--- /dev/null
+*************************************************************************\r
+* This program is to identify the best alignment of two protein \r
+* structures to give the best TM-score. By default, TM-score is \r
+* normalized by the second protein. The program can be freely \r
+* copied or modified or redistributed.\r
+* (For comments, please email to: yzhang@ku.edu)\r
+* \r
+* Reference:\r
+* Yang Zhang, Jeffrey Skolnick, Nucl. Acid Res. 2005 33: 2303-9\r
+*\r
+************************ updating history *******************************\r
+* 2005/06/01: A small bug of two-point superposition was fixed.\r
+* 2005/10/19: the program was reformed so that the alignment\r
+* results are not dependent on the specific compilers.\r
+* 2006/06/20: select 'A' if there is altLoc when reading PDB file.\r
+* 2007/02/27: rotation matrix from Chain-1 to Chain-2 is added.\r
+* 2007/04/18: add options with TM-score normalized by average\r
+* length, shorter length, or longer length of two \r
+* structures.\r
+* 2007/05/23: add additional output file 'TM.sup_all' for showing\r
+* all atoms while 'TM.sup' is only for aligned atoms\r
+* 2007/09/19: add a new feature alignment to deal with the problem\r
+* of aligning fractional structures (e.g. protein\r
+* interfaces).\r
+*************************************************************************\r
+ \r
+ program compares\r
+ PARAMETER(nmax=5000)\r
+ PARAMETER(nmax2=10000)\r
+\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/alignrst/invmap0(nmax)\r
+ common/length/nseq1,nseq2\r
+ common/d0/d0,anseq\r
+ common/d0min/d0_min\r
+ common/d00/d00,d002\r
+\r
+ character*100 fnam,pdb(100),outname\r
+ character*3 aa(-1:20),aanam,ss1(nmax),ss2(nmax)\r
+ character*100 s,du\r
+ character*200 outnameall_tmp,outnameall\r
+ character seq1(0:nmax),seq2(0:nmax)\r
+ character aseq1(nmax2),aseq2(nmax2),aseq3(nmax2)\r
+\r
+ dimension xx(nmax),yy(nmax),zz(nmax)\r
+ dimension m1(nmax),m2(nmax)\r
+ dimension xtm1(nmax),ytm1(nmax),ztm1(nmax)\r
+ dimension xtm2(nmax),ytm2(nmax),ztm2(nmax)\r
+ common/init/invmap_i(nmax)\r
+\r
+ common/TM/TM,TMmax\r
+ common/n1n2/n1(nmax),n2(nmax)\r
+ common/d8/d8\r
+ common/initial4/mm1(nmax),mm2(nmax)\r
+\r
+ccc RMSD:\r
+ double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)\r
+ double precision u(3,3),t(3),rms,drms !armsd is real\r
+ data w /nmax*1.0/\r
+ccc \r
+\r
+ data aa/ 'BCK','GLY','ALA','SER','CYS','VAL','THR','ILE',\r
+ & 'PRO','MET','ASP','ASN','LEU',\r
+ & 'LYS','GLU','GLN','ARG',\r
+ & 'HIS','PHE','TYR','TRP','CYX'/\r
+ character*1 slc(-1:20)\r
+ data slc/'X','G','A','S','C','V','T','I',\r
+ & 'P','M','D','N','L','K','E','Q','R',\r
+ & 'H','F','Y','W','C'/\r
+\r
+ call getarg(1,fnam)\r
+ if(fnam.eq.' '.or.fnam.eq.'?'.or.fnam.eq.'-h')then\r
+ write(*,*)\r
+ write(*,*)'Brief instruction for running TM-align program:'\r
+ write(*,*)'(For detail: Zhang & Skolnick, Nucl. Acid Res.',\r
+ & '2005 33, 2303)'\r
+ write(*,*)\r
+ write(*,*)'1. Align ''structure.pdb'' to ''target.pdb'''\r
+ write(*,*)' (By default, TM-score is normalized by the ',\r
+ & 'length of ''target.pdb'')'\r
+ write(*,*)' >TMalign structure.pdb target.pdb'\r
+ write(*,*)\r
+ write(*,*)'2. Run TM-align and output the superposition ',\r
+ & 'to ''TM.sup'' and ''TM.sup_all'':'\r
+ write(*,*)' >TMalign structure.pdb target.pdb -o TM.sup'\r
+ write(*,*)' To view the superimposed structures of the',\r
+ & ' aligned regions by rasmol:'\r
+ write(*,*)' >rasmol -script TM.sup)'\r
+ write(*,*)' To view the superimposed structures of all',\r
+ & ' regions by rasmol:'\r
+ write(*,*)' >rasmol -script TM.sup_all)'\r
+ write(*,*)\r
+ write(*,*)'3. If you want TM-score normalized by ',\r
+ & 'an assigned length, e.g. 100 aa:'\r
+ write(*,*)' >TMalign structure.pdb target.pdb -L 100'\r
+ write(*,*)' If you want TM-score normalized by the ',\r
+ & 'average length of two structures:'\r
+ write(*,*)' >TMalign structure.pdb target.pdb -a'\r
+ write(*,*)' If you want TM-score normalized by the ',\r
+ & 'shorter length of two structures:'\r
+ write(*,*)' >TMalign structure.pdb target.pdb -b'\r
+ write(*,*)' If you want TM-score normalized by the ',\r
+ & 'longer length of two structures:'\r
+ write(*,*)' >TMalign structure.pdb target.pdb -c'\r
+ write(*,*)\r
+c write(*,*)'5. If you want to set a minimum cutoff for d0, ',\r
+c & 'e.g. d0>3.0'\r
+c write(*,*)' (By default d0>0.5, this option need ',\r
+c & 'be considered only when L<35 aa)'\r
+c write(*,*)' >TMalign structure.pdb target.pdb -dmin 3.0'\r
+c write(*,*)\r
+ write(*,*)'(All above options does not change the ',\r
+ & 'final structure alignment result)'\r
+ write(*,*)\r
+ goto 9999\r
+ endif\r
+\r
+******* options ----------->\r
+ m_out=-1 !decided output\r
+ m_fix=-1 !fixed length-scale only for output\r
+ m_ave=-1 !using average length\r
+ m_d0_min=-1 !diminum d0 for search\r
+ m_d0=-1 !given d0 for both search and output\r
+ narg=iargc()\r
+ i=0\r
+ j=0\r
+ 115 continue\r
+ i=i+1\r
+ call getarg(i,fnam)\r
+ if(fnam.eq.'-o')then\r
+ m_out=1\r
+ i=i+1\r
+ call getarg(i,outname)\r
+ elseif(fnam.eq.'-L')then !change both L_all and d0\r
+ m_fix=1\r
+ i=i+1\r
+ call getarg(i,fnam)\r
+ read(fnam,*)L_fix\r
+ elseif(fnam.eq.'-dmin')then\r
+ m_d0_min=1\r
+ i=i+1\r
+ call getarg(i,fnam)\r
+ read(fnam,*)d0_min_input\r
+ elseif(fnam.eq.'-d0')then\r
+ m_d0=1\r
+ i=i+1\r
+ call getarg(i,fnam)\r
+ read(fnam,*)d0_fix\r
+ elseif(fnam.eq.'-a')then ! this will change the superposed output but not the alignment\r
+ m_ave=1\r
+ i=i+1\r
+ elseif(fnam.eq.'-b')then\r
+ m_ave=2\r
+ i=i+1\r
+ elseif(fnam.eq.'-c')then\r
+ m_ave=3\r
+ i=i+1\r
+ else\r
+ j=j+1\r
+ pdb(j)=fnam\r
+ endif\r
+ if(i.lt.narg)goto 115\r
+ \r
+ccccccccc read data from first CA file:\r
+ open(unit=10,file=pdb(1),status='old')\r
