include 'COMMON.CONTROL'
include 'COMMON.DISTFIT'
include 'COMMON.SETUP'
- integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
- & ishift_pdb
- logical lprn /.true./,fail
- double precision e1(3),e2(3),e3(3)
- double precision dcj,efree_temp
- character*3 seq,res
- character*5 atom
+ character*3 seq,atom,res
character*80 card
- double precision sccor(3,20)
+ dimension sccor(3,20)
+ double precision e1(3),e2(3),e3(3)
+ logical fail
integer rescode
- efree_temp=0.0d0
ibeg=1
- ishift1=0
- ishift=0
-c write (2,*) "UNRES_PDB",unres_pdb
- ires=0
- ires_old=0
- iii=0
lsecondary=.false.
nhfrag=0
nbfrag=0
+ do i=1,maxres
+ itype(i)=21
+ do j=1,3
+ c(j,i)=0.0d0
+ c(j,i+nres)=0.0d0
+ enddo
+ enddo
do i=1,10000
read (ipdbin,'(a80)',end=10) card
-c write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
crc----------------------------------------
endif
if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
-c Read free energy
- if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
C Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
- read (card(12:16),*) atom
-c write (iout,*) "! ",atom," !",ires
-c 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
+ read (card(14:16),'(a3)') atom
+ if (atom.eq.'CA' .or. atom.eq.'CH3') then
C Calculate the CM of the preceding residue.
-c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
if (ibeg.eq.0) then
-c write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires)=sccor(j,iii)
+ dc(j,ires+nres)=sccor(j,iii)
enddo
else
- call sccenter(ires_old,iii,sccor)
+ call sccenter(ires,iii,sccor)
endif
- iii=0
endif
C Start new residue.
- 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
+ read (card(24:26),*) ires
+ read (card(18:20),'(a3)') res
+ if (ibeg.eq.1) then
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
itype(1)=21
endif
- ires=ires-ishift+ishift1
- ires_old=ires
-c write (iout,*) "ishift",ishift," ires",ires,
-c & " ires_old",ires_old
ibeg=0
- else
- ishift=ishift-(ires-ishift+ishift1-ires_old-1)
- ires=ires-ishift+ishift1
- ires_old=ires
endif
- if (res.eq.'ACE' .or. res.eq.'NHE') then
- itype(ires)=10
+ ires=ires-ishift
+ if (res.eq.'ACE') then
+ ity=10
else
itype(ires)=rescode(ires,res,0)
endif
- else
- ires=ires-ishift+ishift1
- endif
-c write (iout,*) "ires_old",ires_old," ires",ires
- if (card(27:27).eq."A" .or. card(27:27).eq."B") then
-c 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)
-c write (iout,*) "backbone ",atom
-#ifdef DEBUG
- write (iout,'(2i3,2x,a,3f8.3)')
- & ires,itype(ires),res,(c(j,ires),j=1,3)
-#endif
- iii=iii+1
+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
- if (ishift.ne.0) then
- ires_ca=ires+ishift-ishift1
- else
- ires_ca=ires
- endif
-c write (*,*) card(23:27),ires,itype(ires)
- 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
-c write (iout,*) "sidechain ",atom
+ else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N ' .and. atom.ne.'C ') then
iii=iii+1
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
endif
endif
enddo
- 10 write (iout,'(a,i5)') ' Number of residues found: ',ires
- if (ires.eq.0) return
+ 10 if(me.eq.king.or..not.out1file)
+ & write (iout,'(a,i5)') ' Nres: ',ires
C Calculate the CM of the last side chain.
- if (iii.gt.0) then
if (unres_pdb) then
do j=1,3
- dc(j,ires)=sccor(j,iii)
+ dc(j,ires+nres)=sccor(j,iii)
enddo
- else
+ else if (.not.catrace) then
call sccenter(ires,iii,sccor)
endif
- endif
nres=ires
nsup=nres
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
itype(nres)=21
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ enddo
+ else if (.not.catrace) then
do j=1,3
dcj=c(j,nres-2)-c(j,nres-3)
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
+ endif
endif
do i=2,nres-1
do j=1,3
do j=1,3
c(j,1)=c(j,2)-3.8d0*e2(j)
enddo
- else
+ else if (.not.catrace) then
do j=1,3
dcj=c(j,4)-c(j,3)
c(j,1)=c(j,2)-dcj
enddo
endif
endif
-C Copy the coordinates to reference coordinates
-c do i=1,2*nres
-c do j=1,3
-c cref(j,i)=c(j,i)
-c enddo
-c enddo
-C Calculate internal coordinates.
- if (lprn) then
- 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,i3,3f8.3,5x,3f8.3)')
- & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
- & (c(j,ires+nres),j=1,3)
- enddo
- endif
C Calculate internal coordinates.
if(me.eq.king.or..not.out1file)then
write (iout,'(a)')
& (c(j,nres+ires),j=1,3)
enddo
endif
- call int_from_cart(.true.,.false.)
- call sc_loc_geom(.false.)
+ call int_from_cart(.not.catrace,.false.)
+ if (.not.catrace) call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
hfrag(i,j)=hfrag(i,j)-ishift
enddo
enddo
- ishift_pdb=ishift
+
return
end
c---------------------------------------------------------------------------
include 'COMMON.NAMES'
include 'COMMON.CONTROL'
include 'COMMON.SETUP'
- character*3 seq,res
-c character*5 atom
+ character*3 seq,atom,res
character*80 card
dimension sccor(3,20)
integer rescode
endif
endif
do i=1,nres-1
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iti=itype(i)
if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
c endif
if (lside) then
do i=2,nres-1
+ if (itype(i).eq.ntyp1) cycle
do j=1,3
c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
& +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
iti=itype(i)
di=dist(i,nres+i)
C 10/03/12 Adam: Correction for zero SC-SC bond length
- if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1. and. di.eq.0.0d0)
& di=dsc(itype(i))
vbld(i+nres)=di
if (itype(i).ne.10) then
projects / unres.git / blobdiff