spherang
+!--------------------------------------------------------------------------------
+ real(kind=8) function sumangp(gam1,theta11,theta12,gam2,&
+ theta21,theta22,fi)
+! implicit none
+ real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,fi,&
+ cost11,cost12,cost21,cost22,sint11,sint12,sint21,sint22,cosd1,&
+ cosd2
+! derivarive of the sum of the difference of the angles of a 4-residue fragment.
+! real(kind=8) :: arcos
+ cost11=dcos(theta11)
+ cost12=dcos(theta12)
+ cost21=dcos(theta21)
+ cost22=dcos(theta22)
+ sint11=dsin(theta11)
+ sint12=dsin(theta12)
+ sint21=dsin(theta21)
+ sint22=dsin(theta22)
+ cosd1=cost11*cost12+sint11*sint12*dcos(fi)
+ cosd2=cost21*cost22+sint21*sint22*dcos(gam2-gam1+fi)
+ sumangp=sint11*sint12*dsin(fi)/dsqrt(1.0d0-cosd1*cosd1) &
+ +sint21*sint22*dsin(gam2-gam1+fi)/dsqrt(1.0d0-cosd2*cosd2)
+ return
+ end function sumangp
+!-----------------------------------------------------------------------------
+! contact.f
+!-----------------------------------------------------------------------------
+ subroutine contact(lprint,ncont,icont,ist,ien)
+
+ use calc_data
+ use geometry_data, only:c,dc,dc_norm
+ use energy_data, only:itype,maxcont
+! implicit none
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'COMMON.CONTROL'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.FFIELD'
+! include 'COMMON.NAMES'
+! include 'COMMON.CALC'
+! include 'COMMON.CONTPAR'
+! include 'COMMON.LOCAL'
+ integer :: ist,ien,kkk,iti,itj,itypi,itypj,i1,i2,it1,it2
+ real(kind=8) :: csc !el,dist
+ real(kind=8),dimension(maxcont) :: cscore,omt1,omt2,omt12,&
+ ddsc,ddla,ddlb
+ integer :: ncont
+ integer,dimension(2,maxcont) :: icont
+ real(kind=8) :: u,v,a(3),b(3),dla,dlb
+ logical :: lprint
+!el-------
+ dla=0.0d0
+ dlb=0.0d0
+!el------
+ ncont=0
+ kkk=3
+ if (lprint) then
+ do i=1,nres
+ write (iout,110) restyp(itype(i)),i,c(1,i),c(2,i),&
+ c(3,i),dc(1,nres+i),dc(2,nres+i),dc(3,nres+i),&
+ dc_norm(1,nres+i),dc_norm(2,nres+i),dc_norm(3,nres+i)
+ enddo
+ endif
+ 110 format (a,'(',i3,')',9f8.3)
+ do i=ist,ien-kkk
+ iti=iabs(itype(i))
+ if (iti.le.0 .or. iti.gt.ntyp) cycle
+ do j=i+kkk,ien
+ itj=iabs(itype(j))
+ if (itj.le.0 .or. itj.gt.ntyp) cycle
+ itypi=iti
+ itypj=itj
+ xj = c(1,nres+j)-c(1,nres+i)
+ yj = c(2,nres+j)-c(2,nres+i)
+ zj = c(3,nres+j)-c(3,nres+i)
+ dxi = dc_norm(1,nres+i)
+ dyi = dc_norm(2,nres+i)
+ dzi = dc_norm(3,nres+i)
+ dxj = dc_norm(1,nres+j)
+ dyj = dc_norm(2,nres+j)
+ dzj = dc_norm(3,nres+j)
+ do k=1,3
+ a(k)=dc(k,nres+i)
+ b(k)=dc(k,nres+j)
+ enddo
+! write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
+ if (icomparfunc.eq.1) then
+ call contfunc(csc,iti,itj)
+ else if (icomparfunc.eq.2) then
+ call scdist(csc,iti,itj)
+ else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
+ csc = dist(nres+i,nres+j)
+ else if (icomparfunc.eq.4) then
+ call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
+ else
+ write (*,*) "Error - Unknown sidechain contact function"
+ write (iout,*) "Error - Unknown sidechain contact function"
+ endif
+ if (csc.lt.sc_cutoff(iti,itj)) then
+! write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
+! & " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
+! & dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
+! & dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
+! & xj,yj,zj
+! write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
+! & sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
+! & chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
+! & csc
+ ncont=ncont+1
+ cscore(ncont)=csc
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ omt1(ncont)=om1
+ omt2(ncont)=om2
+ omt12(ncont)=om12
+ ddsc(ncont)=1.0d0/rij
+ ddla(ncont)=dla
+ ddlb(ncont)=dlb
+ endif
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') 'Contact map:'
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
+ i,restyp(it1),i1,restyp(it2),i2,cscore(i),&
+ sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
+ omt1(i),omt2(i),omt12(i)
+ enddo
+ endif
+ return
+ end subroutine contact
+#else
+!----------------------------------------------------------------------------
+ subroutine contact(lprint,ncont,icont)
+
+ use energy_data, only: nnt,nct,itype,ipot,maxcont,sigma,sigmaii
+! include 'DIMENSIONS'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.FFIELD'
+! include 'COMMON.NAMES'
+ real(kind=8) :: facont=1.569D0 ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
+ integer :: ncont,icont(2,maxcont)
+ logical :: lprint
+ integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
+ real(kind=8) :: rcomp
+ ncont=0
+ kkk=3
+! print *,'nnt=',nnt,' nct=',nct
+ do i=nnt+kkk,nct
+ iti=iabs(itype(i))
+ do j=nnt,i-kkk
+ itj=iabs(itype(j))
+ if (ipot.ne.4) then
+! rcomp=sigmaii(iti,itj)+1.0D0
+ rcomp=facont*sigmaii(iti,itj)
+ else
+! rcomp=sigma(iti,itj)+1.0D0
+ rcomp=facont*sigma(iti,itj)
+ endif
+! rcomp=6.5D0
+! print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
+ if (dist(nres+i,nres+j).lt.rcomp) then
+ ncont=ncont+1
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ endif
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') 'Contact map:'
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ endif
+ return
+ end subroutine contact
+#endif
+!----------------------------------------------------------------------------
+ real(kind=8) function contact_fract(ncont,ncont_ref,&
+ icont,icont_ref)
+
+ use energy_data, only:maxcont
+! implicit none
+! include 'DIMENSIONS'
+! include 'COMMON.IOUNITS'
+ integer :: i,j,nmatch
+ integer :: ncont,ncont_ref
+ integer,dimension(2,maxcont) :: icont,icont_ref
+ nmatch=0
+! print *,'ncont=',ncont,' ncont_ref=',ncont_ref
+! write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
+! write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
+! write (iout,'(20i4)') (icont(1,i),i=1,ncont)
+! write (iout,'(20i4)') (icont(2,i),i=1,ncont)
+ do i=1,ncont
+ do j=1,ncont_ref
+ if (icont(1,i).eq.icont_ref(1,j) .and. &
+ icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
+ enddo
+ enddo
+! print *,' nmatch=',nmatch
+! contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
+ contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
+ return
+ end function contact_fract
+#ifndef CLUSTER
+!------------------------------------------------------------------------------
+ subroutine pept_cont(lprint,ncont,icont)
+
+ use geometry_data, only:c
+ use energy_data, only:maxcont,nnt,nct,itype
+! implicit none
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.FFIELD'
+! include 'COMMON.NAMES'
+ integer :: ncont,icont(2,maxcont)
+ integer :: i,j,k,kkk,i1,i2,it1,it2
+ logical :: lprint
+!el real(kind=8) :: dist
+ real(kind=8) :: rcomp=5.5d0
+ ncont=0
+ kkk=0
+ print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
+ do i=nnt,nct-3
+ do k=1,3
+ c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
+ enddo
+ do j=i+2,nct-1
+ do k=1,3
+ c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
+ enddo
+ if (dist(2*nres+1,2*nres+2).lt.rcomp) then
+ ncont=ncont+1
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ endif
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') 'PP contact map:'
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ endif
+ return
+ end subroutine pept_cont
+!-----------------------------------------------------------------------------
+! cont_frag.f
+!-----------------------------------------------------------------------------
+ subroutine contacts_between_fragments(lprint,is,ncont,icont,&
+ ncont_interfrag,icont_interfrag)
+
+ use energy_data, only:itype,maxcont
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.INTERACT'
+! include 'COMMON.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.CHAIN'
+! include 'COMMON.NAMES'
+ integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
+ icont_interfrag(2,maxcont,mmaxfrag)
+ logical :: OK1,OK2,lprint
+ integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2
+! Determine the contacts that occur within a fragment and between fragments.
+ do i=1,nfrag(1)
+ do j=1,i
+ ind = icant(i,j)
+ nc=0
+! write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
+! & ,k=1,npiece(i,1))
+! write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
+! & ,k=1,npiece(j,1))
+! write (iout,*) "ncont",ncont
+ do k=1,ncont
+ ic1=icont(1,k)
+ ic2=icont(2,k)
+ OK1=.false.
+ l=0
+ do while (.not.OK1 .and. l.lt.npiece(j,1))
+ l=l+1
+ OK1=ic1.ge.ifrag(1,l,j)-is .and. &
+ ic1.le.ifrag(2,l,j)+is
+ enddo
+ OK2=.false.