+ i=0\r
+ do while (.true.)\r
+ read(10,9001,end=1010) s\r
+ if(i.gt.0.and.s(1:3).eq.'TER')goto 1010\r
+ if(s(1:3).eq.'ATO')then\r
+ if(s(13:16).eq.'CA '.or.s(13:16).eq.' CA '.or\r
+ & .s(13:16).eq.' CA')then\r
+ if(s(17:17).eq.' '.or.s(17:17).eq.'A')then\r
+ i=i+1\r
+ read(s,9000)du,aanam,du,mm1(i),du,\r
+ $ xa(1,i,0),xa(2,i,0),xa(3,i,0)\r
+ do j=-1,20\r
+ if(aanam.eq.aa(j))seq1(i)=slc(j)\r
+ enddo\r
+ ss1(i)=aanam\r
+ if(i.ge.nmax)goto 1010\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+ 1010 continue\r
+ 9000 format(A17,A3,A2,i4,A4,3F8.3)\r
+ 9001 format(A100)\r
+ close(10)\r
+ nseq1=i\r
+c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+\r
+ccccccccc read data from the second CA file:\r
+ open(unit=10,file=pdb(2),status='old')\r
+ i=0\r
+ do while (.true.)\r
+ read(10,9001,end=1011) s\r
+ if(i.gt.0.and.s(1:3).eq.'TER')goto 1011\r
+ if(s(1:3).eq.'ATO')then\r
+ if(s(13:16).eq.'CA '.or.s(13:16).eq.' CA '.or.\r
+ & s(13:16).eq.' CA')then\r
+ if(s(17:17).eq.' '.or.s(17:17).eq.'A')then\r
+ i=i+1\r
+ read(s,9000)du,aanam,du,mm2(i),du,\r
+ $ xa(1,i,1),xa(2,i,1),xa(3,i,1)\r
+ do j=-1,20\r
+ if(aanam.eq.aa(j))seq2(i)=slc(j)\r
+ enddo\r
+ ss2(i)=aanam\r
+ if(i.ge.nmax)goto 1011\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+ 1011 continue\r
+ close(10)\r
+ nseq2=i\r
+c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+\r
+*!!! Scale of TM-score in search is based on the smaller protein --------->\r
+ d0_min=0.5\r
+ if(m_d0_min.eq.1)then\r
+ d0_min=d0_min_input !for search\r
+ endif\r
+ anseq_min=min(nseq1,nseq2)\r
+ anseq=anseq_min !length for defining TMscore in search\r
+ d8=1.5*anseq_min**0.3+3.5 !remove pairs with dis>d8 during search & final\r
+ if(anseq.gt.15)then\r
+ d0=1.24*(anseq-15)**(1.0/3.0)-1.8 !scale for defining TM-score\r
+ else\r
+ d0=d0_min\r
+ endif\r
+ if(d0.lt.d0_min)d0=d0_min\r
+ if(m_d0.eq.1)d0=d0_fix\r
+ d00=d0 !for quickly calculate TM-score in searching\r
+ if(d00.gt.8)d00=8\r
+ if(d00.lt.4.5)d00=4.5\r
+ d002=d00**2\r
+ nseq=max(nseq1,nseq2)\r
+ do i=1,nseq\r
+ n1(i)=i\r
+ n2(i)=i\r
+ enddo\r
+ \r
+***** do alignment **************************\r
+ CALL super_align !to find invmap(j)\r
+ \r
+************************************************************\r
+*** resuperpose to find residues of dis<d8 ------------------------>\r
+ n_al=0\r
+ do j=1,nseq2\r
+ if(invmap0(j).gt.0)then\r
+ i=invmap0(j)\r
+ n_al=n_al+1\r
+ xtm1(n_al)=xa(1,i,0)\r
+ ytm1(n_al)=xa(2,i,0)\r
+ ztm1(n_al)=xa(3,i,0)\r
+ xtm2(n_al)=xa(1,j,1)\r
+ ytm2(n_al)=xa(2,j,1)\r
+ ztm2(n_al)=xa(3,j,1)\r
+ m1(n_al)=i !for recording residue order\r
+ m2(n_al)=j\r
+ endif\r
+ enddo\r
+ d0_input=d0\r
+ call TMscore8(d0_input,n_al,xtm1,ytm1,ztm1,n1,n_al,\r
+ & xtm2,ytm2,ztm2,n2,TM,Rcomm,Lcomm) !TM-score with dis<d8 only\r
+\r
+*!!! Output TM-score is based on the second protein------------------>\r
+ d0_min=0.5 !for output\r
+ anseq=nseq2 !length for defining final TMscore\r
+ if(m_ave.eq.1)anseq=(nseq1+nseq2)/2.0 !<L>\r
+ if(m_ave.eq.2)anseq=min(nseq1,nseq2)\r
+ if(m_ave.eq.3)anseq=max(nseq1,nseq2)\r
+ if(anseq.lt.anseq_min)anseq=anseq_min\r
+ if(m_fix.eq.1)anseq=L_fix !input length\r
+ if(anseq.gt.15)then\r
+ d0=1.24*(anseq-15)**(1.0/3.0)-1.8 !scale for defining TM-score\r
+ else\r
+ d0=d0_min\r
+ endif\r
+ if(d0.lt.d0_min)d0=d0_min\r
+ if(m_d0.eq.1)d0=d0_fix\r
+ \r
+*** remove dis>d8 in normal TM-score calculation for final report----->\r
+ j=0\r
+ n_eq=0\r
+ do i=1,n_al\r
+ dis2=sqrt((xtm1(i)-xtm2(i))**2+(ytm1(i)-ytm2(i))**2+\r
+ & (ztm1(i)-ztm2(i))**2)\r
+ if(dis2.le.d8)then\r
+ j=j+1\r
+ xtm1(j)=xtm1(i)\r
+ ytm1(j)=ytm1(i)\r
+ ztm1(j)=ztm1(i)\r
+ xtm2(j)=xtm2(i)\r
+ ytm2(j)=ytm2(i)\r
+ ztm2(j)=ztm2(i)\r
+ m1(j)=m1(i)\r
+ m2(j)=m2(i)\r
+ if(ss1(m1(i)).eq.ss2(m2(i)))then\r
+ n_eq=n_eq+1\r
+ endif\r
+ endif\r
+ enddo\r
+ seq_id=float(n_eq)/(n_al+0.00000001)\r
+ n8_al=j\r
+ d0_input=d0\r
+ call TMscore(d0_input,n8_al,xtm1,ytm1,ztm1,n1,n8_al,\r
+ & xtm2,ytm2,ztm2,n2,TM8,Rcomm,Lcomm) !normal TMscore\r
+ rmsd8_al=Rcomm\r
+ TM8=TM8*n8_al/anseq !TM-score after cutoff\r
+ \r
+********* for output summary ******************************\r
+ write(*,*)\r
+ write(*,*)'*****************************************************',\r
+ & '*********************'\r
+ write(*,*)'* TM-align ',\r
+ & ' *'\r
+ write(*,*)'* A protein structural alignment algorithm based on T',\r
+ & 'M-score *'\r
+ write(*,*)'* Reference: Y. Zhang and J. Skolnick, Nucl. Acids Re',\r
+ & 's. 2005 33, 2302-9 *'\r
+ write(*,*)'* Comments on the program, please email to: yzhang@ku',\r
+ & '.edu *'\r
+ write(*,*)'*****************************************************',\r
+ & '*********************'\r
+ write(*,*)\r
+ write(*,101)pdb(1),nseq1\r
+ 101 format('Chain 1:',A10,' Size=',I4)\r
+ write(*,102)pdb(2),nseq2,int(anseq)\r
+ 102 format('Chain 2:',A10,' Size=',I4,\r
+ & ' (TM-score is normalized by ',I4,')')\r
+ write(*,*)\r
+ write(*,103)n8_al,rmsd8_al,TM8,seq_id\r
+ 103 format('Aligned length=',I4,', RMSD=',f6.2,\r
+ & ', TM-score=',f7.5,', ID=',f5.3)\r
+ write(*,*)\r
+\r
+********* extract rotation matrix ------------>\r
+ L=0\r
+ do i=1,n8_al\r
+ k=m1(i)\r
+ L=L+1\r
+ r_1(1,L)=xa(1,k,0)\r
+ r_1(2,L)=xa(2,k,0)\r
+ r_1(3,L)=xa(3,k,0)\r
+ r_2(1,L)=xtm1(i)\r
+ r_2(2,L)=ytm1(i)\r
+ r_2(3,L)=ztm1(i)\r
+ enddo\r
+ if(L.gt.3)then\r
+ call u3b(w,r_1,r_2,L,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ armsd=dsqrt(rms/L)\r
+ write(*,*)'-------- rotation matrix to rotate Chain-1 to ',\r
+ & 'Chain-2 ------'\r
+ write(*,*)'i t(i) u(i,1) u(i,2) ',\r
+ & ' u(i,3)'\r
+ do i=1,3\r
+ write(*,204)i,t(i),u(i,1),u(i,2),u(i,3)\r
+ enddo\r
+c do i=1,nseq1\r
+c ax=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0)\r
+c ay=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0)\r
