X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Freadpdb.f;h=3e7ecb33bf149218a80e2369d58a96493bf82e86;hb=058b4e72d61c149f66570d580bda9b47464d9df6;hp=93c9cbeac7eef93267f4c62071ab98a36cb4c39b;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git diff --git a/source/wham/src-M/readpdb.f b/source/wham/src-M/readpdb.f index 93c9cbe..3e7ecb3 100644 --- a/source/wham/src-M/readpdb.f +++ b/source/wham/src-M/readpdb.f @@ -3,6 +3,7 @@ C Read the PDB file and convert the peptide geometry into virtual-chain C geometry. implicit none include 'DIMENSIONS' + include 'DIMENSIONS.FREE' include 'DIMENSIONS.ZSCOPT' include 'COMMON.CONTROL' include 'COMMON.LOCAL' @@ -26,8 +27,10 @@ C geometry. goto 10 else if (card(:3).eq.'TER') then C End current chain - ires_old=ires+1 - itype(ires_old)=21 +c ires_old=ires+1 + ires_old=ires+2 + itype(ires_old-1)=ntyp1 + itype(ires_old)=ntyp1 ibeg=2 c write (iout,*) "Chain ended",ires,ishift,ires_old call sccenter(ires,iii,sccor) @@ -48,7 +51,7 @@ c write (iout,'(a80)') card 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 @@ -85,14 +88,51 @@ C system nres=ires do i=2,nres-1 c write (iout,*) i,itype(i) - if (itype(i).eq.21) 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 + + if (itype(i).eq.ntyp1) then + if (itype(i+1).eq.ntyp1) 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 +C if (unres_pdb) then +C 2/15/2013 by Adam: corrected insertion of the last dummy residue +C call refsys(i-3,i-2,i-1,e1,e2,e3,fail) +C if (fail) then +C e2(1)=0.0d0 +C e2(2)=1.0d0 +C e2(3)=0.0d0 +C endif !fail +C do j=1,3 +C c(j,i)=c(j,i-1)-1.9d0*e2(j) +C enddo +C else !unres_pdb + do j=1,3 + dcj=(c(j,i-2)-c(j,i-3))/2.0 + c(j,i)=c(j,i-1)+dcj + c(j,nres+i)=c(j,i) + enddo +C endif !unres_pdb + else !itype(i+1).eq.ntyp1 +C if (unres_pdb) then +C 2/15/2013 by Adam: corrected insertion of the first dummy residue +C call refsys(i+1,i+2,i+3,e1,e2,e3,fail) +C if (fail) then +C e2(1)=0.0d0 +C e2(2)=1.0d0 +C e2(3)=0.0d0 +C endif +C do j=1,3 +C c(j,i)=c(j,i+1)-1.9d0*e2(j) +C enddo +C else !unres_pdb + do j=1,3 + dcj=(c(j,i+3)-c(j,i+2))/2.0 + c(j,i)=c(j,i+1)-dcj + c(j,nres+i)=c(j,i) + enddo +C endif !unres_pdb + endif !itype(i+1).eq.ntyp1 + endif !itype.eq.ntyp1 enddo C Calculate the CM of the last side chain. call sccenter(ires,iii,sccor) @@ -100,9 +140,9 @@ C Calculate the CM of the last side chain. nstart_sup=1 if (itype(nres).ne.10) then nres=nres+1 - itype(nres)=21 + itype(nres)=ntyp1 do j=1,3 - dcj=c(j,nres-2)-c(j,nres-3) + dcj=(c(j,nres-2)-c(j,nres-3))/2.0 c(j,nres)=c(j,nres-1)+dcj c(j,2*nres)=c(j,nres) enddo @@ -116,11 +156,11 @@ C Calculate the CM of the last side chain. 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 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 @@ -131,7 +171,9 @@ C Calculate internal coordinates. & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3), & (c(j,nres+ires),j=1,3) enddo + call int_from_cart1(.false.) call int_from_cart(.true.,.false.) + call sc_loc_geom(.true.) write (iout,*) "After int_from_cart" call flush(iout) do i=1,nres-1 @@ -148,6 +190,16 @@ C Calculate internal coordinates. c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3), c & vbld_inv(i+nres) enddo + do i=1,nres + thetaref(i)=theta(i) + phiref(i)=phi(i) +c + phi_ref(i)=phi(i) + theta_ref(i)=theta(i) + alph_ref(i)=alph(i) + omeg_ref(i)=omeg(i) + enddo + c call chainbuild C Copy the coordinates to reference coordinates c do i=1,2*nres @@ -163,7 +215,7 @@ C Splits to single chain if occurs 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).and.