+ l=0
+ do while (.not.OK2 .and. l.lt.npiece(i,1))
+ l=l+1
+ OK2=ic2.ge.ifrag(1,l,i)-is .and. &
+ ic2.le.ifrag(2,l,i)+is
+ enddo
+! write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
+! & " OK2",OK2
+ if (OK1.and.OK2) then
+ nc=nc+1
+ icont_interfrag(1,nc,ind)=ic1
+ icont_interfrag(2,nc,ind)=ic2
+! write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
+ endif
+ enddo
+ ncont_interfrag(ind)=nc
+! do k=1,ncont_interfrag(ind)
+! i1=icont_interfrag(1,k,ind)
+! i2=icont_interfrag(2,k,ind)
+! it1=itype(i1)
+! it2=itype(i2)
+! write (iout,'(i3,2x,a,i4,2x,a,i4)')
+! & i,restyp(it1),i1,restyp(it2),i2
+! enddo
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,*) "Contacts within fragments:"
+ do i=1,nfrag(1)
+ write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
+ ifrag(2,k,i),k=1,npiece(i,1)),")"
+ ind=icant(i,i)
+ do k=1,ncont_interfrag(ind)
+ i1=icont_interfrag(1,k,ind)
+ i2=icont_interfrag(2,k,ind)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ enddo
+ write (iout,*)
+ write (iout,*) "Contacts between fragments:"
+ do i=1,nfrag(1)
+ do j=1,i-1
+ ind = icant(i,j)
+ write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
+ ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
+ (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
+ write (iout,*) "Number of contacts",&
+ ncont_interfrag(ind)
+ ind=icant(i,j)
+ do k=1,ncont_interfrag(ind)
+ i1=icont_interfrag(1,k,ind)
+ i2=icont_interfrag(2,k,ind)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ enddo
+ enddo
+ endif
+ return
+ end subroutine contacts_between_fragments
+!-----------------------------------------------------------------------------
+! contfunc.f
+!-----------------------------------------------------------------------------
+ subroutine contfunc(cscore,itypi,itypj)
+!
+! This subroutine calculates the contact function based on
+! the Gay-Berne potential of interaction.
+!
+ use calc_data
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'COMMON.CONTPAR'
+! include 'COMMON.CALC'
+ integer :: expon=6
+ integer :: itypi,itypj
+ real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
+!
+ sig0ij=sig_comp(itypi,itypj)
+ chi1=chi_comp(itypi,itypj)
+ chi2=chi_comp(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip_comp(itypi,itypj)
+ chip2=chip_comp(itypj,itypi)
+ chip12=chip1*chip2
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+! Calculate angle-dependent terms of the contact function
+ erij(1)=xj*rij
+ erij(2)=yj*rij
+ erij(3)=zj*rij
+ om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+ om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+ om12=dxi*dxj+dyi*dyj+dzi*dzj
+ chiom12=chi12*om12
+! print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
+! & sig0ij,
+! & rij,rrij,om1,om2,om12
+! Calculate eps1(om12)
+ faceps1=1.0D0-om12*chiom12
+ faceps1_inv=1.0D0/faceps1
+ eps1=dsqrt(faceps1_inv)
+! Following variable is eps1*deps1/dom12
+ eps1_om12=faceps1_inv*chiom12
+! Calculate sigma(om1,om2,om12)
+ om1om2=om1*om2
+ chiom1=chi1*om1
+ chiom2=chi2*om2
+ facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
+ sigsq=1.0D0-facsig*faceps1_inv
+! Calculate eps2 and its derivatives in om1, om2, and om12.
+ chipom1=chip1*om1
+ chipom2=chip2*om2
+ chipom12=chip12*om12
+ facp=1.0D0-om12*chipom12
+ facp_inv=1.0D0/facp
+ facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
+! Following variable is the square root of eps2
+ eps2rt=1.0D0-facp1*facp_inv
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+sig0ij
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D1
+ cscore = -dlog(evdw+1.0d-6)
+ return
+ endif
+ rij_shift=1.0D0/rij_shift
+ e2=(rij_shift*sig0ij)**expon
+ evdw=dabs(eps1*eps2rt**2*e2)
+ if (evdw.gt.1.0d1) evdw = 1.0d1
+ cscore = -dlog(evdw+1.0d-6)
+ return
+ end subroutine contfunc
+!------------------------------------------------------------------------------
+ subroutine scdist(cscore,itypi,itypj)
+!
+! This subroutine calculates the contact distance
+!
+ use calc_data
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'COMMON.CONTPAR'
+! include 'COMMON.CALC'
+ integer :: itypi,itypj
+ real(kind=8) :: cscore,rrij
+
+ chi1=chi_comp(itypi,itypj)
+ chi2=chi_comp(itypj,itypi)
+ chi12=chi1*chi2
+ rrij=xj*xj+yj*yj+zj*zj
+ rij=dsqrt(rrij)
+! Calculate angle-dependent terms of the contact function
+ erij(1)=xj/rij
+ erij(2)=yj/rij
+ erij(3)=zj/rij
+ om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+ om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+ om12=dxi*dxj+dyi*dyj+dzi*dzj
+ chiom12=chi12*om12
+ om1om2=om1*om2
+ chiom1=chi1*om1
+ chiom2=chi2*om2
+ cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
+ return
+ end subroutine scdist
+!------------------------------------------------------------------------------
+! elecont.f
+!------------------------------------------------------------------------------
+ subroutine elecont(lprint,ncont,icont,ist,ien)
+
+ use geometry_data, only:c
+ use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2
+! implicit none
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.FFIELD'
+! include 'COMMON.NAMES'
+! include 'COMMON.LOCAL'
+ logical :: lprint
+ integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
+ real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
+ xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
+ vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
+ eesij,ees,evdw,ene
+ real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
+ -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
+ real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
+ 0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
+ real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
+ real(kind=8) :: elcutoff=-0.3d0
+ real(kind=8) :: elecutoff_14=-0.5d0
+ integer :: ncont,icont(2,maxcont)
+ real(kind=8) :: econt(maxcont)
+!
+! Load the constants of peptide bond - peptide bond interactions.
+! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
+! proline) - determined by averaging ECEPP energy.
+!
+! as of 7/06/91.
+!
+! data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
+! data rpp / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
+!el data (elpp6c) /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
+!el data (elpp3c) / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
+!el data (elcutoff) /-0.3d0/
+!el data (elecutoff_14) /-0.5d0/
+ ees=0.0d0
+ evdw=0.0d0
+ if (lprint) write (iout,'(a)') &
+ "Constants of electrostatic interaction energy expression."
+ do i=1,2
+ do j=1,2
+ rri=rpp(i,j)**6
+ appc(i,j)=epp(i,j)*rri*rri
+ bppc(i,j)=-2.0*epp(i,j)*rri
+ ael6c(i,j)=elpp6c(i,j)*4.2**6
+ ael3c(i,j)=elpp3c(i,j)*4.2**3
+ if (lprint) &
+ write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
+ ael3c(i,j)
+ enddo
+ enddo
+ ncont=0
+ do 1 i=ist,ien-2
+ xi=c(1,i)
+ yi=c(2,i)
+ zi=c(3,i)
+ dxi=c(1,i+1)-c(1,i)
+ dyi=c(2,i+1)-c(2,i)
+ dzi=c(3,i+1)-c(3,i)
+ xmedi=xi+0.5*dxi
+ ymedi=yi+0.5*dyi
+ zmedi=zi+0.5*dzi
+ do 4 j=i+2,ien-1
+ ind=ind+1
+ iteli=itel(i)
+ itelj=itel(j)
+ if (j.eq.i+2 .and. itelj.eq.2) iteli=2
+ if (iteli.eq.2 .and. itelj.eq.2 &
+ .or.iteli.eq.0 .or.itelj.eq.0) goto 4
+ aaa=appc(iteli,itelj)
+ bbb=bppc(iteli,itelj)
+ ael6i=ael6c(iteli,itelj)
+ ael3i=ael3c(iteli,itelj)
+ dxj=c(1,j+1)-c(1,j)
+ dyj=c(2,j+1)-c(2,j)
+ dzj=c(3,j+1)-c(3,j)
+ xj=c(1,j)+0.5*dxj-xmedi
+ yj=c(2,j)+0.5*dyj-ymedi
+ zj=c(3,j)+0.5*dzj-zmedi
+ rrmij=1.0/(xj*xj+yj*yj+zj*zj)
+ rmij=sqrt(rrmij)
+ r3ij=rrmij*rmij
+ r6ij=r3ij*r3ij
+ vrmij=vblinv*rmij
+ cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
+ cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
+ cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
+ fac=cosa-3.0*cosb*cosg
+ ev1=aaa*r6ij*r6ij
+ ev2=bbb*r6ij
+ fac3=ael6i*r6ij
+ fac4=ael3i*r3ij
+ evdwij=ev1+ev2
+ el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
+ el2=fac4*fac
+ eesij=el1+el2
+ if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
+ j.eq.i+2 .and. eesij.le.elecutoff_14) then
+ ncont=ncont+1
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ econt(ncont)=eesij
+ endif
+ ees=ees+eesij
+ evdw=evdw+evdwij
+ 4 continue
+ 1 continue
+ if (lprint) then
+ write (iout,*) 'Total average electrostatic energy: ',ees
+ write (iout,*) 'VDW energy between peptide-group centers: ',evdw
+ write (iout,*)
+ write (iout,*) 'Electrostatic contacts before pruning: '
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
+ i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ enddo
+ endif
+! For given residues keep only the contacts with the greatest energy.