+c az=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0)\r
+c enddo\r
+ write(*,*)\r
+ endif\r
+ 204 format(I2,f18.10,f15.10,f15.10,f15.10)\r
+ \r
+********* for output superposition ******************************\r
+ if(m_out.eq.1)then\r
+ 1237 format('ATOM ',i5,' CA ',A3,I6,4X,3F8.3)\r
+ 1238 format('TER')\r
+ 1239 format('CONECT',I5,I5)\r
+ 900 format(A)\r
+ 901 format('select atomno=',I4)\r
+ 104 format('REMARK Chain 1:',A10,' Size=',I4)\r
+ 105 format('REMARK Chain 2:',A10,' Size=',I4,\r
+ & ' (TM-score is normalized by ',I4,')')\r
+ 106 format('REMARK Aligned length=',I4,', RMSD=',f6.2,\r
+ & ', TM-score=',f7.5,', ID=',f5.3)\r
+ OPEN(unit=7,file=outname,status='unknown') !pdb1.aln + pdb2.aln\r
+*** script:\r
+ write(7,900)'load inline'\r
+ write(7,900)'select atomno<2000'\r
+ write(7,900)'wireframe .45'\r
+ write(7,900)'select none'\r
+ write(7,900)'select atomno>2000'\r
+ write(7,900)'wireframe .20'\r
+ write(7,900)'color white'\r
+ do i=1,n8_al\r
+ dis2=sqrt((xtm1(i)-xtm2(i))**2+\r
+ & (ytm1(i)-ytm2(i))**2+(ztm1(i)-ztm2(i))**2)\r
+ if(dis2.le.5)then\r
+ write(7,901)m1(i)\r
+ write(7,900)'color red'\r
+ write(7,901)2000+m2(i)\r
+ write(7,900)'color red'\r
+ endif\r
+ enddo\r
+ write(7,900)'select all'\r
+ write(7,900)'exit'\r
+ write(7,104)pdb(1),nseq1\r
+ write(7,105)pdb(2),nseq2,int(anseq)\r
+ write(7,106)n8_al,rmsd8_al,TM8,seq_id\r
+*** chain1:\r
+ do i=1,n8_al\r
+ write(7,1237)m1(i),ss1(m1(i)),mm1(m1(i)),\r
+ & xtm1(i),ytm1(i),ztm1(i)\r
+ enddo\r
+ write(7,1238) !TER\r
+ do i=2,n8_al\r
+ write(7,1239)m1(i-1),m1(i) !connect atoms\r
+ enddo\r
+*** chain2:\r
+ do i=1,n8_al\r
+ write(7,1237)2000+m2(i),ss2(m2(i)),mm2(m2(i)),\r
+ $ xtm2(i),ytm2(i),ztm2(i)\r
+ enddo\r
+ write(7,1238)\r
+ do i=2,n8_al\r
+ write(7,1239)2000+m2(i-1),2000+m2(i)\r
+ enddo\r
+ close(7)\r
+ccc \r
+ k=0\r
+ outnameall_tmp=outname//'_all'\r
+ outnameall=''\r
+ do i=1,200\r
+ if(outnameall_tmp(i:i).ne.' ')then\r
+ k=k+1\r
+ outnameall(k:k)=outnameall_tmp(i:i)\r
+ endif\r
+ enddo\r
+ OPEN(unit=8,file=outnameall,status='unknown') !pdb1.aln + pdb2.aln\r
+*** script:\r
+ write(8,900)'load inline'\r
+ write(8,900)'select atomno<2000'\r
+ write(8,900)'wireframe .45'\r
+ write(8,900)'select none'\r
+ write(8,900)'select atomno>2000'\r
+ write(8,900)'wireframe .20'\r
+ write(8,900)'color white'\r
+ do i=1,n8_al\r
+ dis2=sqrt((xtm1(i)-xtm2(i))**2+\r
+ & (ytm1(i)-ytm2(i))**2+(ztm1(i)-ztm2(i))**2)\r
+ if(dis2.le.5)then\r
+ write(8,901)m1(i)\r
+ write(8,900)'color red'\r
+ write(8,901)2000+m2(i)\r
+ write(8,900)'color red'\r
+ endif\r
+ enddo\r
+ write(8,900)'select all'\r
+ write(8,900)'exit'\r
+ write(8,104)pdb(1),nseq1\r
+ write(8,105)pdb(2),nseq2,int(anseq)\r
+ write(8,106)n8_al,rmsd8_al,TM8,seq_id\r
+*** chain1:\r
+ do i=1,nseq1\r
+ ax=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0)\r
+ ay=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0)\r
+ az=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0)\r
+ write(8,1237)i,ss1(i),mm1(i),ax,ay,az\r
+ enddo\r
+ write(8,1238) !TER\r
+ do i=2,nseq1\r
+ write(8,1239)i-1,i\r
+ enddo\r
+*** chain2:\r
+ do i=1,nseq2\r
+ write(8,1237)2000+i,ss2(i),mm2(i),\r
+ $ xa(1,i,1),xa(2,i,1),xa(3,i,1)\r
+ enddo\r
+ write(8,1238)\r
+ do i=2,nseq2\r
+ write(8,1239)2000+i-1,2000+i\r
+ enddo\r
+ close(8)\r
+ endif\r
+*^^^^^^^^^^^^^^^^^^ output finished ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+\r
+************ output aligned sequences **************************\r
+ ii=0\r
+ i1_old=1\r
+ i2_old=1\r
+ do i=1,n8_al\r
+ do j=i1_old,m1(i)-1\r
+ ii=ii+1\r
+ aseq1(ii)=seq1(j)\r
+ aseq2(ii)='-'\r
+ aseq3(ii)=' '\r
+ enddo\r
+ do j=i2_old,m2(i)-1\r
+ ii=ii+1\r
+ aseq1(ii)='-'\r
+ aseq2(ii)=seq2(j)\r
+ aseq3(ii)=' '\r
+ enddo\r
+ ii=ii+1\r
+ aseq1(ii)=seq1(m1(i))\r
+ aseq2(ii)=seq2(m2(i))\r
+ dis2=sqrt((xtm1(i)-xtm2(i))**2+\r
+ & (ytm1(i)-ytm2(i))**2+(ztm1(i)-ztm2(i))**2)\r
+ if(dis2.le.5)then\r
+ aseq3(ii)=':'\r
+ else\r
+ aseq3(ii)='.'\r
+ endif\r
+ i1_old=m1(i)+1\r
+ i2_old=m2(i)+1\r
+ enddo\r
+ do i=i1_old,nseq1\r
+ ii=ii+1\r
+ aseq1(ii)=seq1(i)\r
+ aseq2(ii)='-'\r
+ aseq3(ii)=' '\r
+ enddo\r
+ do i=i2_old,nseq2\r
+ ii=ii+1\r
+ aseq1(ii)='-'\r
+ aseq2(ii)=seq2(i)\r
+ aseq3(ii)=' '\r
+ enddo\r
+ write(*,50)\r
+ 50 format('(":" denotes the residue pairs of distance < 5.0 ',\r
+ & 'Angstrom)')\r
+ write(*,10)(aseq1(i),i=1,ii)\r
+ write(*,10)(aseq3(i),i=1,ii)\r
+ write(*,10)(aseq2(i),i=1,ii)\r
+ 10 format(10000A1)\r
+ write(*,*)\r
+\r
+c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ 9999 END\r
+\r
+***********************************************************************\r
+***********************************************************************\r
+* Structure superposition\r
+***********************************************************************\r
+***********************************************************************\r
+***********************************************************************\r
+ SUBROUTINE super_align\r
+ PARAMETER(nmax=5000)\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/length/nseq1,nseq2\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/alignrst/invmap0(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/TM/TM,TMmax\r
+ common/init/invmap_i(nmax)\r
+ dimension gapp(100)\r
+\r
+ TMmax=0\r
+ n_gapp=2\r
+ gapp(1)=-0.6\r
+ gapp(2)=0\r
+\r
+c n_gapp=11\r
+c do i=1,n_gapp\r
+c gapp(i)=-(n_gapp-i)\r
+c enddo\r
+\r
+*11111111111111111111111111111111111111111111111111111111\r
+* get initial alignment from gapless threading\r
+**********************************************************\r
+ call get_initial !gapless threading\r
+ do i=1,nseq2\r
+ invmap(i)=invmap_i(i) !with highest zcore\r
+ enddo\r
+ call get_score !TM, matrix score(i,j)\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+\r
+*****************************************************************\r
