X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_Eshel%2Freadpdb.F;h=5d6acc0c3adf1dc719bdf941c8d0c6e51ce35f9c;hb=34d3ad3987785642be58fb2f26557d3314215577;hp=3ce8334606e37962aaaf15bb1ab712acfeadec49;hpb=f690e8b70bab14132839afebf080d4a28363b226;p=unres.git diff --git a/source/unres/src_Eshel/readpdb.F b/source/unres/src_Eshel/readpdb.F index 3ce8334..5d6acc0 100644 --- a/source/unres/src_Eshel/readpdb.F +++ b/source/unres/src_Eshel/readpdb.F @@ -13,30 +13,25 @@ C geometry. 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. @@ -55,118 +50,86 @@ 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(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 @@ -191,7 +154,7 @@ 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 + else if (.not.catrace) then do j=1,3 dcj=c(j,4)-c(j,3) c(j,1)=c(j,2)-dcj @@ -199,24 +162,6 @@ 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)') @@ -227,8 +172,8 @@ C Calculate internal coordinates. & (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) @@ -267,7 +212,7 @@ C Copy the coordinates to reference coordinates hfrag(i,j)=hfrag(i,j)-ishift enddo enddo - ishift_pdb=ishift + return end c--------------------------------------------------------------------------- @@ -286,8 +231,7 @@ 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 @@ -307,6 +251,7 @@ c character*5 atom 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 @@ -333,6 +278,7 @@ 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)) @@ -340,7 +286,7 @@ 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.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