+ i=0
+ do while (i.lt.ncont)
+ i=i+1
+ ene=econt(i)
+ ic1=icont(1,i)
+ ic2=icont(2,i)
+ j=i
+ do while (j.lt.ncont)
+ j=j+1
+ if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
+ ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
+! write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
+! & " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
+ if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
+ if (ic1.eq.icont(1,j)) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
+ .and. iabs(icont(1,k)-ic1).le.2 .and. &
+ econt(k).lt.econt(j) ) goto 21
+ enddo
+ else if (ic2.eq.icont(2,j) ) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
+ .and. iabs(icont(2,k)-ic2).le.2 .and. &
+ econt(k).lt.econt(j) ) goto 21
+ enddo
+ endif
+! Remove ith contact
+ do k=i+1,ncont
+ icont(1,k-1)=icont(1,k)
+ icont(2,k-1)=icont(2,k)
+ econt(k-1)=econt(k)
+ enddo
+ i=i-1
+ ncont=ncont-1
+! write (iout,*) "ncont",ncont
+! do k=1,ncont
+! write (iout,*) icont(1,k),icont(2,k)
+! enddo
+ goto 20
+ else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
+ then
+ if (ic1.eq.icont(1,j)) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
+ .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
+ econt(k).lt.econt(i) ) goto 21
+ enddo
+ else if (ic2.eq.icont(2,j) ) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
+ .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
+ econt(k).lt.econt(i) ) goto 21
+ enddo
+ endif
+! Remove jth contact
+ do k=j+1,ncont
+ icont(1,k-1)=icont(1,k)
+ icont(2,k-1)=icont(2,k)
+ econt(k-1)=econt(k)
+ enddo
+ ncont=ncont-1
+! write (iout,*) "ncont",ncont
+! do k=1,ncont
+! write (iout,*) icont(1,k),icont(2,k)
+! enddo
+ j=j-1
+ endif
+ endif
+ 21 continue
+ enddo
+ 20 continue
+ enddo
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) 'Electrostatic contacts after pruning: '
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
+ i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ enddo
+ endif
+ return
+ end subroutine elecont
+!------------------------------------------------------------------------------
+! match_contact.f
+!------------------------------------------------------------------------------
+ subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
+ ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
+ nc_frac,nc_req_set,istr,llocal,lprn)
+
+ use energy_data, only:maxcont
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'COMMON.IOUNITS'
+ integer :: ncont_ref,ncont,ishift,ishif2,nc_match
+ integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
+ real(kind=8) :: nc_frac
+ logical :: llocal,lprn
+ integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
+ nc_req_set,istr,nc_match_max
+ integer :: i,nc_req,nc_match1,is,js
+ nc_match_max=0
+ do i=1,ncont_ref
+ nc_match_max=nc_match_max+ &
+ min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
+ enddo
+ if (istr.eq.3) then
+ nc_req=0
+ else if (nc_req_set.eq.0) then
+ nc_req=nc_match_max*nc_frac
+ else
+ nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
+ dfloat(nc_req_set)+1.0d-7)
+ endif
+! write (iout,*) "match_contact: nc_req:",nc_req
+! write (iout,*) "nc_match_max",nc_match_max
+! write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
+! & " n_shif2",n_shif2
+! Match current contact map against reference contact map; exit, if at least
+! half of the contacts match
+ call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
+ ncont,icont,jfrag,llocal,lprn)
+ nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",0,0," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
+ nc_req.eq.0 .and. nc_match.eq.1) then
+ ishif1=0
+ ishif2=0
+ return
+ endif
+! If sufficient matches are not found, try to shift contact maps up to three
+! positions.
+ if (n_shif1.gt.0) then
+ do is=1,n_shif1
+! The following four tries help to find shifted beta-sheet patterns
+! Shift "left" strand backward
+ call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",-is,0," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
+ nc_req.eq.0 .and. nc_match.eq.1) then
+ ishif1=-is
+ ishif2=0
+ return
+ endif
+! Shift "left" strand forward
+ call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",is,0," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
+ nc_req.eq.0 .and. nc_match.eq.1) then
+ ishif1=is
+ ishif2=0
+ return
+ endif
+ enddo
+ if (nc_req.eq.0) return
+! Shift "right" strand backward
+ do is=1,n_shif1
+ call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",0,-is," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=0
+ ishif2=-is
+ return
+ endif
+! Shift "right" strand upward
+ call ncont_match(nc_match,nc_match1,0,is,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",0,is," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=0
+ ishif2=is
+ return
+ endif
+ enddo ! is
+! Now try to shift both residues in contacts.
+ do is=1,n_shif1
+ do js=1,is
+ if (js.ne.is) then
+ call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",-is,-js," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-is
+ ishif2=-js
+ return
+ endif
+ call ncont_match(nc_match,nc_match1,is,js,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",is,js," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=is
+ ishif2=js
+ return
+ endif
+!
+ call ncont_match(nc_match,nc_match1,-js,-is,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",-js,-is," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-js
+ ishif2=-is
+ return
+ endif
+!
+ call ncont_match(nc_match,nc_match1,js,is,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",js,is," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=js
+ ishif2=is
+ return
+ endif
+ endif
+!
+ if (is+js.le.n_shif1) then
+ call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",-is,js," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-is
+ ishif2=js
+ return
+ endif
+!
+ call ncont_match(nc_match,nc_match1,js,-is,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",js,-is," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=js
+ ishif2=-is
+ return
+ endif
+ endif
+!
+ enddo !js
+ enddo !is
+ endif
+
+ if (n_shif2.gt.0) then
+ do is=1,n_shif2
+ call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",-is,-is," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-is
+ ishif2=-is
+ return
+ endif
+ call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
+ icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*) &
+ "Shift:",is,is," nc_match1",nc_match1,&
+ " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=is
+ ishif2=is
+ return
+ endif
+ enddo
+ endif
+! If this point is reached, the contact maps are different.
+ nc_match=0
+ ishif1=0
+ ishif2=0
+ return
+ end subroutine match_contact
+!-------------------------------------------------------------------------
+ subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
+ ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
+
+ use energy_data, only:nnt,nct,maxcont
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.INTERACT'
+! include 'COMMON.GEO'
+! include 'COMMON.COMPAR'
+ logical :: llocal,lprn
+ integer ncont_ref,ncont,ishift,ishif2,nang_pair
+ integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
+ integer,dimension(2,nres) :: iang_pair !(2,maxres)
+ integer :: nc_match,nc_match1,ishif1,jfrag
+ integer :: i,j,ic1,ic2
+ real(kind=8) :: diffang,fract,rad2deg
+
+! Compare the contact map against the reference contact map; they're stored
+! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
+ if (lprn) write (iout,'(80(1h*))')
+ nc_match=0
+ nc_match1=0
+! Check the local structure by comparing dihedral angles.
+! write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
+ if (llocal .and. ncont_ref.eq.0) then
+! If there are no contacts just compare the dihedral angles and exit.
+ call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
+ lprn)
+ if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
+ " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
+ if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
+ then
+ nc_match=1
+ else
+ nc_match=0
+ endif
+ return
+ endif
+ nang_pair=0
+ do i=1,ncont
+ ic1=icont(1,i)+ishif1
+ ic2=icont(2,i)+ishif2
+! write (iout,*) "i",i," ic1",ic1," ic2",ic2
+ if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
+ do j=1,ncont_ref
+ if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
+ nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
+ nc_match1=nc_match1+1
+ icont_match(1,nc_match1)=ic1
+ icont_match(2,nc_match1)=ic2
+! call add_angpair(icont(1,i),icont_ref(1,j),
+! & nang_pair,iang_pair)
+! call add_angpair(icont(2,i),icont_ref(2,j),
+! & nang_pair,iang_pair)
+ if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
+ " match",icont_ref(1,j),icont_ref(2,j),&
+ " shifts",ishif1,ishif2
+ goto 10
+ endif
+ enddo
+ 10 continue
+ enddo
+ if (lprn) then
+ write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
+ write (iout,*) "icont_match"
+ do i=1,nc_match1
+ write (iout,*) icont_match(1,i),icont_match(2,i)
+ enddo
+ endif
+ if (llocal .and. nc_match.gt.0) then
+ call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
+ ang_cut1(jfrag),diffang,fract)
+ if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
+ " ang_cut:",ang_cut(jfrag)*rad2deg,&
+ " ang_cut1",ang_cut1(jfrag)*rad2deg
+ if (diffang.gt.ang_cut(jfrag) &
+ .or. fract.lt.frac_min(jfrag)) nc_match=0
+ endif
+! if (nc_match.gt.0) then
+! diffang = angnorm1(nang_pair,iang_pair,lprn)
+! if (diffang.gt.ang_cut(jfrag)) nc_match=0
+! endif
+ if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
+ " diffang",rad2deg*diffang," nc_match",nc_match
+ return
+ end subroutine ncont_match
+!------------------------------------------------------------------------------
+ subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
+! This subroutine compares the secondary structure (isecstr) of fragment jfrag
+! conformation considered to that of the reference conformation.
+! Returns the number of equivalent residues (nsec_match).
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.CHAIN'
+! include 'COMMON.PEPTCONT'
+! include 'COMMON.COMPAR'
+ logical :: lprn
+ integer :: isecstr(nres)
+ integer :: jfrag,nsec_match,npart,i,j
+ npart = npiece(jfrag,1)
+ nsec_match=0
+ if (lprn) then
+ write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
+ (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
+ write (iout,'(80i1)') (isec_ref(j),j=1,nres)
+ write (iout,'(80i1)') (isecstr(j),j=1,nres)
+ endif
+ do i=1,npart
+ do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+! The residue has equivalent conformational state to that of the reference
+! structure, if:
+! a) the conformational states are equal or
+! b) the reference state is a coil and that of the conformation considered
+! is a strand or
+! c) the conformational state of the conformation considered is a strand
+! and that of the reference conformation is a coil.
+! 10/28/02 - case (b) deleted.