+* initerative alignment, for different gap_open:\r
+*****************************************************************\r
+ DO 111 i_gapp=1,n_gapp !different gap panalties\r
+ GAP_OPEN=gapp(i_gapp) !gap panalty\r
+ do 222 id=1,30 !maximum interation is 200\r
+ call DP(NSEQ1,NSEQ2) !produce alignment invmap(j)\r
+* Input: score(i,j), and gap_open\r
+* Output: invmap(j)\r
+\r
+ call get_score !calculate TM-score, score(i,j)\r
+c record the best alignment in whole search ---------->\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+ if(id.gt.1)then\r
+ diff=abs(TM-TM_old)\r
+ if(diff.lt.0.000001)goto 33\r
+ endif\r
+ TM_old=TM\r
+ 222 continue\r
+ 33 continue\r
+ 111 continue\r
+\r
+*222222222222222222222222222222222222222222222222222222222\r
+* get initial alignment from secondary structure alignment\r
+**********************************************************\r
+ call get_initial2 !DP for secondary structure\r
+ do i=1,nseq2\r
+ invmap(i)=invmap_i(i) !with highest zcore\r
+ enddo\r
+ call get_score !TM, score(i,j)\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+\r
+*****************************************************************\r
+* initerative alignment, for different gap_open:\r
+*****************************************************************\r
+ DO 1111 i_gapp=1,n_gapp !different gap panalties\r
+ GAP_OPEN=gapp(i_gapp) !gap panalty\r
+ do 2222 id=1,30 !maximum interation is 200\r
+ call DP(NSEQ1,NSEQ2) !produce alignment invmap(j)\r
+* Input: score(i,j), and gap_open\r
+* Output: invmap(j)\r
+\r
+ call get_score !calculate TM-score, score(i,j)\r
+c write(*,21)gap_open,rmsd_al,n_al,TM\r
+c record the best alignment in whole search ---------->\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+ if(id.gt.1)then\r
+ diff=abs(TM-TM_old)\r
+ if(diff.lt.0.000001)goto 333\r
+ endif\r
+ TM_old=TM\r
+ 2222 continue\r
+ 333 continue\r
+ 1111 continue\r
+ \r
+*333333333333333333333333333333333333333333333333333333333333\r
+* get initial alignment from invmap0+SS\r
+*************************************************************\r
+ call get_initial3 !invmap0+SS\r
+ do i=1,nseq2\r
+ invmap(i)=invmap_i(i) !with highest zcore\r
+ enddo\r
+ call get_score !TM, score(i,j)\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+\r
+*****************************************************************\r
+* initerative alignment, for different gap_open:\r
+*****************************************************************\r
+ DO 1110 i_gapp=1,n_gapp !different gap panalties\r
+ GAP_OPEN=gapp(i_gapp) !gap panalty\r
+ do 2220 id=1,30 !maximum interation is 200\r
+ call DP(NSEQ1,NSEQ2) !produce alignment invmap(j)\r
+* Input: score(i,j), and gap_open\r
+* Output: invmap(j)\r
+\r
+ call get_score !calculate TM-score, score(i,j)\r
+c write(*,21)gap_open,rmsd_al,n_al,TM\r
+c record the best alignment in whole search ---------->\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+ if(id.gt.1)then\r
+ diff=abs(TM-TM_old)\r
+ if(diff.lt.0.000001)goto 330\r
+ endif\r
+ TM_old=TM\r
+ 2220 continue\r
+ 330 continue\r
+ 1110 continue\r
+\r
+*444444444444444444444444444444444444444444444444444444444\r
+* get initial alignment of pieces from gapless threading\r
+**********************************************************\r
+ call get_initial4 !gapless threading\r
+ do i=1,nseq2\r
+ invmap(i)=invmap_i(i) !with highest zcore\r
+ enddo\r
+ call get_score !TM, matrix score(i,j)\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+\r
+*****************************************************************\r
+* initerative alignment, for different gap_open:\r
+*****************************************************************\r
+ DO 44 i_gapp=2,n_gapp !different gap panalties\r
+ GAP_OPEN=gapp(i_gapp) !gap panalty\r
+ do 444 id=1,2 !maximum interation is 200\r
+ call DP(NSEQ1,NSEQ2) !produce alignment invmap(j)\r
+* Input: score(i,j), and gap_open\r
+* Output: invmap(j)\r
+ \r
+ call get_score !calculate TM-score, score(i,j)\r
+c record the best alignment in whole search ---------->\r
+ if(TM.gt.TMmax)then\r
+ TMmax=TM\r
+ do j=1,nseq2\r
+ invmap0(j)=invmap(j)\r
+ enddo\r
+ endif\r
+ 444 continue\r
+ 44 continue\r
+\r
+c^^^^^^^^^^^^^^^ best alignment invmap0(j) found ^^^^^^^^^^^^^^^^^^\r
+ RETURN\r
+ END\r
+\r
+**************************************************************\r
+* get initial alignment invmap0(i) from gapless threading\r
+**************************************************************\r
+ subroutine get_initial\r
+ PARAMETER(nmax=5000)\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/length/nseq1,nseq2\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/alignrst/invmap0(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/TM/TM,TMmax\r
+ common/init/invmap_i(nmax)\r
+\r
+ aL=min(nseq1,nseq2)\r
+ idel=aL/2.5 !minimum size of considered fragment\r
+ if(idel.le.5)idel=5\r
+ n1=-nseq2+idel\r
+ n2=nseq1-idel\r
+ GL_max=0\r
+ do ishift=n1,n2\r
+ L=0\r
+ do j=1,nseq2\r
+ i=j+ishift\r
+ if(i.ge.1.and.i.le.nseq1)then\r
+ L=L+1\r
+ invmap(j)=i\r
+ else\r
+ invmap(j)=-1\r
+ endif\r
+ enddo\r
+ if(L.ge.idel)then\r
+ call get_GL(GL)\r
+ if(GL.gt.GL_max)then\r
+ GL_max=GL\r
+ do i=1,nseq2\r
+ invmap_i(i)=invmap(i)\r
+ enddo\r
+ endif\r
+ endif\r
+ enddo\r
+\r
+ return\r
+ end\r
+\r
+**************************************************************\r
+* get initial alignment invmap0(i) from secondary structure\r
+**************************************************************\r
+ subroutine get_initial2\r
+ PARAMETER(nmax=5000)\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/length/nseq1,nseq2\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/alignrst/invmap0(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/TM/TM,TMmax\r
