X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_Eshel%2Freadpdb.F;h=3ce8334606e37962aaaf15bb1ab712acfeadec49;hb=5e2358117d5efe154a9c192de01e50c1f84f6a43;hp=5d6acc0c3adf1dc719bdf941c8d0c6e51ce35f9c;hpb=a09fdb5f3686a0c1242c8dd3b6dfadf0d3678aaf;p=unres.git diff --git a/source/unres/src_Eshel/readpdb.F b/source/unres/src_Eshel/readpdb.F index 5d6acc0..3ce8334 100644 --- a/source/unres/src_Eshel/readpdb.F +++ b/source/unres/src_Eshel/readpdb.F @@ -13,25 +13,30 @@ C geometry. 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) - logical fail + double precision dcj,efree_temp + character*3 seq,res + character*5 atom + character*80 card + double precision sccor(3,20) 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. @@ -50,86 +55,118 @@ crc to be corrected !!! 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(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) + dc(j,ires)=sccor(j,iii) enddo else - call sccenter(ires,iii,sccor) + call sccenter(ires_old,iii,sccor) endif + iii=0 endif C Start new residue. - 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 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 - ires=ires-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) -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 +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 + 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 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 the CM of the last side chain. + if (iii.gt.0) then if (unres_pdb) then do j=1,3 - dc(j,ires+nres)=sccor(j,iii) + dc(j,ires)=sccor(j,iii) enddo - else if (.not.catrace) then + else 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 @@ -154,7 +191,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue do j=1,3 c(j,1)=c(j,2)-3.8d0*e2(j) enddo - else if (.not.catrace) then + else do j=1,3 dcj=c(j,4)-c(j,3) c(j,1)=c(j,2)-dcj @@ -162,6 +199,24 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue 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)') @@ -172,8 +227,8 @@ C Calculate internal coordinates. & (c(j,nres+ires),j=1,3) enddo endif - call int_from_cart(.not.catrace,.false.) - if (.not.catrace) call sc_loc_geom(.false.) + call int_from_cart(.true.,.false.) + call sc_loc_geom(.false.) do i=1,nres thetaref(i)=theta(i) phiref(i)=phi(i) @@ -212,7 +267,7 @@ C Copy the coordinates to reference coordinates hfrag(i,j)=hfrag(i,j)-ishift enddo enddo - + ishift_pdb=ishift return end c--------------------------------------------------------------------------- @@ -231,7 +286,8 @@ c--------------------------------------------------------------------------- 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 @@ -251,7 +307,6 @@ c--------------------------------------------------------------------------- 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 @@ -278,7 +333,6 @@ c endif 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)) @@ -286,7 +340,7 @@ c endif 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) + if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0) & di=dsc(itype(i)) vbld(i+nres)=di if (itype(i).ne.10) then