+ if (isecstr(j).eq.isec_ref(j) .or. &
+! & isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
+ isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
+ nsec_match=nsec_match+1
+ enddo
+ enddo
+ return
+ end subroutine match_secondary
+!------------------------------------------------------------------------------
+! odlodc.f
+!------------------------------------------------------------------------------
+ subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
+
+ use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
+! isccont_frag_ref
+! implicit real*8 (a-h,o-z)
+ real(kind=8),dimension(3) :: r1,r2,a,b,x,y
+ real(kind=8) :: uu,vv,aa,bb,dd
+ real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
+!el odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
+!el + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
+! print *,"r1",(r1(i),i=1,3)
+! print *,"r2",(r2(i),i=1,3)
+! print *,"a",(a(i),i=1,3)
+! print *,"b",(b(i),i=1,3)
+ aa = a(1)**2+a(2)**2+a(3)**2
+ bb = b(1)**2+b(2)**2+b(3)**2
+ ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
+ ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
+ br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
+ det = aa*bb-ab**2
+! print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
+ uu = (-ar*bb+br*ab)/det
+ vv = (br*aa-ar*ab)/det
+! print *,u,v
+ uu=dmin1(uu,1.0d0)
+ uu=dmax1(uu,0.0d0)
+ vv=dmin1(vv,1.0d0)
+ vv=dmax1(vv,0.0d0)
+!el dd1 = odl(uu,vv)
+ dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
+!el dd2 = odl(0.0d0,0.0d0)
+ dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
+!el dd3 = odl(0.0d0,1.0d0)
+ dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
+!el dd4 = odl(1.0d0,0.0d0)
+ dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
+!el dd5 = odl(1.0d0,1.0d0)
+ dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
+ dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
+ if (dd.eq.dd2) then
+ uu=0.0d0
+ vv=0.0d0
+ else if (dd.eq.dd3) then
+ uu=0.0d0
+ vv=1.0d0
+ else if (dd.eq.dd4) then
+ uu=1.0d0
+ vv=0.0d0
+ else if (dd.eq.dd5) then
+ uu=1.0d0
+ vv=1.0d0
+ endif
+! Control check
+! do i=1,3
+! x(i)=r1(i)+u*a(i)
+! y(i)=r2(i)+v*b(i)
+! enddo
+! dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
+! dd1 = dsqrt(dd1)
+ aa = dsqrt(aa)
+ bb = dsqrt(bb)
+! write (8,*) uu,vv,dd,dd1
+! print *,dd,dd1
+ return
+ end subroutine odlodc
+!------------------------------------------------------------------------------
+ real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
+
+ real(kind=8),dimension(3) :: r1,r2
+ real(kind=8) :: aa,bb,u,v,ar,br,ab
+
+ odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
+ + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
+
+ end function odl
+!------------------------------------------------------------------------------
+! proc_cont.f
+!------------------------------------------------------------------------------
+ subroutine proc_cont
+
+ use geometry_data, only:rad2deg
+ use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
+! isccont_frag_ref
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.TIME1'
+! include 'COMMON.SBRIDGE'
+! include 'COMMON.CONTROL'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.HEADER'
+! include 'COMMON.CONTACTS1'
+! include 'COMMON.PEPTCONT'
+! include 'COMMON.GEO'
+ integer :: i,j,k,ind,len_cut,ndigit,length_frag
+
+ write (iout,*) "proc_cont: nlevel",nlevel
+ if (nlevel.lt.0) then
+ write (iout,*) "call define_fragments"
+ call define_fragments
+ else
+ write (iout,*) "call secondary2"
+ call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
+ isec_ref)
+ endif
+ write (iout,'(80(1h=))')
+ write (iout,*) "Electrostatic contacts"
+ call contacts_between_fragments(.true.,0,ncont_pept_ref,&
+ icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
+ write (iout,'(80(1h=))')
+ write (iout,*) "Side chain contacts"
+ call contacts_between_fragments(.true.,0,ncont_ref,&
+ icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
+ if (nlevel.lt.0) then
+ do i=1,nfrag(1)
+ ind=icant(i,i)
+ len_cut=1000
+ if (istruct(i).le.1) then
+ len_cut=max0(len_frag(i,1)*4/5,3)
+ else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
+ len_cut=max0(len_frag(i,1)*2/5,3)
+ endif
+ write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
+ ncont_frag_ref(ind)," len_cut",len_cut,&
+ " icont_single",icont_single," iloc_single",iloc_single
+ iloc(i)=iloc_single
+ if (iloc(i).gt.0) write (iout,*) &
+ "Local structure used to compare structure of fragment",i,&
+ " to native."
+ if (istruct(i).ne.3 .and. istruct(i).ne.0 &
+ .and. icont_single.gt.0 .and. &
+ ncont_frag_ref(ind).ge.len_cut) then
+ write (iout,*) "Electrostatic contacts used to compare",&
+ " structure of fragment",i," to native."
+ ielecont(i,1)=1
+ isccont(i,1)=0
+ else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
+ .ge.len_cut) then
+ write (iout,*) "Side chain contacts used to compare",&
+ " structure of fragment",i," to native."
+ isccont(i,1)=1
+ ielecont(i,1)=0
+ else
+ write (iout,*) "Contacts not used to compare",&
+ " structure of fragment",i," to native."
+ ielecont(i,1)=0
+ isccont(i,1)=0
+ nc_req_setf(i,1)=0
+ endif
+ if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
+ .and. ielecont(i,1).eq.0) then
+ write (iout,*) "RMSD used to compare",&
+ " structure of fragment",i," to native."
+ irms(i,1)=1
+ else
+ write (iout,*) "RMSD not used to compare",&
+ " structure of fragment",i," to native."
+ irms(i,1)=0
+ endif
+ enddo
+ endif
+ if (nlevel.lt.-1) then
+ call define_pairs
+ nlevel = -nlevel
+ if (nlevel.gt.3) nlevel=3
+ if (nlevel.eq.3) then
+ nfrag(3)=1
+ npiece(1,3)=nfrag(1)
+ do i=1,nfrag(1)
+ ipiece(i,1,3)=i
+ enddo
+ ielecont(1,3)=0
+ isccont(1,3)=0
+ irms(1,3)=1
+ n_shift(1,1,3)=0
+ n_shift(2,1,3)=0
+ endif
+ else if (nlevel.eq.-1) then
+ nlevel=1
+ endif
+ isnfrag(1)=0
+ do i=1,nlevel
+ isnfrag(i+1)=isnfrag(i)+nfrag(i)
+ enddo
+ ndigit=3*nfrag(1)
+ do i=2,nlevel
+ ndigit=ndigit+2*nfrag(i)
+ enddo
+ write (iout,*) "ndigit",ndigit
+ if (.not.binary .and. ndigit.gt.30) then
+ write (iout,*) "Highest class too large; switching to",&
+ " binary representation."
+ binary=.true.
+ endif
+ write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
+ write(iout,*) "rmscut_base_up",rmscut_base_up,&
+ " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
+ do i=1,nlevel
+ do j=1,nfrag(i)
+ length_frag = 0
+ if (i.eq.1) then
+ do k=1,npiece(j,i)
+ length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
+ enddo
+ else
+ do k=1,npiece(j,i)
+ length_frag=length_frag+len_frag(ipiece(k,j,i),1)
+ enddo
+ endif
+ len_frag(j,i)=length_frag
+ rmscutfrag(1,j,i)=rmscut_base_up*length_frag
+ rmscutfrag(2,j,i)=rmscut_base_low*length_frag
+ if (rmscutfrag(1,j,i).lt.rmsup_lim) &
+ rmscutfrag(1,j,i)=rmsup_lim
+ if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
+ rmscutfrag(1,j,i)=rmsupup_lim
+ enddo
+ enddo
+ write (iout,*) "Level",1," number of fragments:",nfrag(1)
+ do j=1,nfrag(1)
+ write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
+ k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
+ rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
+ ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
+ nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
+ enddo
+ do i=2,nlevel
+ write (iout,*) "Level",i," number of fragments:",nfrag(i)
+ do j=1,nfrag(i)
+ write (iout,*) npiece(j,i),(ipiece(k,j,i),&
+ k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
+ rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
+ nc_fragm(j,i),nc_req_setf(j,i)
+ enddo
+ enddo
+ return
+ end subroutine proc_cont
+!------------------------------------------------------------------------------
+! define_pairs.f
+!------------------------------------------------------------------------------
+ subroutine define_pairs
+
+! use energy_data, only:nsccont_frag_ref
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.TIME1'
+! include 'COMMON.SBRIDGE'
+! include 'COMMON.CONTROL'
+! include 'COMMON.COMPAR'
+! include 'COMMON.FRAG'
+! include 'COMMON.CHAIN'
+! include 'COMMON.HEADER'
+! include 'COMMON.GEO'
+! include 'COMMON.CONTACTS1'
+! include 'COMMON.PEPTCONT'
+ integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
+
+ do j=1,nfrag(1)
+ length_frag = 0
+ do k=1,npiece(j,1)
+ length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
+ enddo
+ len_frag(j,1)=length_frag
+ write (iout,*) "Fragment",j," length",len_frag(j,1)
+ enddo
+ nfrag(2)=0
+ do i=1,nfrag(1)
+ do j=i+1,nfrag(1)
+ ind = icant(i,j)
+ if (istruct(i).le.1 .or. istruct(j).le.1) then
+ if (istruct(i).le.1) then
+ ll1=len_frag(i,1)
+ else
+ ll1=len_frag(i,1)/2
+ endif
+ if (istruct(j).le.1) then
+ ll2=len_frag(j,1)
+ else
+ ll2=len_frag(j,1)/2
+ endif
+ len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
+ else
+ if (istruct(i).eq.2 .or. istruct(i).eq.4) then
+ ll1=len_frag(i,1)/2
+ else
+ ll1=len_frag(i,1)
+ endif
+ if (istruct(j).eq.2 .or. istruct(j).eq.4) then
+ ll2=len_frag(j,1)/2
+ else
+ ll2=len_frag(j,1)
+ endif
+ len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
+ endif
+ write (iout,*) "Fragments",i,j," structure",istruct(i),&
+ istruct(j)," # contacts",&
+ ncont_frag_ref(ind),nsccont_frag_ref(ind),&
+ " lengths",len_frag(i,1),len_frag(j,1),&
+ " ll1",ll1," ll2",ll2," len_cut",len_cut
+ if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
+ nsccont_frag_ref(ind).ge.len_cut ) then
+ if (istruct(i).eq.1 .and. istruct(j).eq.1) then
+ write (iout,*) "Adding pair of helices",i,j,&
+ " based on SC contacts"
+ else
+ write (iout,*) "Adding helix+strand/sheet pair",i,j,&
+ " based on SC contacts"
+ endif
+ nfrag(2)=nfrag(2)+1
+ if (icont_pair.gt.0) then
+ write (iout,*) "# SC contacts will be used",&
+ " in comparison."