+ common/sec/isec(nmax),jsec(nmax)\r
+ common/init/invmap_i(nmax)\r
+\r
+********** assign secondary structures ***************\r
+c 1->coil, 2->helix, 3->turn, 4->strand\r
+ do i=1,nseq1\r
+ isec(i)=1\r
+ j1=i-2\r
+ j2=i-1\r
+ j3=i\r
+ j4=i+1\r
+ j5=i+2\r
+ if(j1.ge.1.and.j5.le.nseq1)then\r
+ dis13=diszy(0,j1,j3)\r
+ dis14=diszy(0,j1,j4)\r
+ dis15=diszy(0,j1,j5)\r
+ dis24=diszy(0,j2,j4)\r
+ dis25=diszy(0,j2,j5)\r
+ dis35=diszy(0,j3,j5)\r
+ isec(i)=make_sec(dis13,dis14,dis15,dis24,dis25,dis35)\r
+ endif\r
+ enddo\r
+ do i=1,nseq2\r
+ jsec(i)=1\r
+ j1=i-2\r
+ j2=i-1\r
+ j3=i\r
+ j4=i+1\r
+ j5=i+2\r
+ if(j1.ge.1.and.j5.le.nseq2)then\r
+ dis13=diszy(1,j1,j3)\r
+ dis14=diszy(1,j1,j4)\r
+ dis15=diszy(1,j1,j5)\r
+ dis24=diszy(1,j2,j4)\r
+ dis25=diszy(1,j2,j5)\r
+ dis35=diszy(1,j3,j5)\r
+ jsec(i)=make_sec(dis13,dis14,dis15,dis24,dis25,dis35)\r
+ endif\r
+ enddo\r
+ call smooth !smooth the assignment\r
+\r
+********** score matrix **************************\r
+ do i=1,nseq1\r
+ do j=1,nseq2\r
+ if(isec(i).eq.jsec(j))then\r
+ score(i,j)=1\r
+ else\r
+ score(i,j)=0\r
+ endif\r
+ enddo\r
+ enddo\r
+\r
+********** find initial alignment: invmap(j) ************\r
+ gap_open=-1.0 !should be -1\r
+ call DP(NSEQ1,NSEQ2) !produce alignment invmap(j)\r
+ do i=1,nseq2\r
+ invmap_i(i)=invmap(i)\r
+ enddo\r
+\r
+*^^^^^^^^^^^^ initial alignment done ^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ end\r
+\r
+**************************************************************\r
+* get initial alignment invmap0(i) from secondary structure \r
+* and previous alignments\r
+**************************************************************\r
+ subroutine get_initial3\r
+ PARAMETER(nmax=5000)\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/length/nseq1,nseq2\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/alignrst/invmap0(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/TM/TM,TMmax\r
+ common/sec/isec(nmax),jsec(nmax)\r
+ common/init/invmap_i(nmax)\r
+\r
+********** score matrix **************************\r
+ do i=1,nseq2\r
+ invmap(i)=invmap0(i)\r
+ enddo\r
+ call get_score1 !get score(i,j) using RMSD martix\r
+ do i=1,nseq1\r
+ do j=1,nseq2\r
+ if(isec(i).eq.jsec(j))then\r
+ score(i,j)=0.5+score(i,j)\r
+ else\r
+ score(i,j)=score(i,j)\r
+ endif\r
+ enddo\r
+ enddo\r
+\r
+********** find initial alignment: invmap(j) ************\r
+ gap_open=-1.0 !should be -1\r
+ call DP(NSEQ1,NSEQ2) !produce alignment invmap(j)\r
+ do i=1,nseq2\r
+ invmap_i(i)=invmap(i)\r
+ enddo\r
+\r
+*^^^^^^^^^^^^ initial alignment done ^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ end\r
+\r
+**************************************************************\r
+* get initial alignment invmap0(i) from fragment gapless threading\r
+**************************************************************\r
+ subroutine get_initial4\r
+ PARAMETER(nmax=5000)\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/length/nseq1,nseq2\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/alignrst/invmap0(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/TM/TM,TMmax\r
+ common/init/invmap_i(nmax)\r
+ common/initial4/mm1(nmax),mm2(nmax)\r
+ logical contin\r
+\r
+ dimension ifr2(2,nmax,nmax),Lfr2(2,nmax),Lfr_max2(2),i_fr2(2)\r
+ dimension ifr(nmax)\r
+ dimension mm(2,nmax)\r
+ \r
+ fra_min=4 !>=4,minimum fragment for search\r
+ fra_min1=fra_min-1 !cutoff for shift, save time\r
+ dcu0=3.85\r
+ dcu_min=3.65\r
+\r
+ccc Find the smallest continuous fragments -------->\r
+ do i=1,nseq1\r
+ mm(1,i)=mm1(i)\r
+ enddo\r
+ do i=1,nseq2\r
+ mm(2,i)=mm2(i)\r
+ enddo\r
+ do k=1,2\r
+ dcu=dcu0\r
+ if(k.eq.1)then\r
+ nseq0=nseq1\r
+ r_min=nseq1/3.0 !minimum fragment, in case too small protein\r
+ else\r
+ nseq0=nseq2\r
+ r_min=nseq2/3.0 !minimum fragment, in case too small protein\r
+ endif\r
+ if(r_min.gt.fra_min)r_min=fra_min\r
+ 20 nfr=1 !number of fragments\r
+ j=1 !number of residue at nf-fragment\r
+ ifr2(k,nfr,j)=1 !what residue\r
+ Lfr2(k,nfr)=j !length of the fragment\r
+ do i=2,nseq0\r
+ dis=diszy(k-1,i-1,i)\r
+ contin=.false.\r
+ if(dcu.gt.dcu0)then\r
+ if(dis.lt.dcu)then\r
+ if(dis.gt.dcu_min)then\r
+ contin=.true.\r
+ endif\r
+ endif\r
+ elseif(mm(k,i).eq.(mm(k,i-1)+1))then\r
+ if(dis.lt.dcu)then\r
+ if(dis.gt.dcu_min)then\r
+ contin=.true.\r
+ endif\r
+ endif\r
+ endif\r
+ if(contin)then\r
+ j=j+1\r
+ ifr2(k,nfr,j)=i\r
+ Lfr2(k,nfr)=j\r
+ else\r
+ nfr=nfr+1\r
+ j=1\r
+ ifr2(k,nfr,j)=i\r
+ Lfr2(k,nfr)=j\r
+ endif\r
+ enddo\r
+ Lfr_max=0\r
+ i_fr2(k)=1 !ID of the maximum piece\r
+ do i=1,nfr\r
+ if(Lfr_max.lt.Lfr2(k,i))then\r
+ Lfr_max=Lfr2(k,i)\r
+ i_fr2(k)=i\r
+ endif\r
+ enddo\r
+ if(Lfr_max.lt.r_min)then\r
+ dcu=1.1*dcu\r
+ goto 20\r
+ endif\r
+ enddo\r
+c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ \r
+ccc select what piece will be used (this may araise ansysmetry, but\r
+ccc only when L1=L2 and Lfr1=Lfr2 and L1 ne Lfr1\r
+ccc if L1=Lfr1 and L2=Lfr2 (normal proteins), it will be the same as initial1\r
+ mark=1\r
+ if(Lfr2(1,i_fr2(1)).lt.Lfr2(2,i_fr2(2)))then\r
+ mark=1\r
+ elseif(Lfr2(1,i_fr2(1)).gt.Lfr2(2,i_fr2(2)))then\r
+ mark=2\r
+ else !Lfr1=Lfr2\r
+ if(nseq1.le.nseq2)then\r
+ mark=1\r
+ else\r
+ mark=2\r
+ endif\r
+ endif\r
+ccc \r
+ L_fr=Lfr2(mark,i_fr2(mark))\r
+ do i=1,L_fr\r
+ ifr(i)=ifr2(mark,i_fr2(mark),i)\r
+ enddo\r
+ccc \r
+ if(mark.eq.1)then !non-redundant to get_initial1\r
+ nseq0=nseq1\r
+ else\r
+ nseq0=nseq2\r
+ endif\r
+ if(L_fr.eq.nseq0)then\r
+ n1=int(nseq0*0.1) !0\r
+ n2=int(nseq0*0.89) !2\r
+ j=0\r
+ do i=n1,n2\r
+ j=j+1\r
+ ifr(j)=ifr(n1+j)\r
+ enddo\r
+ L_fr=j\r
+ endif\r
+ \r
+ccc get initial ------------->\r
+ if(mark.eq.1)then !nseq1 as the smallest one\r
+ nseq1_=L_fr\r
+ aL=min(nseq1_,nseq2)\r
+ idel=aL/2.5 !minimum size of considered fragment\r
+ if(idel.le.fra_min1)idel=fra_min1\r
