--- /dev/null
+ subroutine define_fragments
+ 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,maxres/2)
+ integer nhairp,ihairp(2,maxres/5)
+ character*16 strstr(4) /'helix','hairpin','strand','strand pair'/
+ 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
+c Find secondary structure elements (helices and beta-sheets)
+ call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,
+ & isec_ref)
+c Define primary fragments. First include the helices.
+ nhairp=0
+ nstrand=0
+c Merge helices
+c 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
+c 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
+c 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
+c 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
+c------------------------------------------------------------------------------
+ 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,maxres/3)
+ integer nhairp,ihairp(2,maxres/5)
+ 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
+c------------------------------------------------------------------------------
+ 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,maxres/3)
+ integer nstrand,istrand(2,maxres/2)
+ integer nhairp,ihairp(2,maxres/5)
+ logical found
+ 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
+c------------------------------------------------------------------------------
+ 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,maxres/2)
+ integer nhairp,ihairp(2,maxres/5)
+ logical found
+ 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
+c 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
+c 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
+c------------------------------------------------------------------------------
+ subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
+ 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(maxres,4),nsec(maxres),
+ & isecstr(maxres)
+ logical lprint,lprint_sec,not_done,freeres
+ double precision p1,p2
+ external freeres
+ character*1 csec(0:2) /'-','E','H'/
+ 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
+
+c finding parallel beta
+cd 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
+cd write (iout,*) "parallel",i1,j1
+ if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
+ ii1=i1
+ jj1=j1
+cd 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
+cd 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
+
+c finding antiparallel beta
+cd 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
+cd 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
+cd 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
+
+cd write (iout,*) "After beta:",nbfrag
+cd do i=1,nbfrag
+cd write (iout,*) (bfrag(j,i),j=1,4)
+cd 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
+
+
+c 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
+cd if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
+co 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.
+
+cd write (iout,*) i1,j1,not_done,p1,p2
+ enddo
+ j1=j1+1
+ if (j1-ii1.gt.4) then
+ nhelix=nhelix+1
+cd 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:'
+ 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)
+ 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
+c-------------------------------------------------
+ logical function freeres(i,j,nsec,isec)
+ include 'DIMENSIONS'
+ integer isec(maxres,4),nsec(maxres)
+ 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
+
projects / unres.git / blobdiff