+ isccont(nfrag(2),2)=1
+ endif
+ if (irms_pair.gt.0) then
+ write (iout,*) "Fragment RMSD will be used",&
+ " in comparison."
+ irms(nfrag(2),2)=1
+ endif
+ npiece(nfrag(2),2)=2
+ ipiece(1,nfrag(2),2)=i
+ ipiece(2,nfrag(2),2)=j
+ ielecont(nfrag(2),2)=0
+ n_shift(1,nfrag(2),2)=nshift_pair
+ n_shift(2,nfrag(2),2)=nshift_pair
+ nc_fragm(nfrag(2),2)=ncfrac_pair
+ nc_req_setf(nfrag(2),2)=ncreq_pair
+ else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
+ .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
+ .and. ncont_frag_ref(ind).ge.len_cut ) then
+ nfrag(2)=nfrag(2)+1
+ write (iout,*) "Adding pair strands/sheets",i,j,&
+ " based on pp contacts"
+ if (icont_pair.gt.0) then
+ write (iout,*) "# pp contacts will be used",&
+ " in comparison."
+ ielecont(nfrag(2),2)=1
+ endif
+ if (irms_pair.gt.0) then
+ write (iout,*) "Fragment RMSD will be used",&
+ " in comparison."
+ irms(nfrag(2),2)=1
+ endif
+ npiece(nfrag(2),2)=2
+ ipiece(1,nfrag(2),2)=i
+ ipiece(2,nfrag(2),2)=j
+ ielecont(nfrag(2),2)=1
+ isccont(nfrag(2),2)=0
+ n_shift(1,nfrag(2),2)=nshift_pair
+ n_shift(2,nfrag(2),2)=nshift_pair
+ nc_fragm(nfrag(2),2)=ncfrac_bet
+ nc_req_setf(nfrag(2),2)=ncreq_bet
+ endif
+ enddo
+ enddo
+ write (iout,*) "Pairs found"
+ do i=1,nfrag(2)
+ write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
+ enddo
+ return
+ end subroutine define_pairs
+!------------------------------------------------------------------------------
+! icant.f
+!------------------------------------------------------------------------------
+ INTEGER FUNCTION ICANT(I,J)
+ integer :: i,j
+ IF (I.GE.J) THEN
+ ICANT=(I*(I-1))/2+J
+ ELSE
+ ICANT=(J*(J-1))/2+I
+ ENDIF
+ RETURN
+ END FUNCTION ICANT
+!------------------------------------------------------------------------------
+! mysort.f
+!------------------------------------------------------------------------------
+ subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
+! implicit none
+ integer :: n,m,mm
+ integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
+ real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
+ real(kind=8) :: xxtemp
+ integer :: i,j,k,imax
+ do i=1,n
+ xmin=x(1,1,i)
+ imax=i
+ do j=i+1,n
+ if (x(1,1,j).lt.xmin) then
+ imax=j
+ xmin=x(1,1,j)
+ endif
+ enddo
+ xxtemp=z2(imax)
+ z2(imax)=z2(i)
+ z2(i)=xxtemp
+ xxtemp=z3(imax)
+ z3(imax)=z3(i)
+ z3(i)=xxtemp
+ xxtemp=z4(imax)
+ z4(imax)=z4(i)
+ z4(i)=xxtemp
+ xxtemp=z5(imax)
+ z5(imax)=z5(i)
+ z5(i)=xxtemp
+ xtemp=y(imax)
+ y(imax)=y(i)
+ y(i)=xtemp
+ xtemp=z(imax)
+ z(imax)=z(i)
+ z(i)=xtemp
+ xtemp=z6(imax)
+ z6(imax)=z6(i)
+ z6(i)=xtemp
+ do j=1,2
+ xtemp=z1(j,imax)
+ z1(j,imax)=z1(j,i)
+ z1(j,i)=xtemp
+ enddo
+ do j=1,m
+ do k=1,mm
+ xtemp=x(j,k,imax)
+ x(j,k,imax)=x(j,k,i)
+ x(j,k,i)=xtemp
+ enddo
+ enddo
+ enddo
+ return
+ end subroutine imysort
+!------------------------------------------------------------------------------
+! qwolynes.f
+!-------------------------------------------------------------------------------
+ real(kind=8) function qwolynes(ilevel,jfrag)
+
+ use geometry_data, only:cref,nperm
+ use control_data, only:symetr
+ use energy_data, only:nnt,nct,itype
+! implicit none
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.CONTROL'
+ integer :: ilevel,jfrag,kkk
+ integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
+ integer :: nsep=3
+ real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
+ real(kind=8) :: maxiQ !dist,
+ real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
+ logical :: lprn=.false.
+ real(kind=8) :: x !el sigm
+!el sigm(x)=0.25d0*x
+ nperm=1
+ maxiQ=0
+ do i=1,symetr
+ nperm=i*nperm
+ enddo
+! write (iout,*) "QWolyes: " jfrag",jfrag,
+! & " ilevel",ilevel
+ allocate(tempus(nperm))
+ do kkk=1,nperm
+ qq = 0.0d0
+ if (ilevel.eq.0) then
+ if (lprn) write (iout,*) "Q computed for whole molecule"
+ nl=0
+ do il=nnt+nsep,nct
+ do jl=nnt,il-nsep
+ dij=0.0d0
+ dijCM=0.0d0
+ d0ij=0.0d0
+ d0ijCM=0.0d0
+ qqij=0.0d0
+ qqijCM=0.0d0
+ nl=nl+1
+ d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
+ (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
+ (cref(3,jl,kkk)-cref(3,il,kkk))**2)
+ dij=dist(il,jl)
+ qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+ if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ nl=nl+1
+ d0ijCM=dsqrt( &
+ (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
+ (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
+ (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
+ dijCM=dist(il+nres,jl+nres)
+ qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
+ endif
+ qq = qq+qqij+qqijCM
+ if (lprn) then
+ write (iout,*) "il",il," jl",jl,&
+ " itype",itype(il),itype(jl)
+ write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
+ " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
+ endif
+ enddo
+ enddo
+ qq = qq/nl
+ if (lprn) write (iout,*) "nl",nl," qq",qq
+ else if (ilevel.eq.1) then
+ if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
+ nl=0
+! write (iout,*) "nlist_frag",nlist_frag(jfrag)
+ do i=2,nlist_frag(jfrag)
+ do j=1,i-1
+ il=list_frag(i,jfrag)
+ jl=list_frag(j,jfrag)
+ if (iabs(il-jl).gt.nsep) then
+ dij=0.0d0
+ dijCM=0.0d0
+ d0ij=0.0d0
+ d0ijCM=0.0d0
+ qqij=0.0d0
+ qqijCM=0.0d0
+ nl=nl+1
+ d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
+ (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
+ (cref(3,jl,kkk)-cref(3,il,kkk))**2)
+ dij=dist(il,jl)
+ qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+ if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ nl=nl+1
+ d0ijCM=dsqrt( &
+ (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
+ (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
+ (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
+ dijCM=dist(il+nres,jl+nres)
+ qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
+ endif
+ qq = qq+qqij+qqijCM
+ if (lprn) then
+ write (iout,*) "i",i," j",j," il",il," jl",jl,&
+ " itype",itype(il),itype(jl)
+ write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
+ " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
+ endif
+ endif
+ enddo
+ enddo
+ qq = qq/nl
+ if (lprn) write (iout,*) "nl",nl," qq",qq
+ else if (ilevel.eq.2) then
+ np=npiece(jfrag,ilevel)
+ nl=0
+ do i=2,np
+ ip=ipiece(i,jfrag,ilevel)
+ do j=1,nlist_frag(ip)
+ il=list_frag(j,ip)
+ do k=1,i-1
+ kp=ipiece(k,jfrag,ilevel)
+ do l=1,nlist_frag(kp)
+ kl=list_frag(l,kp)
+ if (iabs(kl-il).gt.nsep) then
+ nl=nl+1
+ dij=0.0d0
+ dijCM=0.0d0
+ d0ij=0.0d0
+ d0ijCM=0.0d0
+ qqij=0.0d0
+ qqijCM=0.0d0
+ d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
+ (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
+ (cref(3,kl,kkk)-cref(3,il,kkk))**2)
+ dij=dist(il,kl)
+ qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+ if (itype(il).ne.10 .or. itype(kl).ne.10) then
+ nl=nl+1
+ d0ijCM=dsqrt( &
+ (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
+ (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
+ (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
+ dijCM=dist(il+nres,kl+nres)
+ qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
+ (sigm(d0ijCM)))**2)
+ endif
+ qq = qq+qqij+qqijCM
+ if (lprn) then
+ write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
+ " kl",kl," itype",itype(il),itype(kl)
+ write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
+ d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
+ endif
+ endif
+ enddo ! l
+ enddo ! k
+ enddo ! j
+ enddo ! i
+ qq = qq/nl
+ if (lprn) write (iout,*) "nl",nl," qq",qq
+ else
+ write (iout,*)"Error: Q can be computed only for level 1 and 2."