+ n1=-nseq2+idel !shift1\r
+ n2=nseq1_-idel !shift2\r
+ GL_max=0\r
+ do ishift=n1,n2\r
+ L=0\r
+ do j=1,nseq2\r
+ i=j+ishift\r
+ if(i.ge.1.and.i.le.nseq1_)then\r
+ L=L+1\r
+ invmap(j)=ifr(i)\r
+ else\r
+ invmap(j)=-1\r
+ endif\r
+ enddo\r
+ if(L.ge.idel)then\r
+ call get_GL(GL)\r
+ if(GL.gt.GL_max)then\r
+ GL_max=GL\r
+ do i=1,nseq2\r
+ invmap_i(i)=invmap(i)\r
+ enddo\r
+ endif\r
+ endif\r
+ enddo\r
+ else !@@@@@@@@@@@@@@@@@@@@\r
+ nseq2_=L_fr\r
+ aL=min(nseq1,nseq2_)\r
+ idel=aL/2.5 !minimum size of considered fragment\r
+ if(idel.le.fra_min1)idel=fra_min1\r
+ n1=-nseq2_+idel\r
+ n2=nseq1-idel\r
+ GL_max=0\r
+ do ishift=n1,n2\r
+ L=0\r
+ do j=1,nseq2\r
+ invmap(j)=-1\r
+ enddo\r
+ do j=1,nseq2_\r
+ i=j+ishift\r
+ if(i.ge.1.and.i.le.nseq1)then\r
+ L=L+1\r
+ invmap(ifr(j))=i\r
+ endif\r
+ enddo\r
+ if(L.ge.idel)then\r
+ call get_GL(GL)\r
+ if(GL.gt.GL_max)then\r
+ GL_max=GL\r
+ do i=1,nseq2\r
+ invmap_i(i)=invmap(i)\r
+ enddo\r
+ endif\r
+ endif\r
+ enddo\r
+ endif\r
+ \r
+ return\r
+ end\r
+\r
+**************************************************************\r
+* smooth the secondary structure assignment\r
+**************************************************************\r
+ subroutine smooth\r
+ PARAMETER(nmax=5000)\r
+ common/sec/isec(nmax),jsec(nmax)\r
+ common/length/nseq1,nseq2\r
+\r
+*** smooth single -------------->\r
+*** --x-- => -----\r
+ do i=1,nseq1\r
+ if(isec(i).eq.2.or.isec(i).eq.4)then\r
+ j=isec(i)\r
+ if(isec(i-2).ne.j)then\r
+ if(isec(i-1).ne.j)then\r
+ if(isec(i+1).ne.j)then\r
+ if(isec(i+1).ne.j)then\r
+ isec(i)=1\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+ do i=1,nseq2\r
+ if(jsec(i).eq.2.or.jsec(i).eq.4)then\r
+ j=jsec(i)\r
+ if(jsec(i-2).ne.j)then\r
+ if(jsec(i-1).ne.j)then\r
+ if(jsec(i+1).ne.j)then\r
+ if(jsec(i+1).ne.j)then\r
+ jsec(i)=1\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+\r
+*** smooth double -------------->\r
+*** --xx-- => ------\r
+ do i=1,nseq1\r
+ if(isec(i).ne.2)then\r
+ if(isec(i+1).ne.2)then\r
+ if(isec(i+2).eq.2)then\r
+ if(isec(i+3).eq.2)then\r
+ if(isec(i+4).ne.2)then\r
+ if(isec(i+5).ne.2)then\r
+ isec(i+2)=1\r
+ isec(i+3)=1\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+\r
+ if(isec(i).ne.4)then\r
+ if(isec(i+1).ne.4)then\r
+ if(isec(i+2).eq.4)then\r
+ if(isec(i+3).eq.4)then\r
+ if(isec(i+4).ne.4)then\r
+ if(isec(i+5).ne.4)then\r
+ isec(i+2)=1\r
+ isec(i+3)=1\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+ do i=1,nseq2\r
+ if(jsec(i).ne.2)then\r
+ if(jsec(i+1).ne.2)then\r
+ if(jsec(i+2).eq.2)then\r
+ if(jsec(i+3).eq.2)then\r
+ if(jsec(i+4).ne.2)then\r
+ if(jsec(i+5).ne.2)then\r
+ jsec(i+2)=1\r
+ jsec(i+3)=1\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+\r
+ if(jsec(i).ne.4)then\r
+ if(jsec(i+1).ne.4)then\r
+ if(jsec(i+2).eq.4)then\r
+ if(jsec(i+3).eq.4)then\r
+ if(jsec(i+4).ne.4)then\r
+ if(jsec(i+5).ne.4)then\r
+ jsec(i+2)=1\r
+ jsec(i+3)=1\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+\r
+*** connect -------------->\r
+*** x-x => xxx\r
+ do i=1,nseq1\r
+ if(isec(i).eq.2)then\r
+ if(isec(i+1).ne.2)then\r
+ if(isec(i+2).eq.2)then\r
+ isec(i+1)=2\r
+ endif\r
+ endif\r
+ endif\r
+\r
+ if(isec(i).eq.4)then\r
+ if(isec(i+1).ne.4)then\r
+ if(isec(i+2).eq.4)then\r
+ isec(i+1)=4\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+ do i=1,nseq2\r
+ if(jsec(i).eq.2)then\r
+ if(jsec(i+1).ne.2)then\r
+ if(jsec(i+2).eq.2)then\r
+ jsec(i+1)=2\r
+ endif\r
+ endif\r
+ endif\r
+\r
+ if(jsec(i).eq.4)then\r
+ if(jsec(i+1).ne.4)then\r
+ if(jsec(i+2).eq.4)then\r
+ jsec(i+1)=4\r
+ endif\r
+ endif\r
+ endif\r
+ enddo\r
+\r
+ return\r
+ end\r
+\r
+*************************************************************\r
+* assign secondary structure:\r
+*************************************************************\r
+ function diszy(i,i1,i2)\r
+ PARAMETER(nmax=5000)\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ diszy=sqrt((xa(1,i1,i)-xa(1,i2,i))**2\r
+ & +(xa(2,i1,i)-xa(2,i2,i))**2\r
+ & +(xa(3,i1,i)-xa(3,i2,i))**2)\r
+ return\r
+ end\r
+\r
+*************************************************************\r
+* assign secondary structure:\r
+*************************************************************\r
+ function make_sec(dis13,dis14,dis15,dis24,dis25,dis35)\r
+ make_sec=1\r
+ delta=2.1\r
+ if(abs(dis15-6.37).lt.delta)then\r
+ if(abs(dis14-5.18).lt.delta)then\r
+ if(abs(dis25-5.18).lt.delta)then\r
+ if(abs(dis13-5.45).lt.delta)then\r
+ if(abs(dis24-5.45).lt.delta)then\r
+ if(abs(dis35-5.45).lt.delta)then\r
+ make_sec=2 !helix\r
+ return\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ delta=1.42\r
+ if(abs(dis15-13).lt.delta)then\r
+ if(abs(dis14-10.4).lt.delta)then\r
+ if(abs(dis25-10.4).lt.delta)then\r
+ if(abs(dis13-6.1).lt.delta)then\r
+ if(abs(dis24-6.1).lt.delta)then\r
+ if(abs(dis35-6.1).lt.delta)then\r
+ make_sec=4 !strand\r
+ return\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ endif\r
+ if(dis15.lt.8)then\r
+ make_sec=3\r
+ endif\r
+\r
+ return\r
+ end\r
+\r
+****************************************************************\r
+* quickly calculate TM-score with given invmap(i) in 3 iterations\r
+****************************************************************\r
+ subroutine get_GL(GL)\r
+ PARAMETER(nmax=5000)\r
+ common/length/nseq1,nseq2\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/d0/d0,anseq\r
+ dimension xtm1(nmax),ytm1(nmax),ztm1(nmax)\r
+ dimension xtm2(nmax),ytm2(nmax),ztm2(nmax)\r
+ common/TM/TM,TMmax\r
+ common/n1n2/n1(nmax),n2(nmax)\r
+ common/d00/d00,d002\r
+\r
+ dimension xo1(nmax),yo1(nmax),zo1(nmax)\r
+ dimension xo2(nmax),yo2(nmax),zo2(nmax)\r
+ dimension dis2(nmax)\r
+\r
+ccc RMSD:\r
+ double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)\r
+ double precision u(3,3),t(3),rms,drms !armsd is real\r
+ data w /nmax*1.0/\r
