include 'COMMON.CONTROL'
include 'COMMON.DISTFIT'
include 'COMMON.SETUP'
- character*3 seq,atom,res
- character*80 card
- dimension sccor(3,20)
+ 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*80 card
+ double precision sccor(3,20)
integer rescode
- logical fail
+ efree_temp=0.0d0
ibeg=1
+ ishift1=0
+ ishift=0
+c write (2,*) "UNRES_PDB",unres_pdb
+ ires=0
+ ires_old=0
+ nres=0
+ iii=0
lsecondary=.false.
nhfrag=0
nbfrag=0
- do
+ do i=1,100000
read (ipdbin,'(a80)',end=10) card
+c write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
goto 10
else if (card(:3).eq.'TER') then
C End current chain
- ires_old=ires+1
- itype(ires_old)=21
+ ires_old=ires+1
+ ishift1=ishift1+1
+ itype(ires_old)=ntyp1
ibeg=2
c write (iout,*) "Chain ended",ires,ishift,ires_old
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
endif
+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(14:16),'(a3)') atom
- if (atom.eq.'CA' .or. atom.eq.'CH3') 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
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+nres)=sccor(j,iii)
enddo
else
- call sccenter(ires,iii,sccor)
+ call sccenter(ires_old,iii,sccor)
endif
+ iii=0
endif
C Start new residue.
-c write (iout,'(a80)') card
- read (card(24:26),*) ires
- read (card(18:20),'(a3)') res
- if (ibeg.eq.1) then
+ 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)=21
+ itype(1)=ntyp1
endif
-c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
- ibeg=0
+ ires=ires-ishift+ishift1
+ ires_old=ires
+c write (iout,*) "ishift",ishift," ires",ires,
+c & " ires_old",ires_old
+ 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
+c ishift=-ires_old+ires-1
+c ishift1=ishift1+1
+c write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+ ires=ires-ishift+ishift1
+ ires_old=ires
ibeg=0
+ else
+ ishift=ishift-(ires-ishift+ishift1-ires_old-1)
+ ires=ires-ishift+ishift1
+ ires_old=ires
endif
- ires=ires-ishift
-c write (2,*) "ires",ires," ishift",ishift
- if (res.eq.'ACE') then
- ity=10
+ if (res.eq.'ACE' .or. res.eq.'NHE') then
+ itype(ires)=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)
- if(me.eq.king.or..not.out1file)
- & write (iout,'(2i3,2x,a,3f8.3)')
- & ires,itype(ires),res,(c(j,ires),j=1,3)
- iii=1
+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
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 (*,*) 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
iii=iii+1
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
endif
endif
enddo
- 10 if(me.eq.king.or..not.out1file)
- & write (iout,'(a,i5)') ' Nres: ',ires
+ 10 write (iout,'(a,i5)') ' Number of residues found: ',ires
+ if (ires.eq.0) return
C Calculate dummy residue coordinates inside the "chain" of a multichain
C system
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
c write (iout,*) "dummy",i,itype(i)
do j=1,3
c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
endif
enddo
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)
enddo
- else
+ else
call sccenter(ires,iii,sccor)
endif
+ endif
+c nres=ires
nsup=nres
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
- itype(nres)=21
+ itype(nres)=ntyp1
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)
c(j,nres+1)=c(j,1)
c(j,2*nres)=c(j,nres)
enddo
- if (itype(1).eq.21) then
+ if (itype(1).eq.ntyp1) then
nsup=nsup-1
nstart_sup=2
if (unres_pdb) then
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)')
+ & "Backbone and SC coordinates as read from the PDB"
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),
endif
call int_from_cart(.true.,.false.)
call sc_loc_geom(.true.)
+c wczesbiej bylo false
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
c call chainbuild
C Copy the coordinates to reference coordinates
C Splits to single chain if occurs
+
+c do i=1,2*nres
+c do j=1,3
+c cref(j,i,cou)=c(j,i)
+c enddo
+c enddo
+c
kkk=1
lll=0
cou=1
lll=lll+1
cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
- if ((itype(i-1).eq.21)) then
+ if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
endif
enddo
enddo
+ write (iout,*) chain_length
+ if (chain_length.eq.0) chain_length=nres
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
c enddo
c enddo
-c enddiagnostic
+c enddiagnostic
C makes copy of chains
write (iout,*) "symetr", symetr
-
+
if (symetr.gt.1) then
call permut(symetr)
nperm=1
1 ' ', 6X,'X',11X,'Y',11X,'Z',
& 10X,'X',11X,'Y',11X,'Z')
110 format (a,'(',i3,')',6f12.5)
-
+
enddo
cc enddiag
do j=1,nbfrag
hfrag(i,j)=hfrag(i,j)-ishift
enddo
enddo
-
+ ishift_pdb=ishift
return
end
c---------------------------------------------------------------------------
include 'DIMENSIONS'
#ifdef MPI
include "mpif.h"
-#endif
+#endif
include 'COMMON.LOCAL'
include 'COMMON.VAR'
include 'COMMON.CHAIN'
include 'COMMON.NAMES'
include 'COMMON.CONTROL'
include 'COMMON.SETUP'
- character*3 seq,atom,res
+ character*3 seq,res
+c character*5 atom
character*80 card
dimension sccor(3,20)
integer rescode
logical lside,lprn
-#ifdef MPI
if(me.eq.king.or..not.out1file)then
-#endif
if (lprn) then
write (iout,'(/a)')
& 'Internal coordinates calculated from crystal structure.'
if (lside) then
write (iout,'(8a)') ' Res ',' dvb',' Theta',
- & ' Phi',' Dsc_id',' Dsc',' Alpha',
- & ' Omega'
+ & ' Gamma',' Dsc_id',' Dsc',' Alpha',
+ & ' Beta '
else
write (iout,'(4a)') ' Res ',' dvb',' Theta',
- & ' Phi'
+ & ' Gamma'
endif
endif
-#ifdef MPI
endif
-#endif
do i=1,nres-1
iti=itype(i)
- if (iti.ne.21 .and. itype(i+1).ne.21 .and.
- & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
+ 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
ctest stop
endif
enddo
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.ntyp1. and. di.eq.0.0d0)
+ & di=dsc(itype(i))
vbld(i+nres)=di
if (itype(i).ne.10) then
vbld_inv(i+nres)=1.0d0/di
include 'DIMENSIONS'
#ifdef MPI
include "mpif.h"
-#endif
+#endif
include 'COMMON.LOCAL'
include 'COMMON.VAR'
include 'COMMON.CHAIN'
enddo
enddo
do i=2,nres-1
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10) then
do j=1,3
dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
enddo
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
it=itype(i)
- if (it.ne.10 .and. itype(i).ne.21) then
+ if (it.ne.10) then
c
C Compute the axes of tghe local cartesian coordinates system; store in
c x_prime, y_prime and z_prime
if (lprn) then
do i=2,nres
iti=itype(i)
-#ifdef MPI
if(me.eq.king.or..not.out1file)
& write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
& yyref(i),zzref(i)
-#else
- write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
- & zzref(i)
-#endif
enddo
endif
return
enddo
return
end
-
projects / unres.git / blobdiff