+ endif
+ tempus(kkk)=qq
+ enddo
+ do kkk=1,nperm
+ if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
+ enddo
+ qwolynes=1.0d0-maxiQ
+ deallocate(tempus)
+ return
+ end function qwolynes
+!-------------------------------------------------------------------------------
+ real(kind=8) function sigm(x)
+ real(kind=8) :: x
+ sigm=0.25d0*x
+ return
+ end function sigm
+!-------------------------------------------------------------------------------
+ subroutine fragment_list
+! implicit none
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.COMPAR'
+ logical :: lprn=.true.
+ integer :: i,ilevel,j,k,jfrag
+ do jfrag=1,nfrag(1)
+ nlist_frag(jfrag)=0
+ do i=1,npiece(jfrag,1)
+ if (lprn) write (iout,*) "jfrag=",jfrag,&
+ "i=",i," fragment",ifrag(1,i,jfrag),&
+ ifrag(2,i,jfrag)
+ do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ do k=1,nlist_frag(jfrag)
+ if (list_frag(k,jfrag).eq.j) goto 10
+ enddo
+ nlist_frag(jfrag)=nlist_frag(jfrag)+1
+ list_frag(nlist_frag(jfrag),jfrag)=j
+ enddo
+ 10 continue
+ enddo
+ enddo
+ write (iout,*) "Fragment list"
+ do j=1,nfrag(1)
+ write (iout,*)"Fragment",j," list",(list_frag(k,j),&
+ k=1,nlist_frag(j))
+ enddo
+ return
+ end subroutine fragment_list
+!-------------------------------------------------------------------------------
+ real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
+
+ use w_comm_local
+ use control_data, only:symetr
+ use geometry_data, only:nperm
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.VAR'
+! include 'COMMON.CONTROL'
+ real(kind=8) :: przes(3),obrot(3,3)
+!el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
+!el logical :: iadded(nres)
+!el integer :: inumber(2,nres)
+!el common /ccc/ creff,cc,iadded,inumber
+ logical :: lprn
+ logical :: non_conv
+ integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
+ real(kind=8) :: rminrms,rms
+ if (lprn) then
+ write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
+ write (iout,*) "npiece",npiece(j,i)
+ call flush(iout)
+ endif
+! write (iout,*) "symetr",symetr
+! call flush(iout)
+ nperm=1
+ do idup=1,symetr
+ nperm=nperm*idup
+ enddo
+! write (iout,*) "nperm",nperm
+! call flush(iout)
+ do kkk=1,nperm
+ idup=0
+ do l=1,nres
+ iadded(l)=.false.
+ enddo
+! write (iout,*) "kkk",kkk
+! call flush(iout)
+ do k=1,npiece(j,i)
+ if (i.eq.1) then
+ if (lprn) then
+ write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
+ ifrag(1,k,j),ifrag(2,k,j)
+ call flush(iout)
+ endif
+ call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
+! write (iout,*) "Exit cprep"
+! call flush(iout)
+! write (iout,*) "ii=",ii
+ else
+ kk = ipiece(k,j,i)
+! write (iout,*) "kk",kk," npiece",npiece(kk,1)
+ do l=1,npiece(kk,1)
+ if (lprn) then
+ write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
+ " l=",l," adding fragment",&
+ ifrag(1,l,kk),ifrag(2,l,kk)
+ call flush(iout)
+ endif
+ call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
+! write (iout,*) "After cprep"
+! call flush(iout)
+ enddo
+ endif
+ enddo
+ enddo
+ if (lprn) then
+ write (iout,*) "tuszukaj"
+ do kkk=1,nperm
+ do k=1,idup
+ write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
+ inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
+ enddo
+ enddo
+ call flush(iout)
+ endif
+ rminrms=1.0d10
+ do kkk=1,nperm
+ call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
+ if (non_conv) then
+ print *,'Error: FITSQ non-convergent, jcon',jcon,i
+ rms = 1.0d10
+ else if (rms.lt.-1.0d-6) then
+ print *,'Error: rms^2 = ',rms,jcon,i
+ rms = 1.0d10
+ else if (rms.ge.1.0d-6 .and. rms.lt.0) then
+ rms = 0.0d0
+ endif
+! write (iout,*) "rmsmin", rminrms, "rms", rms
+ if (rms.le.rminrms) rminrms=rms
+ enddo
+ rmscalc = dsqrt(rminrms)
+! write (iout, *) "analysys", rmscalc,anatemp
+ return
+ end function rmscalc
+!-------------------------------------------------------------------------
+ subroutine cprep(if1,if2,ishif,idup,kwa)
+
+ use w_comm_local
+ use control_data, only:symetr
+ use geometry_data, only:nperm,cref,c
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.CONTROL'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.VAR'
+ real(kind=8) :: przes(3),obrot(3,3)
+!el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
+!el logical :: iadded(nres)
+!el integer :: inumber(2,nres)
+ integer :: iistrart,kwa,blar
+!el common /ccc/ creff,cc,iadded,inumber
+ integer :: if1,if2,ishif,idup,kkk,l,m
+! write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
+ nperm=1
+ do blar=1,symetr
+ nperm=nperm*blar
+ enddo
+! write (iout,*) "nperm",nperm
+ kkk=kwa
+! ii=0
+ do l=if1,if2
+! write (iout,*) "l",l," iadded",iadded(l)
+! call flush(iout)
+ if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
+ then
+ idup=idup+1
+ iadded(l)=.true.
+ inumber(1,idup)=l
+ inumber(2,idup)=l+ishif
+ do m=1,3
+ creff(m,idup)=cref(m,l,kkk)
+ cc(m,idup)=c(m,l+ishif)
+ enddo
+ endif
+ enddo
+ return
+ end subroutine cprep
+!-------------------------------------------------------------------------
+ real(kind=8) function rmsnat(jcon)
+
+ use control_data, only:symetr
+ use geometry_data, only:nperm,cref,c
+ use energy_data, only:itype
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.VAR'
+! include 'COMMON.CONTROL'
+ real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
+ logical :: non_conv
+ integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
+ real(kind=8) :: rminrms,rmsminsing,rms
+ rminrms=10.0d10
+ rmsminsing=10d10
+ nperm=1
+ do i=1,symetr
+ nperm=nperm*i
+ enddo
+ do kkk=1,nperm
+ nnsup=0
+ do i=1,nres
+ if (itype(i).ne.ntyp1) then
+ nnsup=nnsup+1
+ do j=1,3
+ cc(j,nnsup)=c(j,i)
+ ccref(j,nnsup)=cref(j,i,kkk)
+ enddo
+ endif
+ enddo
+ call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
+ if (non_conv) then
+ print *,'Error: FITSQ non-convergent, jcon',jcon,i
+ rms=1.0d10
+ else if (rms.lt.-1.0d-6) then
+ print *,'Error: rms^2 = ',rms,jcon,i
+ rms = 1.0d10
+ else if (rms.ge.1.0d-6 .and. rms.lt.0) then
+ rms=0.0d0
+ endif
+ if (rms.le.rminrms) rminrms=rms
+! write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
+ enddo
+ rmsnat = dsqrt(rminrms)
+! write (iout,*) "analysys",rmsnat, anatemp
+! liczenie rmsdla pojedynczego lancucha
+ return
+ end function rmsnat
+!-------------------------------------------------------------------------------
+ subroutine define_fragments
+
+ use geometry_data, only:rad2deg
+ use energy_data, only:itype
+ use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.TIME1'
+! include 'COMMON.FRAG'
+! include 'COMMON.SBRIDGE'
+! include 'COMMON.CONTROL'
+! include 'COMMON.COMPAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.HEADER'
+! include 'COMMON.GEO'
+! include 'COMMON.CONTACTS'
+! include 'COMMON.PEPTCONT'
+! include 'COMMON.INTERACT'
+! include 'COMMON.NAMES'
+ integer :: nstrand,istrand(2,nres/2)
+ integer :: nhairp,ihairp(2,nres/5)
+ character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
+ 'strand','strand pair'/),shape(strstr))
+ integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
+
+ write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
+ 'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
+ 'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
+ ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
+ write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
+ ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
+ write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
+ ' MAXANG_HEL',angcut1_hel*rad2deg
+ write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
+ ' MAXANG_BET',angcut1_bet*rad2deg
+ write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
+ ' MAXANG_STRAND',angcut1_strand*rad2deg
+ write (iout,*) 'FRAC_MIN',frac_min_set
+! Find secondary structure elements (helices and beta-sheets)
+ call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
+ isec_ref)
+! Define primary fragments. First include the helices.
+ nhairp=0
+ nstrand=0
+! Merge helices
+! AL 12/23/03 - to avoid splitting helices into very small fragments
+ if (merge_helices) then
+ write (iout,*) "Before merging helices: nhfrag",nhfrag
+ do i=1,nhfrag
+ write (2,*) hfrag(1,i),hfrag(2,i)
+ enddo
+ i=1
+ do while (i.lt.nhfrag)
+ if (hfrag(1,i+1)-hfrag(2,i).le.1) then
+ nhfrag=nhfrag-1
+ hfrag(2,i)=hfrag(2,i+1)
+ do j=i+1,nhfrag
+ hfrag(1,j)=hfrag(1,j+1)
+ hfrag(2,j)=hfrag(2,j+1)
+ enddo
+ endif
+ i=i+1
+ enddo
+ write (iout,*) "After merging helices: nhfrag",nhfrag
+ do i=1,nhfrag
+ write (2,*) hfrag(1,i),hfrag(2,i)
+ enddo
+ endif
+ nfrag(1)=nhfrag
+ do i=1,nhfrag
+ npiece(i,1)=1
+ ifrag(1,1,i)=hfrag(1,i)
+ ifrag(2,1,i)=hfrag(2,i)
+ n_shift(1,i,1)=0
+ n_shift(2,i,1)=nshift_hel
+ ang_cut(i)=angcut_hel
+ ang_cut1(i)=angcut1_hel
+ frac_min(i)=frac_min_set
+ nc_fragm(i,1)=ncfrac_hel
+ nc_req_setf(i,1)=ncreq_hel
+ istruct(i)=1
+ enddo
+ write (iout,*) "isplit_bet",isplit_bet
+ if (isplit_bet.gt.1) then
+! Split beta-sheets into strands and store strands as primary fragments.