+ccc \r
+\r
+c calculate RMSD between aligned structures and rotate the structures -->\r
+ n_al=0\r
+ do j=1,NSEQ2\r
+ i=invmap(j) !j aligned to i\r
+ if(i.gt.0)then\r
+ n_al=n_al+1\r
+ r_1(1,n_al)=xa(1,i,0)\r
+ r_1(2,n_al)=xa(2,i,0)\r
+ r_1(3,n_al)=xa(3,i,0)\r
+ r_2(1,n_al)=xa(1,j,1)\r
+ r_2(2,n_al)=xa(2,j,1)\r
+ r_2(3,n_al)=xa(3,j,1)\r
+ xo1(n_al)=xa(1,i,0)\r
+ yo1(n_al)=xa(2,i,0)\r
+ zo1(n_al)=xa(3,i,0)\r
+ xo2(n_al)=xa(1,j,1)\r
+ yo2(n_al)=xa(2,j,1)\r
+ zo2(n_al)=xa(3,j,1)\r
+ endif\r
+ enddo\r
+ call u3b(w,r_1,r_2,n_al,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ GL=0\r
+ do i=1,n_al\r
+ xx=t(1)+u(1,1)*xo1(i)+u(1,2)*yo1(i)+u(1,3)*zo1(i)\r
+ yy=t(2)+u(2,1)*xo1(i)+u(2,2)*yo1(i)+u(2,3)*zo1(i)\r
+ zz=t(3)+u(3,1)*xo1(i)+u(3,2)*yo1(i)+u(3,3)*zo1(i)\r
+ dis2(i)=(xx-xo2(i))**2+(yy-yo2(i))**2+(zz-zo2(i))**2\r
+ GL=GL+1/(1+dis2(i)/(d0**2))\r
+ enddo\r
+ccc for next iteration------------->\r
+ d002t=d002\r
+ 21 j=0\r
+ do i=1,n_al\r
+ if(dis2(i).le.d002t)then\r
+ j=j+1\r
+ r_1(1,j)=xo1(i)\r
+ r_1(2,j)=yo1(i)\r
+ r_1(3,j)=zo1(i)\r
+ r_2(1,j)=xo2(i)\r
+ r_2(2,j)=yo2(i)\r
+ r_2(3,j)=zo2(i)\r
+ endif\r
+ enddo\r
+ if(j.lt.3.and.n_al.gt.3)then\r
+ d002t=d002t+.5\r
+ goto 21\r
+ endif\r
+ L=j\r
+ call u3b(w,r_1,r_2,L,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ G2=0\r
+ do i=1,n_al\r
+ xx=t(1)+u(1,1)*xo1(i)+u(1,2)*yo1(i)+u(1,3)*zo1(i)\r
+ yy=t(2)+u(2,1)*xo1(i)+u(2,2)*yo1(i)+u(2,3)*zo1(i)\r
+ zz=t(3)+u(3,1)*xo1(i)+u(3,2)*yo1(i)+u(3,3)*zo1(i)\r
+ dis2(i)=(xx-xo2(i))**2+(yy-yo2(i))**2+(zz-zo2(i))**2\r
+ G2=G2+1/(1+dis2(i)/(d0**2))\r
+ enddo\r
+ccc for next iteration------------->\r
+ d002t=d002+1\r
+ 22 j=0\r
+ do i=1,n_al\r
+ if(dis2(i).le.d002t)then\r
+ j=j+1\r
+ r_1(1,j)=xo1(i)\r
+ r_1(2,j)=yo1(i)\r
+ r_1(3,j)=zo1(i)\r
+ r_2(1,j)=xo2(i)\r
+ r_2(2,j)=yo2(i)\r
+ r_2(3,j)=zo2(i)\r
+ endif\r
+ enddo\r
+ if(j.lt.3.and.n_al.gt.3)then\r
+ d002t=d002t+.5\r
+ goto 22\r
+ endif\r
+ L=j\r
+ call u3b(w,r_1,r_2,L,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ G3=0\r
+ do i=1,n_al\r
+ xx=t(1)+u(1,1)*xo1(i)+u(1,2)*yo1(i)+u(1,3)*zo1(i)\r
+ yy=t(2)+u(2,1)*xo1(i)+u(2,2)*yo1(i)+u(2,3)*zo1(i)\r
+ zz=t(3)+u(3,1)*xo1(i)+u(3,2)*yo1(i)+u(3,3)*zo1(i)\r
+ dis2(i)=(xx-xo2(i))**2+(yy-yo2(i))**2+(zz-zo2(i))**2\r
+ G3=G3+1/(1+dis2(i)/(d0**2))\r
+ enddo\r
+ if(G2.gt.GL)GL=G2\r
+ if(G3.gt.GL)GL=G3\r
+\r
+c^^^^^^^^^^^^^^^^ GL done ^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ end\r
+\r
+****************************************************************\r
+* with invmap(i) calculate TM-score and martix score(i,j) for rotation \r
+****************************************************************\r
+ subroutine get_score\r
+ PARAMETER(nmax=5000)\r
+ common/length/nseq1,nseq2\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/d0/d0,anseq\r
+ dimension xtm1(nmax),ytm1(nmax),ztm1(nmax)\r
+ dimension xtm2(nmax),ytm2(nmax),ztm2(nmax)\r
+ common/TM/TM,TMmax\r
+ common/n1n2/n1(nmax),n2(nmax)\r
+\r
+ccc RMSD:\r
+ double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)\r
+ double precision u(3,3),t(3),rms,drms !armsd is real\r
+ data w /nmax*1.0/\r
+ccc \r
+\r
+c calculate RMSD between aligned structures and rotate the structures -->\r
+ n_al=0\r
+ do j=1,NSEQ2\r
+ i=invmap(j) !j aligned to i\r
+ if(i.gt.0)then\r
+ n_al=n_al+1\r
+ccc for TM-score:\r
+ xtm1(n_al)=xa(1,i,0) !for TM-score\r
+ ytm1(n_al)=xa(2,i,0)\r
+ ztm1(n_al)=xa(3,i,0)\r
+ xtm2(n_al)=xa(1,j,1)\r
+ ytm2(n_al)=xa(2,j,1)\r
+ ztm2(n_al)=xa(3,j,1)\r
+ccc for rotation matrix:\r
+ r_1(1,n_al)=xa(1,i,0)\r
+ r_1(2,n_al)=xa(2,i,0)\r
+ r_1(3,n_al)=xa(3,i,0)\r
+ endif\r
+ enddo\r
+*** calculate TM-score for the given alignment----------->\r
+ d0_input=d0\r
+ call TMscore8_search(d0_input,n_al,xtm1,ytm1,ztm1,n1,\r
+ & n_al,xtm2,ytm2,ztm2,n2,TM,Rcomm,Lcomm) !simplified search engine\r
+ TM=TM*n_al/anseq !TM-score\r
+*** calculate score matrix score(i,j)------------------>\r
+ do i=1,n_al\r
+ r_2(1,i)=xtm1(i)\r
+ r_2(2,i)=ytm1(i)\r
+ r_2(3,i)=ztm1(i)\r
+ enddo\r
+ call u3b(w,r_1,r_2,n_al,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ do i=1,nseq1\r
+ xx=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0)\r
+ yy=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0)\r
+ zz=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0)\r
+ do j=1,nseq2\r
+ dd=(xx-xa(1,j,1))**2+(yy-xa(2,j,1))**2+(zz-xa(3,j,1))**2\r
+ score(i,j)=1/(1+dd/d0**2)\r
+ enddo\r
+ enddo\r
+ \r
+c^^^^^^^^^^^^^^^^ score(i,j) done ^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ end\r
+\r
+****************************************************************\r
+* with invmap(i) calculate score(i,j) using RMSD rotation \r
+****************************************************************\r
+ subroutine get_score1\r
+ PARAMETER(nmax=5000)\r
+ common/length/nseq1,nseq2\r
+ COMMON/BACKBONE/XA(3,nmax,0:1)\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ common/zscore/zrms,n_al,rmsd_al\r
+ common/d0/d0,anseq\r
+ common/d0min/d0_min\r
+ dimension xtm1(nmax),ytm1(nmax),ztm1(nmax)\r
+ dimension xtm2(nmax),ytm2(nmax),ztm2(nmax)\r
+ common/TM/TM,TMmax\r
+ common/n1n2/n1(nmax),n2(nmax)\r
+\r
+ccc RMSD:\r
+ double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)\r
+ double precision u(3,3),t(3),rms,drms !armsd is real\r
+ data w /nmax*1.0/\r
+ccc \r
+\r
+c calculate RMSD between aligned structures and rotate the structures -->\r
+ n_al=0\r
+ do j=1,NSEQ2\r
+ i=invmap(j) !j aligned to i\r
+ if(i.gt.0)then\r
+ n_al=n_al+1\r
+ccc for rotation matrix:\r
+ r_1(1,n_al)=xa(1,i,0)\r
+ r_1(2,n_al)=xa(2,i,0)\r
+ r_1(3,n_al)=xa(3,i,0)\r
+ r_2(1,n_al)=xa(1,j,1)\r
+ r_2(2,n_al)=xa(2,j,1)\r
+ r_2(3,n_al)=xa(3,j,1)\r
+ endif\r
+ enddo\r
+*** calculate score matrix score(i,j)------------------>\r
+ call u3b(w,r_1,r_2,n_al,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ d01=d0+1.5\r
