double precision sccor(3,50)
double precision e1(3),e2(3),e3(3)
integer rescode,iterter(maxres),cou
- logical fail
- integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg
- double precision dcj
+ logical fail,sccalc
+ integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg,ifree
+ double precision dcj!,efree_temp
+ logical zero
bfac=0.0d0
do i=1,maxres
iterter(i)=0
enddo
ibeg=1
+ ishift=0
ishift1=0
lsecondary=.false.
nhfrag=0
nbfrag=0
+ iii=0
+ sccalc=.false.
do
read (ipdbin,'(a80)',end=10) card
+c write (iout,'(a)') card
+c call flush(iout)
if (card(:5).eq.'HELIX') then
- nhfrag=nhfrag+1
- lsecondary=.true.
- read(card(22:25),*) hfrag(1,nhfrag)
- read(card(34:37),*) hfrag(2,nhfrag)
+ nhfrag=nhfrag+1
+ lsecondary=.true.
+ read(card(22:25),*) hfrag(1,nhfrag)
+ read(card(34:37),*) hfrag(2,nhfrag)
endif
if (card(:5).eq.'SHEET') then
- nbfrag=nbfrag+1
- lsecondary=.true.
- read(card(24:26),*) bfrag(1,nbfrag)
- read(card(35:37),*) bfrag(2,nbfrag)
-crc----------------------------------------
-crc to be corrected !!!
- bfrag(3,nbfrag)=bfrag(1,nbfrag)
- bfrag(4,nbfrag)=bfrag(2,nbfrag)
-crc----------------------------------------
+ nbfrag=nbfrag+1
+ lsecondary=.true.
+ read(card(24:26),*) bfrag(1,nbfrag)
+ read(card(35:37),*) bfrag(2,nbfrag)
+!rc----------------------------------------
+!rc to be corrected !!!
+ bfrag(3,nbfrag)=bfrag(1,nbfrag)
+ bfrag(4,nbfrag)=bfrag(2,nbfrag)
+!rc----------------------------------------
endif
if (card(:3).eq.'END') then
goto 10
else if (card(:3).eq.'TER') then
-C End current chain
+! End current chain
ires_old=ires+2
- itype(ires_old-1)=ntyp1
+ itype(ires_old-1)=ntyp1
iterter(ires_old-1)=1
itype(ires_old)=ntyp1
iterter(ires_old)=1
+c ishift1=ishift1+1
ibeg=2
- write (iout,*) "Chain ended",ires,ishift,ires_old
+ write (iout,*) "Chain ended",ires,ishift,ires_old,ibeg
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
enddo
- else
+ else
call sccenter(ires,iii,sccor)
endif
+ iii=0
+ sccalc=.true.
endif
-C Fish out the ATOM cards.
-c if (index(card(1:4),'ATOM').gt.0) then
-c read (card(14:16),'(a3)') atom
-c if (atom.eq.'CA' .or. atom.eq.'CH3') then
-C Calculate the CM of the preceding residue.
- read (card(23:26),*) ires
- read (card(18:20),'(a3)') res
- if (ires-ishift+ishift1.ne.ires_old) then
- if (ibeg.eq.0) then
- if (unres_pdb) then
- do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
- enddo
+! Read free energy
+c if (index(card,"FREE ENERGY").gt.0) then
+c ifree=index(card,"FREE ENERGY")+12
+c read(card(ifree:),*,err=1115,end=1115) efree_temp
+c 1115 continue
+c endif
+! Fish out the ATOM cards.
+ if (index(card(1:4),'ATOM').gt.0) then
+ sccalc=.false.
+ read (card(12:16),*) atom
+c write (2,'(a)') card
+c write (iout,*) "ibeg",ibeg
+c write (iout,*) "! ",atom," !",ires
+! if (atom.eq.'CA' .or. atom.eq.'CH3') then
+ read (card(23:26),*) ires
+ read (card(18:20),'(a3)') res
+c write (iout,*) "ires",ires,ires-ishift+ishift1,
+c & " ires_old",ires_old
+c write (iout,*) "ishift",ishift," ishift1",ishift1
+c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+ if (ires-ishift+ishift1.ne.ires_old) then
+! Calculate the CM of the preceding residue.
+! if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+ if (ibeg.eq.0) then
+c write (iout,*) "Calculating sidechain center iii",iii
+c write (iout,*) "ires",ires
+ if (unres_pdb) then
+c write (iout,'(i5,3f10.5)') ires,(sccor(j,iii),j=1,3)
+ do j=1,3
+ dc(j,ires_old)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires_old,iii,sccor)
+ endif
+ iii=0
+ sccalc=.true.
+ endif
+! Start new residue.
