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)
- integer rescode
- efree_temp=0.0d0
+ dimension sccor(3,20)
+ double precision e1(3),e2(3),e3(3)
+ integer rescode,iterter(maxres),cou
+ logical fail
+ do i=1,maxres
+ iterter(i)=0
+ enddo
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 i=1,100000
+ do
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
- ishift1=ishift1+1
+ ires_old=ires+2
+ itype(ires_old-1)=ntyp1
+ iterter(ires_old-1)=1
itype(ires_old)=ntyp1
+ iterter(ires_old)=1
ibeg=2
-c write (iout,*) "Chain ended",ires,ishift,ires_old
+ 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(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+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
+c write (iout,'(a80)') card
+ read (card(23:26),*) 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)=ntyp1
endif
- ires=ires-ishift+ishift1
- ires_old=ires
-c write (iout,*) "ishift",ishift," ires",ires,
-c & " ires_old",ires_old
- ibeg=0
+c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
+ ibeg=0
else if (ibeg.eq.2) then
c Start a new chain
-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
+ ishift=-ires_old+ires-1
+c write (iout,*) "New chain started",ires,ishift
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
+ ires=ires-ishift
+c write (2,*) "ires",ires," ishift",ishift
+ if (res.eq.'ACE') 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)
-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
+ 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
do j=1,3
sccor(j,iii)=c(j,ires)
enddo
-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 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.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
-c c(j,i)=(c(j,i-1)+c(j,i+1))/2
- dc(j,i)=c(j,i)
- enddo
- endif
+ write (iout,*) i,itype(i),itype(i+1)
+ if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
+ if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
+C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+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'
+ 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?'
+ do j=1,3
+ c(j,i)=c(j,i-1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ else !itype(i+1).eq.ntyp1
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(i+1,i+2,i+3,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,i)=c(j,i+1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ endif !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
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
e2(3)=0.0d0
endif
do j=1,3
- c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ c(j,1)=c(j,2)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,4)-c(j,3)
+ dcj=(c(j,4)-c(j,3))/2.0
c(j,1)=c(j,2)-dcj
c(j,nres+1)=c(j,1)
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),
& (c(j,nres+ires),j=1,3)
enddo
endif
+C print *,"before int_from_cart"
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
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
-
+ nperm=1
+ 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,res
-c character*5 atom
+ character*3 seq,atom,res
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',
- & ' Gamma',' Dsc_id',' Dsc',' Alpha',
- & ' Beta '
+ & ' Phi',' Dsc_id',' Dsc',' Alpha',
+ & ' Omega'
else
write (iout,'(4a)') ' Res ',' dvb',' Theta',
- & ' Gamma'
+ & ' Phi'
endif
endif
+#ifdef MPI
endif
+#endif
do i=1,nres-1
iti=itype(i)
- if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
+ if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
+ & (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
c vbld_inv(nres)=1.0d0/vbld(2)
c endif
c endif
+c print *,"A TU2"
if (lside) then
do i=2,nres-1
do j=1,3
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) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) 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) then
+ if (it.ne.10 .and. itype(i).ne.ntyp1) 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
do i=1,nres-1
vbld(i+1)=vbl
vbld_inv(i+1)=1.0d0/vbld(i+1)
- vbld(i+1+nres)=dsc(itype(i+1))
- vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+ vbld(i+1+nres)=dsc(iabs(itype(i+1)))
+ vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
c print *,vbld(i+1),vbld(i+1+nres)
enddo
return
end
+
projects / unres.git / blobdiff