(i.ne.nres)) then chain_length=lll-1 kkk=kkk+1 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) @@ -179,6 +231,8 @@ c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) endif enddo enddo + if (chain_length.eq.0) chain_length=nres + write (iout,*) chain_length do j=1,3 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1) chain_rep(j,chain_length+nres,symetr) @@ -278,27 +332,18 @@ c--------------------------------------------------------------------------- & ' Phi' endif endif - do i=2,nres + do i=1,nres-1 iti=itype(i) - write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1) - if (itype(i-1).ne.21 .and. itype(i).ne.21 .and. - & (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 stop endif - theta(i+1)=alpha(i-1,i,i+1) + vbld(i+1)=dist(i,i+1) + vbld_inv(i+1)=1.0d0/vbld(i+1) + if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1) if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1) enddo - if (itype(1).eq.21) then - do j=1,3 - c(j,1)=c(j,2)+(c(j,3)-c(j,4)) - enddo - endif - if (itype(nres).eq.21) then - do j=1,3 - c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3)) - enddo - endif if (lside) then do i=2,nres-1 do j=1,3 @@ -324,6 +369,97 @@ c--------------------------------------------------------------------------- endif return end + +c------------------------------------------------------------------------------- + subroutine sc_loc_geom(lprn) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'DIMENSIONS.ZSCOPT' + include 'DIMENSIONS.FREE' + include 'COMMON.LOCAL' + include 'COMMON.VAR' + include 'COMMON.CHAIN' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.GEO' + include 'COMMON.NAMES' + include 'COMMON.CONTROL' + include 'COMMON.SETUP' + double precision x_prime(3),y_prime(3),z_prime(3) + logical lprn + do i=1,nres-1 + do j=1,3 + dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i)) + enddo + enddo + do i=2,nres-1 + 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 + else + do j=1,3 + dc_norm(j,i+nres)=0.0d0 + enddo + endif + enddo + do i=2,nres-1 + costtab(i+1) =dcos(theta(i+1)) + sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1)) + cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1))) + sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1))) + cosfac2=0.5d0/(1.0d0+costtab(i+1)) + cosfac=dsqrt(cosfac2) + sinfac2=0.5d0/(1.0d0-costtab(i+1)) + sinfac=dsqrt(sinfac2) + it=itype(i) + 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 +c + do j=1,3 + x_prime(j) = 0.00 + y_prime(j) = 0.00 + z_prime(j) = 0.00 + enddo + do j = 1,3 + x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac + y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac + enddo + call vecpr(x_prime,y_prime,z_prime) +c +C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i), +C to local coordinate system. Store in xx, yy, zz. +c + xx=0.0d0 + yy=0.0d0 + zz=0.0d0 + do j = 1,3 + xx = xx + x_prime(j)*dc_norm(j,i+nres) + yy = yy + y_prime(j)*dc_norm(j,i+nres) + zz = zz + z_prime(j)*dc_norm(j,i+nres) + enddo + + xxref(i)=xx + yyref(i)=yy + zzref(i)=zz + else + xxref(i)=0.0d0 + yyref(i)=0.0d0 + zzref(i)=0.0d0 + endif + enddo + if (lprn) then + do i=2,nres + iti=itype(i) + if(me.eq.king.or..not.out1file) + & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i), + & yyref(i),zzref(i) + enddo + endif + return + end c--------------------------------------------------------------------------- subroutine sccenter(ires,nscat,sccor) implicit none @@ -340,3 +476,374 @@ c--------------------------------------------------------------------------- enddo return end +c---------------------------------------------------------------------- + subroutine readpdb_template(k) +C Read the PDB file for read_constr_homology with read2sigma +C and convert the peptide geometry into virtual-chain geometry. + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'DIMENSIONS.ZSCOPT' + include 'DIMENSIONS.FREE' + include 'COMMON.LOCAL' + include 'COMMON.VAR' + include 'COMMON.CHAIN' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.GEO' + include 'COMMON.NAMES' + include 'COMMON.CONTROL' + include 'COMMON.SETUP' + integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity + logical lprn /.false./,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,iterter(maxres) + logical unres_pdb + unres_pdb=.false. + 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 + iii=0 + lsecondary=.false. + nhfrag=0 + nbfrag=0 + do + read (ipdbin,'(a80)',end=10) card + if (card(:3).eq.'END') then + goto 10 + else if (card(:3).eq.'TER') then +C End current chain + ires_old=ires+2 + itype(ires_old-1)=ntyp1 + iterter(ires_old-1)=1 + itype(ires_old)=ntyp1 + iterter(ires_old)=1 + ibeg=2 + write (iout,*) "Chain ended",ires,ishift,ires_old + if (unres_pdb) then + do j=1,3 + dc(j,ires)=sccor(j,iii) + enddo + else + call sccenter(ires,iii,sccor) + endif + endif +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 +C Calculate the CM of the preceding residue. + if (ibeg.eq.0) then + if (unres_pdb) then + do j=1,3 + dc(j,ires)=sccor(j,iii) + enddo + else + call sccenter(ires_old,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 + 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 +c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift + ibeg=0 + else if (ibeg.eq.2) then +c Start a new chain + ishift=-ires_old+ires-1 + ires=ires_old+1 + 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 + 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 +c if (card(27:27).eq."A" .or. card(27:27).eq."B") then +c ishift1=ishift1+1 +c 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 ,ires,res, (c(j,ires),j=1,3) +c#ifdef DEBUG +c write (iout,'(2i3,2x,a,3f8.3)') +c & ires,itype(ires),res,(c(j,ires),j=1,3) +c#endif + iii=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 + 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 +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),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 + 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 + 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 (unres_pdb) then + do j=1,3 + dc(j,ires)=sccor(j,iii) + enddo + else + call sccenter(ires,iii,sccor) + endif + nsup=nres + nstart_sup=1 + if (itype(nres).ne.10) then + nres=nres+1 + 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) + 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)-1.9d0*e2(j) + enddo + else + do j=1,3 + 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 + endif + endif + do i=2,nres-1 + do j=1,3 + c(j,i+nres)=dc(j,i) + enddo + enddo + do j=1,3 + c(j,nres+1)=c(j,1) + c(j,2*nres)=c(j,nres) + enddo + if (itype(1).eq.ntyp1) then + nsup=nsup-1 + nstart_sup=2 + if (unres_pdb) then +C 2/15/2013 by Adam: corrected insertion of the first dummy residue + call refsys(2,3,4,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,1)=c(j,2)-1.9d0*e2(j) + enddo + else + do j=1,3 + 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 + call int_from_cart1(.false.) + call int_from_cart(.true.,.false.) + call sc_loc_geom(.false.) + do i=1,nres + thetaref(i)=theta(i) + phiref(i)=phi(i) + enddo + do i=1,nres-1 + do j=1,3 + dc(j,i)=c(j,i+1)-c(j,i) + dc_norm(j,i)=dc(j,i)*vbld_inv(i+1) + enddo + enddo + do i=2,nres-1 + do j=1,3 + dc(j,i+nres)=c(j,i+nres)-c(j,i) + dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) + enddo +c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3), +c & vbld_inv(i+nres) + enddo +c call chainbuild +C Copy the coordinates to reference coordinates +C Splits to single chain if occurs + kkk=1 + lll=0 + cou=1 + do i=1,nres + lll=lll+1 +cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) + if (i.gt.1) 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) + lll=1 + endif + endif + do j=1,3 + cref(j,i,cou)=c(j,i) + cref(j,i+nres,cou)=c(j,i+nres) + if (i.le.nres) then + chain_rep(j,lll,kkk)=c(j,i) + chain_rep(j,lll+nres,kkk)=c(j,i+nres) + endif + enddo + enddo +c do i=1,2*nres +c do j=1,3 +c chomo(j,i,k)=c(j,i) +c enddo +c 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) + &=chain_rep(j,chain_length+nres,1) + enddo +c diagnostic +c write (iout,*) "spraw lancuchy",chain_length,symetr +c do i=1,4 +c do kkk=1,chain_length +c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3) +c enddo +c enddo +c enddiagnostic + + return + end