+c write (iout,*) "ibeg",ibeg
+ if (res.eq.'Cl-' .or. res.eq.'Na+') then
+ ires=ires_old
+ cycle
+ else if (ibeg.eq.1) then
+c write (iout,*) "BEG ires",ires
+ ishift=ires-1
+ if (res.ne.'GLY' .and. res.ne. 'ACE') then
+ ishift=ishift-1
+ itype(1)=ntyp1
+ endif
+ ires=ires-ishift+ishift1
+ ires_old=ires
+! write (iout,*) "ishift",ishift," ires",ires,&
+! " ires_old",ires_old
+ ibeg=0
+ else if (ibeg.eq.2) then
+! Start a new chain
+ ishift=-ires_old+ires-1 !!!!!
+c ishift1=ishift1-1 !!!!!
+c write (iout,*) "New chain started",ires,ires_old,ishift,
+c & ishift1
+ ires=ires-ishift+ishift1
+ write (iout,*) "New chain started ires",ires
+ ires_old=ires
+c ires=ires_old+1
+ ibeg=0
else
- call sccenter(ires,iii,sccor)
+ ishift=ishift-(ires-ishift+ishift1-ires_old-1)
+ ires=ires-ishift+ishift1
+ ires_old=ires
endif
- endif
-C Start new residue.
-c write (iout,'(a80)') card
- if (ibeg.eq.1) then
- ishift=ires-1
- if (res.ne.'GLY' .and. res.ne. 'ACE') then
- ishift=ishift-1
- itype(1)=ntyp1
+ if (res.eq.'ACE' .or. res.eq.'NHE') then
+ itype(ires)=10
+ else
+ itype(ires)=rescode(ires,res,0)
endif
-c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
- ibeg=0
- else if (ibeg.eq.2) then
-c Start a new chain
- ishift=-ires_old+ires-1
-c write (iout,*) "New chain started",ires,ishift
- ibeg=0
- endif
- else
- ires=ires-ishift
-c write (2,*) "ires",ires," ishift",ish
- endif
- if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
- & res.eq.'NHE'.and.atom(:2).eq.'HN') then
- if (res.eq.'ACE') then
- itype(ires)=10
else
- itype(ires)=rescode(ires,res,0)
+ ires=ires-ishift+ishift1
endif
- read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
- read(card(61:66),*) bfac(ires)
-c if(me.eq.king.or..not.out1file)
-c & write (iout,'(2i3,2x,a,3f8.3)')
-c & ires,itype(ires),res,(c(j,ires),j=1,3)
- iii=1
- do j=1,3
- sccor(j,iii)=c(j,ires)
- enddo
- else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
- & atom.ne.'N ' .and. atom.ne.'C ') then
+c write (iout,*) "ires_old",ires_old," ires",ires
+ if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+! ishift1=ishift1+1
+ endif
+c write (2,*) "ires",ires," res ",res!," ity"!,ity
+ if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
+ & res.eq.'NHE'.and.atom(:2).eq.'HN') then
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+ read(card(61:66),*) bfac(ires)
+c write (iout,*) "backbone ",atom
+c write (iout,*) ires,res,(c(j,ires),j=1,3)
+#ifdef DEBUG
+ write (iout,'(i6,i3,2x,a,3f8.3)')
+ & ires,itype(ires),res,(c(j,ires),j=1,3)
+#endif
+ iii=iii+1
+ do j=1,3
+ sccor(j,iii)=c(j,ires)
+ enddo
+c write (2,*) card(23:27),ires,itype(ires),iii
+ else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N' .and. atom.ne.'C' .and.
+ & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
+ & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
+! write (iout,*) "sidechain ",atom
iii=iii+1
- read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+ read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+c write (2,*) "iii",iii
+ endif
endif
enddo
10 if(me.eq.king.or..not.out1file)
- & write (iout,'(a,i5)') ' Nres: ',ires
+ & write (iout,'(a,i7)') ' Nres: ',ires
+c write (iout,*) "iii",iii
C Calculate dummy residue coordinates inside the "chain" of a multichain
C system
nres=ires
+c write (iout,*) "dc"
+c do i=1,nres
+c write (iout,'(i5,3f10.5)') i,(dc(j,i),j=1,3)
+c enddo
do i=2,nres-1
c write (iout,*) i,itype(i),itype(i+1),ntyp1,iterter(i)
if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the last dummy residue
- print *,i,'tu dochodze'
+c print *,i,'tu dochodze'
call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
if (fail) then
e2(1)=0.0d0
e2(2)=1.0d0
e2(3)=0.0d0
endif !fail
- print *,i,'a tu?'