+ call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
+ do i=1,nstrand
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=istrand(1,i)
+ ifrag(2,1,ii)=istrand(2,i)
+ n_shift(1,ii,1)=nshift_strand
+ n_shift(2,ii,1)=nshift_strand
+ ang_cut(ii)=angcut_strand
+ ang_cut1(ii)=angcut1_strand
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=0
+ nc_req_setf(ii,1)=0
+ istruct(ii)=3
+ enddo
+ nfrag(1)=nfrag(1)+nstrand
+ else if (isplit_bet.eq.1) then
+! Split only far beta-sheets; does not split hairpins.
+ call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
+ call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
+ do i=1,nhairp
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=ihairp(1,i)
+ ifrag(2,1,ii)=ihairp(2,i)
+ n_shift(1,ii,1)=nshift_bet
+ n_shift(2,ii,1)=nshift_bet
+ ang_cut(ii)=angcut_bet
+ ang_cut1(ii)=angcut1_bet
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=ncfrac_bet
+ nc_req_setf(ii,1)=ncreq_bet
+ istruct(ii)=2
+ enddo
+ nfrag(1)=nfrag(1)+nhairp
+ do i=1,nstrand
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=istrand(1,i)
+ ifrag(2,1,ii)=istrand(2,i)
+ n_shift(1,ii,1)=nshift_strand
+ n_shift(2,ii,1)=nshift_strand
+ ang_cut(ii)=angcut_strand
+ ang_cut1(ii)=angcut1_strand
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=0
+ nc_req_setf(ii,1)=0
+ istruct(ii)=3
+ enddo
+ nfrag(1)=nfrag(1)+nstrand
+ else
+! Do not split beta-sheets; each pair of strands is a primary element.
+ call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
+ do i=1,nhairp
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=ihairp(1,i)
+ ifrag(2,1,ii)=ihairp(2,i)
+ n_shift(1,ii,1)=nshift_bet
+ n_shift(2,ii,1)=nshift_bet
+ ang_cut(ii)=angcut_bet
+ ang_cut1(ii)=angcut1_bet
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=ncfrac_bet
+ nc_req_setf(ii,1)=ncreq_bet
+ istruct(ii)=2
+ enddo
+ nfrag(1)=nfrag(1)+nhairp
+ do i=1,nbfrag
+ ii=i+nfrag(1)
+ npiece(ii,1)=2
+ ifrag(1,1,ii)=bfrag(1,i)
+ ifrag(2,1,ii)=bfrag(2,i)
+ if (bfrag(3,i).lt.bfrag(4,i)) then
+ ifrag(1,2,ii)=bfrag(3,i)
+ ifrag(2,2,ii)=bfrag(4,i)
+ else
+ ifrag(1,2,ii)=bfrag(4,i)
+ ifrag(2,2,ii)=bfrag(3,i)
+ endif
+ n_shift(1,ii,1)=nshift_bet
+ n_shift(2,ii,1)=nshift_bet
+ ang_cut(ii)=angcut_bet
+ ang_cut1(ii)=angcut1_bet
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=ncfrac_bet
+ nc_req_setf(ii,1)=ncreq_bet
+ istruct(ii)=4
+ enddo
+ nfrag(1)=nfrag(1)+nbfrag
+ endif
+ write (iout,*) "The following primary fragments were found:"
+ write (iout,*) "Helices:",nhfrag
+ do i=1,nhfrag
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ write (iout,*) "Hairpins:",nhairp
+ do i=nhfrag+1,nhfrag+nhairp
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ write (iout,*) "Far strand pairs:",nbfrag
+ do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ i3=ifrag(1,2,i)
+ i4=ifrag(2,2,i)
+ it3=itype(i3)
+ it4=itype(i4)
+ write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
+ i,restyp(it1),i1,restyp(it2),i2,&
+ restyp(it3),i3,restyp(it4),i4
+ enddo
+ write (iout,*) "Strands:",nstrand
+ do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
+ istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
+ nc_fragm(1,1),nc_req_setf(1,1))
+ write (iout,*) "Fragments after sorting:"
+ do i=1,nfrag(1)
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
+ i,restyp(it1),i1,restyp(it2),i2
+ if (npiece(i,1).eq.1) then
+ write (iout,'(2x,a)') strstr(istruct(i))
+ else
+ i1=ifrag(1,2,i)
+ i2=ifrag(2,2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
+ restyp(it1),i1,restyp(it2),i2,strstr(istruct(i))
+ endif
+ enddo
+ return
+ end subroutine define_fragments
+!------------------------------------------------------------------------------
+ subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+ integer :: nbfrag,bfrag(4,nres/3)
+ integer :: nhairp,ihairp(2,nres/5)
+ integer :: i,j,k
+ write (iout,*) "Entered find_and_remove_hairpins"
+ write (iout,*) "nbfrag",nbfrag
+ do i=1,nbfrag
+ write (iout,*) i,(bfrag(k,i),k=1,4)
+ enddo
+ nhairp=0
+ i=1
+ do while (i.le.nbfrag)
+ write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
+ if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
+ then
+ write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
+ nhairp=nhairp+1
+ ihairp(1,nhairp)=bfrag(1,i)
+ ihairp(2,nhairp)=bfrag(3,i)
+ nbfrag=nbfrag-1
+ do j=i,nbfrag
+ do k=1,4
+ bfrag(k,j)=bfrag(k,j+1)
+ enddo
+ enddo
+ else
+ i=i+1
+ endif
+ enddo
+ write (iout,*) "After finding hairpins:"
+ write (iout,*) "nhairp",nhairp
+ do i=1,nhairp
+ write (iout,*) i,ihairp(1,i),ihairp(2,i)
+ enddo
+ write (iout,*) "nbfrag",nbfrag
+ do i=1,nbfrag
+ write (iout,*) i,(bfrag(k,i),k=1,4)
+ enddo
+ return
+ end subroutine find_and_remove_hairpins
+!------------------------------------------------------------------------------
+ subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+ integer :: nbfrag,bfrag(4,nres/3)
+ integer :: nstrand,istrand(2,nres/2)
+ integer :: nhairp,ihairp(2,nres/5)
+ logical :: found
+ integer :: i,k
+ write (iout,*) "Entered split_beta"
+ write (iout,*) "nbfrag",nbfrag
+ do i=1,nbfrag
+ write (iout,*) i,(bfrag(k,i),k=1,4)
+ enddo
+ nstrand=0
+ do i=1,nbfrag
+ write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
+ call add_strand(nstrand,istrand,nhairp,ihairp,&
+ bfrag(1,i),bfrag(2,i),found)
+ if (bfrag(3,i).lt.bfrag(4,i)) then
+ write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
+ call add_strand(nstrand,istrand,nhairp,ihairp,&
+ bfrag(3,i),bfrag(4,i),found)
+ else
+ write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
+ call add_strand(nstrand,istrand,nhairp,ihairp,&
+ bfrag(4,i),bfrag(3,i),found)
+ endif
+ enddo
+ nbfrag=0
+ write (iout,*) "Strands found:",nstrand
+ do i=1,nstrand
+ write (iout,*) i,istrand(1,i),istrand(2,i)
+ enddo
+ return
+ end subroutine split_beta
+!------------------------------------------------------------------------------
+ subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'DIMENSIONS.COMPAR'
+! include 'COMMON.IOUNITS'
+ integer :: nstrand,istrand(2,nres/2)
+ integer :: nhairp,ihairp(2,nres/5)
+ logical :: found
+ integer :: is1,is2,j,idelt
+ found=.false.
+ do j=1,nhairp
+ idelt=(ihairp(2,j)-ihairp(1,j))/6
+ if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
+ write (iout,*) "strand",is1,is2," is part of hairpin",&
+ ihairp(1,j),ihairp(2,j)
+ return
+ endif
+ enddo
+ do j=1,nstrand
+ idelt=(istrand(2,j)-istrand(1,j))/3
+ if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
+ then
+! The strand already exists in the array; update its ends if necessary.
+ write (iout,*) "strand",is1,is2," found at position",j,&
+ ":",istrand(1,j),istrand(2,j)
+ istrand(1,j)=min0(istrand(1,j),is1)
+ istrand(2,j)=max0(istrand(2,j),is2)
+ return
+ endif
+ enddo
+! The strand has not been found; add it to the array.
+ write (iout,*) "strand",is1,is2," added to the array."
+ found=.true.
+ nstrand=nstrand+1
+ istrand(1,nstrand)=is1
+ istrand(2,nstrand)=is2
+ return
+ end subroutine add_strand
+!------------------------------------------------------------------------------
+ subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
+
+ use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
+ use energy_data, only:itype,maxcont
+ use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
+ use compare, only:freeres
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'DIMENSIONS.ZSCOPT'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.FRAG'
+! include 'COMMON.VAR'
+! include 'COMMON.GEO'
+! include 'COMMON.CHAIN'
+! include 'COMMON.NAMES'
+! include 'COMMON.INTERACT'
+ integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres),&
+ isecstr(nres)
+ logical :: lprint,lprint_sec,not_done !el,freeres
+ integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
+ integer :: nstrand,nbeta,nhelix,iii1,jjj1
+ real(kind=8) :: p1,p2
+!rel external freeres
+ character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
+ if (lprint) then
+ write (iout,*) "entered secondary2",ncont
+ write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
+ do i=1,ncont
+ write (iout,*) icont(1,i),icont(2,i)
+ enddo
+ endif
+ do i=1,nres
+ isecstr(i)=0
+ enddo
+ nbfrag=0
+ nhfrag=0
+ do i=1,nres
+ isec(i,1)=0
+ isec(i,2)=0
+ nsec(i)=0
+ enddo
+
+! finding parallel beta
+!d write (iout,*) '------- looking for parallel beta -----------'
+ nbeta=0
+ nstrand=0
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ if (i1.ge.nstart_sup .and. i1.le.nend_sup &
+ .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
+!d write (iout,*) "parallel",i1,j1
+ if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
+ ii1=i1
+ jj1=j1
+!d write (iout,*) i1,j1
+ not_done=.true.
+ do while (not_done)
+ i1=i1+1
+ j1=j1+1
+ do j=1,ncont
+ if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
+ freeres(i1,j1,nsec,isec)) goto 5
+ enddo
+ not_done=.false.
+ 5 continue
+!d write (iout,*) i1,j1,not_done
+ enddo
+ j1=j1-1
+ i1=i1-1
+ if (i1-ii1.gt.1) then
+ ii1=max0(ii1-1,1)
+ jj1=max0(jj1-1,1)
+ nbeta=nbeta+1
+ if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
+ nbeta,ii1,i1,jj1,j1
+
+ nbfrag=nbfrag+1
+ bfrag(1,nbfrag)=ii1+1
+ bfrag(2,nbfrag)=i1+1
+ bfrag(3,nbfrag)=jj1+1
+ bfrag(4,nbfrag)=min0(j1+1,nres)
+
+ do ij=ii1,i1
+ nsec(ij)=nsec(ij)+1
+ isec(ij,nsec(ij))=nbeta
+ enddo
+ do ij=jj1,j1
+ nsec(ij)=nsec(ij)+1
+ isec(ij,nsec(ij))=nbeta
+ enddo
+
+ if(lprint_sec) then
+ nstrand=nstrand+1
+ if (nbeta.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",ii1-1,"..",i1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",ii1-1,"..",i1-1,"'"
+ endif
+ nstrand=nstrand+1
+ if (nbeta.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",jj1-1,"..",j1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",jj1-1,"..",j1-1,"'"
+ endif
+ write(12,'(a8,4i4)') &
+ "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
+ endif
+ endif
+ endif
+ endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
+ enddo
+
+! finding antiparallel beta
+!d write (iout,*) '--------- looking for antiparallel beta ---------'
+
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ if (freeres(i1,j1,nsec,isec)) then
+ ii1=i1
+ jj1=j1
+!d write (iout,*) i1,j1
+
+ not_done=.true.
+ do while (not_done)
+ i1=i1+1
+ j1=j1-1
+ do j=1,ncont
+ if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
+ freeres(i1,j1,nsec,isec)) goto 6
+ enddo
+ not_done=.false.
+ 6 continue
+!d write (iout,*) i1,j1,not_done
+ enddo
+ i1=i1-1
+ j1=j1+1
+ if (i1-ii1.gt.1) then
+
+ nbfrag=nbfrag+1
+ bfrag(1,nbfrag)=ii1
+ bfrag(2,nbfrag)=min0(i1+1,nres)
+ bfrag(3,nbfrag)=min0(jj1+1,nres)
+ bfrag(4,nbfrag)=j1
+
+ nbeta=nbeta+1
+ iii1=max0(ii1-1,1)
+ do ij=iii1,i1
+ nsec(ij)=nsec(ij)+1
+ if (nsec(ij).le.2) then
+ isec(ij,nsec(ij))=nbeta
+ endif
+ enddo
+ jjj1=max0(j1-1,1)
+ do ij=jjj1,jj1
+ nsec(ij)=nsec(ij)+1
+ if (nsec(ij).le.2) then
+ isec(ij,nsec(ij))=nbeta
+ endif
+ enddo
+
+
+ if (lprint_sec) then
+ write (iout,'(a,i3,4i4)')'antiparallel beta',&
+ nbeta,ii1-1,i1,jj1,j1-1
+ nstrand=nstrand+1
+ if (nstrand.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",ii1-2,"..",i1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",ii1-2,"..",i1-1,"'"
+ endif
+ nstrand=nstrand+1
+ if (nstrand.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",j1-2,"..",jj1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'strand",nstrand,&
+ "' 'num = ",j1-2,"..",jj1-1,"'"
+ endif
+ write(12,'(a8,4i4)') &
+ "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
+ endif
+ endif
+ endif
+ enddo
+
+!d write (iout,*) "After beta:",nbfrag
+!d do i=1,nbfrag
+!d write (iout,*) (bfrag(j,i),j=1,4)
+!d enddo
+
+ if (nstrand.gt.0.and.lprint_sec) then
+ write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
+ do i=2,nstrand
+ if (i.le.9) then
+ write(12,'(a9,i1,$)') " | strand",i
+ else
+ write(12,'(a9,i2,$)') " | strand",i
+ endif
+ enddo
+ write(12,'(a1)') "'"
+ endif
+
+
+! finding alpha or 310 helix
+
+ nhelix=0
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ p1=phi(i1+2)*rad2deg
+ p2=0.0
+ if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
+
+
+ if (j1.eq.i1+3 .and. &
+ ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
+ ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
+!d if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
+!o if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
+ ii1=i1
+ jj1=j1
+ if (nsec(ii1).eq.0) then
+ not_done=.true.
+ else
+ not_done=.false.
+ endif
+ do while (not_done)
+ i1=i1+1
+ j1=j1+1
+ do j=1,ncont
+ if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
+ enddo
+ not_done=.false.
+ 10 continue
+ p1=phi(i1+2)*rad2deg
+ p2=phi(j1+2)*rad2deg
+ if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
+ not_done=.false.
+
+!d write (iout,*) i1,j1,not_done,p1,p2
+ enddo
+ j1=j1+1
+ if (j1-ii1.gt.4) then
+ nhelix=nhelix+1
+!d write (iout,*)'helix',nhelix,ii1,j1
+
+ nhfrag=nhfrag+1
+ hfrag(1,nhfrag)=ii1
+ hfrag(2,nhfrag)=j1
+
+ do ij=ii1,j1
+ nsec(ij)=-1
+ enddo
+ if (lprint_sec) then
+ write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
+ if (nhelix.le.9) then
+ write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'helix",nhelix,&
+ "' 'num = ",ii1-1,"..",j1-2,"'"
+ else
+ write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
+ "DefPropRes 'helix",nhelix,&
+ "' 'num = ",ii1-1,"..",j1-2,"'"
+ endif
+ endif
+ endif
+ endif
+ enddo
+
+ if (nhelix.gt.0.and.lprint_sec) then
+ write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
+ do i=2,nhelix
+ if (nhelix.le.9) then
+ write(12,'(a8,i1,$)') " | helix",i
+ else
+ write(12,'(a8,i2,$)') " | helix",i
+ endif
+ enddo
+ write(12,'(a1)') "'"
+ endif
+
+ if (lprint_sec) then
+ write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
+ write(12,'(a20)') "XMacStand ribbon.mac"
+ endif
+
+ if (lprint) then
+
+ write(iout,*) 'UNRES seq:',anatemp
+ do j=1,nbfrag
+ write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
+ enddo
+
+ do j=1,nhfrag
+ write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
+ enddo
+
+ endif
+
+ do j=1,nbfrag
+ do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
+ isecstr(k)=1
+ enddo
+ do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
+ isecstr(k)=1
+ enddo
+ enddo
+ do j=1,nhfrag
+ do k=hfrag(1,j),hfrag(2,j)
+ isecstr(k)=2
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) "Secondary structure"
+ do i=1,nres,80
+ ist=i
+ ien=min0(i+79,nres)
+ write (iout,*)
+ write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
+ write (iout,'(80a1)') (onelet(itype(k)),k=ist,ien)
+ write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
+ enddo
+ write (iout,*)
+ endif
+ return
+ end subroutine secondary2
+!-------------------------------------------------
+! logical function freeres(i,j,nsec,isec)
+! include 'DIMENSIONS'
+! integer :: isec(nres,4),nsec(nres)
+! integer :: i,j,k,l
+! freeres=.false.
+!
+! if (nsec(i).gt.1.or.nsec(j).gt.1) return
+! do k=1,nsec(i)
+! do l=1,nsec(j)
+! if (isec(i,k).eq.isec(j,l)) return
+! enddo
+! enddo
+! freeres=.true.
+! return
+! end function freeres
+!-------------------------------------------------
+ subroutine alloc_compar_arrays(nfrg,nlev)
+
+ use energy_data, only:maxcont
+ use w_comm_local
+ integer :: nfrg,nlev
+
+write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
+!------------------------
+! commom.contacts
+! common /contacts/
+ allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
+ allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
+!------------------------
+! COMMON.COMPAR
+! common /compar/
+ allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
+ allocate(qfrag(nfrg,2)) !(maxfrag,2)
+ allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
+ allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
+ allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
+ ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
+ ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
+ allocate(ncont_nat(2,nfrg,nlev+1))
+ allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
+! allocate(nfrag(nlev)) !(maxlevel)
+ allocate(isnfrag(nlev+2)) !(maxlevel+1)
+ allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
+ allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
+ allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
+ allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
+ allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
+!------------------------
+! COMMON.PEPTCONT
+! common /peptcont/
+! integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
+ allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
+ allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
+! integer,dimension(:),allocatable :: isec_ref !(maxres)
+!------------------------
+! module w_comm_local
+! common /ccc/
+ allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
+ allocate(iadded(nres)) !(nres)
+ allocate(inumber(2,nres)) !(2,nres)
+
+
+!-------------------------------------------------------------------------------
+ end subroutine alloc_compar_arrays
+#endif
+!-------------------------------------------------------------------------------
+ end module conform_compar
+
projects / unres4.git / blobdiff