+c print *,i,'a tu?'
do j=1,3
c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
enddo
if (dcj.eq.0) dcj=1.23591524223
c(j,i)=c(j,i-1)+dcj
c(j,nres+i)=c(j,i)
+ dC(j,i)=c(j,i)
enddo
endif !unres_pdb
else !itype(i+1).eq.ntyp1
e2(3)=0.0d0
endif
do j=1,3
- c(j,i)=c(j,i+1)-1.9d0*e2(j)
+ c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
enddo
else !unres_pdb
do j=1,3
if (dcj.eq.0) dcj=1.23591524223
c(j,i)=c(j,i+1)-dcj
c(j,nres+i)=c(j,i)
+ dC(j,i)=c(j,i)
enddo
endif !unres_pdb
endif !itype(i+1).eq.ntyp1
enddo
write (iout,*) "After loop in readpbd"
C Calculate the CM of the last side chain.
+ if (.not. sccalc) then
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
enddo
else
+c write (iout,*) "Calling sccenter iii",iii
call sccenter(ires,iii,sccor)
endif
+ endif
nsup=nres
nstart_sup=1
if (itype(nres).ne.10) then
endif
C Calculate internal coordinates.
if(me.eq.king.or..not.out1file)then
- do ires=1,nres
- write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
- & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
- & (c(j,nres+ires),j=1,3)
- enddo
- endif
+ write (iout,'(/a)')
+ & "Cartesian coordinates of the reference structure"
+ write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
+ & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
+ do ires=1,nres
+ write (iout,'(a3,1x,i6,3f8.3,5x,3f8.3)')
+ & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
+ & (c(j,ires+nres),j=1,3)
+ enddo
call flush(iout)
+ endif
+ zero=.false.
+ do ires=1,nres
+ zero=zero.or.itype(ires).eq.0
+ enddo
+ if (zero) then
+ write (iout,'(2a)') "Gaps in PDB coordinates detected;",
+ & " look for ZERO in the control output above."
+ write (iout,'(2a)') "Repair the PDB file using MODELLER",
+ & " or other softwared and resubmit."
+ call flush(iout)
+ stop
+ endif
c write(iout,*)"before int_from_cart nres",nres
call int_from_cart(.true.,.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
enddo
+ dc(:,0)=c(:,1)
do i=1,nres-1
do j=1,3
dc(j,i)=c(j,i+1)-c(j,i)
enddo
100 format (//' alpha-carbon coordinates ',
& ' centroid coordinates'/
- 1 ' ', 6X,'X',11X,'Y',11X,'Z',
+ 1 ' ', 7X,'X',11X,'Y',11X,'Z',
& 10X,'X',11X,'Y',11X,'Z')
- 110 format (a,'(',i3,')',6f12.5)
+ 110 format (a,'(',i4,')',6f12.5)
cc enddiag
do j=1,nbfrag
do i=1,4
character*3 seq,res
character*5 atom
character*80 card
- double precision sccor(3,20)
+ double precision sccor(3,50)
integer rescode,iterter(maxres)
+ logical zero
do i=1,maxres
iterter(i)=0
enddo
if (ibeg.eq.0) then
if (unres_pdb) then
do j=1,3
- dc(j,ires)=sccor(j,iii)
+ dc(j,ires_old)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
endif
enddo
10 if(me.eq.king.or..not.out1file)
- & write (iout,'(a,i5)') ' Nres: ',ires
+ & write (iout,'(a,i7)') ' Nres: ',ires
C Calculate dummy residue coordinates inside the "chain" of a multichain
C system
nres=ires
e2(3)=0.0d0
endif
do j=1,3
- c(j,i)=c(j,i+1)-1.9d0*e2(j)
+ c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
enddo
else !unres_pdb
do j=1,3
e2(3)=0.0d0
endif
do j=1,3
- c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
+ c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
enddo
else
do j=1,3
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-1.9d0*e2(j)
+ c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
enddo
else
do j=1,3
write (iout,'(/a)')
& "Cartesian coordinates of the reference structure"
write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
- & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
+ & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
do ires=1,nres
- write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
+ write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
& restyp(itype(ires)),ires,(c(j,ires),j=1,3),
& (c(j,ires+nres),j=1,3)
enddo
endif
+ zero=.false.
+ do ires=1,nres
+ zero=zero.or.itype(ires).eq.0
+ enddo
+ if (zero) then
+ write (iout,'(2a)') "Gaps in PDB coordinates detected;",
+ & " look for ZERO in the control output above."
+ write (iout,'(2a)') "Repair the PDB file using MODELLER",
+ & " or other softwared and resubmit."
+ call flush(iout)
+ stop
+ endif
C Calculate internal coordinates.
- call int_from_cart(.true.,.true.)
+ call int_from_cart(.true.,out_template_coord)
call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
enddo
+ dc(:,0)=c(:,1)
do i=1,nres-1
do j=1,3
dc(j,i)=c(j,i+1)-c(j,i)
projects / unres.git / blobdiff