+ if(d01.lt.d0_min)d01=d0_min\r
+ d02=d01*d01\r
+ do i=1,nseq1\r
+ xx=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0)\r
+ yy=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0)\r
+ zz=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0)\r
+ do j=1,nseq2\r
+ dd=(xx-xa(1,j,1))**2+(yy-xa(2,j,1))**2+(zz-xa(3,j,1))**2\r
+ score(i,j)=1/(1+dd/d02)\r
+ enddo\r
+ enddo\r
+\r
+c^^^^^^^^^^^^^^^^ score(i,j) done ^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ end\r
+\r
+\r
+*************************************************************************\r
+*************************************************************************\r
+* This is a subroutine to compare two structures and find the \r
+* superposition that has the maximum TM-score.\r
+*\r
+* L1--Length of the first structure\r
+* (x1(i),y1(i),z1(i))--coordinates of i'th residue at the first structure\r
+* n1(i)--Residue sequence number of i'th residue at the first structure\r
+* L2--Length of the second structure\r
+* (x2(i),y2(i),z2(i))--coordinates of i'th residue at the second structure\r
+* n2(i)--Residue sequence number of i'th residue at the second structure\r
+* TM--TM-score of the comparison\r
+* Rcomm--RMSD of two structures in the common aligned residues\r
+* Lcomm--Length of the common aligned regions\r
+*\r
+* Note: \r
+* 1, Always put native as the second structure, by which TM-score\r
+* is normalized.\r
+* 2, The returned (x1(i),y1(i),z1(i)) are the rotated structure after\r
+* TM-score superposition.\r
+*************************************************************************\r
+*************************************************************************\r
+*** dis<8, simplified search engine\r
+ subroutine TMscore8_search(dx,L1,x1,y1,z1,n1,L2,x2,y2,z2,n2,\r
+ & TM,Rcomm,Lcomm)\r
+ PARAMETER(nmax=5000)\r
+ common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax)\r
+ common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB\r
+ common/para/d,d0\r
+ common/d0min/d0_min\r
+ common/align/n_ali,iA(nmax),iB(nmax)\r
+ common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score\r
+ dimension k_ali(nmax),k_ali0(nmax)\r
+ dimension L_ini(100),iq(nmax)\r
+ common/scores/score\r
+ double precision score,score_max\r
+ dimension xa(nmax),ya(nmax),za(nmax)\r
+ dimension iL0(nmax)\r
+\r
+ dimension x1(nmax),y1(nmax),z1(nmax),n1(nmax)\r
+ dimension x2(nmax),y2(nmax),z2(nmax),n2(nmax)\r
+\r
+ccc RMSD:\r
+ double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)\r
+ double precision u(3,3),t(3),rms,drms !armsd is real\r
+ data w /nmax*1.0/\r
+ccc \r
+\r
+********* convert input data ***************************\r
+* because L1=L2 in this special case---------->\r
+ nseqA=L1\r
+ nseqB=L2\r
+ do i=1,nseqA\r
+ xa(i)=x1(i)\r
+ ya(i)=y1(i)\r
+ za(i)=z1(i)\r
+ nresA(i)=n1(i)\r
+ xb(i)=x2(i)\r
+ yb(i)=y2(i)\r
+ zb(i)=z2(i)\r
+ nresB(i)=n2(i)\r
+ iA(i)=i\r
+ iB(i)=i\r
+ enddo\r
+ n_ali=L1 !number of aligned residues\r
+ Lcomm=L1\r
+\r
+************/////\r
+* parameters:\r
+*****************\r
+*** d0------------->\r
+ d0=dx\r
+ if(d0.lt.d0_min)d0=d0_min\r
+*** d0_search ----->\r
+ d0_search=d0\r
+ if(d0_search.gt.8)d0_search=8\r
+ if(d0_search.lt.4.5)d0_search=4.5\r
+*** iterative parameters ----->\r
+ n_it=20 !maximum number of iterations\r
+ d_output=5 !for output alignment\r
+ n_init_max=6 !maximum number of L_init\r
+ n_init=0\r
+ L_ini_min=4\r
+ if(n_ali.lt.4)L_ini_min=n_ali\r
+ do i=1,n_init_max-1\r
+ n_init=n_init+1\r
+ L_ini(n_init)=n_ali/2**(n_init-1)\r
+ if(L_ini(n_init).le.L_ini_min)then\r
+ L_ini(n_init)=L_ini_min\r
+ goto 402\r
+ endif\r
+ enddo\r
+ n_init=n_init+1\r
+ L_ini(n_init)=L_ini_min\r
+ 402 continue\r
+\r
+******************************************************************\r
+* find the maximum score starting from local structures superposition\r
+******************************************************************\r
+ score_max=-1 !TM-score\r
+ do 333 i_init=1,n_init\r
+ L_init=L_ini(i_init)\r
+ iL_max=n_ali-L_init+1\r
+ k=0\r
+ do i=1,iL_max,40 !this is the simplification!\r
+ k=k+1\r
+ iL0(k)=i\r
+ enddo\r
+ if(iL0(k).lt.iL_max)then\r
+ k=k+1\r
+ iL0(k)=iL_max\r
+ endif\r
+ n_shift=k\r
+ do 300 i_shift=1,n_shift\r
+ iL=iL0(i_shift)\r
+ LL=0\r
+ ka=0\r
+ do i=1,L_init\r
+ k=iL+i-1 ![1,n_ali] common aligned\r
+ r_1(1,i)=xa(iA(k))\r
+ r_1(2,i)=ya(iA(k))\r
+ r_1(3,i)=za(iA(k))\r
+ r_2(1,i)=xb(iB(k))\r
+ r_2(2,i)=yb(iB(k))\r
+ r_2(3,i)=zb(iB(k))\r
+ LL=LL+1\r
+ ka=ka+1\r
+ k_ali(ka)=k\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ if(i_init.eq.1)then !global superposition\r
+ armsd=dsqrt(rms/LL)\r
+ Rcomm=armsd\r
+ endif\r
+ do j=1,nseqA\r
+ xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ d=d0_search-1\r
+ call score_fun8 !init, get scores, n_cut+i_ali(i) for iteration\r
+ if(score_max.lt.score)then\r
+ score_max=score\r
+ ka0=ka\r
+ do i=1,ka0\r
+ k_ali0(i)=k_ali(i)\r
+ enddo\r
+ endif\r
+*** iteration for extending ---------------------------------->\r
+ d=d0_search+1\r
+ do 301 it=1,n_it\r
+ LL=0\r
+ ka=0\r
+ do i=1,n_cut\r
+ m=i_ali(i) ![1,n_ali]\r
+ r_1(1,i)=xa(iA(m))\r
+ r_1(2,i)=ya(iA(m))\r
+ r_1(3,i)=za(iA(m))\r
+ r_2(1,i)=xb(iB(m))\r
+ r_2(2,i)=yb(iB(m))\r
+ r_2(3,i)=zb(iB(m))\r
+ ka=ka+1\r
+ k_ali(ka)=m\r
+ LL=LL+1\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ do j=1,nseqA\r
+ xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ call score_fun8 !get scores, n_cut+i_ali(i) for iteration\r
+ if(score_max.lt.score)then\r
+ score_max=score\r
+ ka0=ka\r
+ do i=1,ka\r
+ k_ali0(i)=k_ali(i)\r
+ enddo\r
+ endif\r
+ if(it.eq.n_it)goto 302\r
+ if(n_cut.eq.ka)then\r
+ neq=0\r
+ do i=1,n_cut\r
+ if(i_ali(i).eq.k_ali(i))neq=neq+1\r
+ enddo\r
+ if(n_cut.eq.neq)goto 302\r
+ endif\r
+ 301 continue !for iteration\r
+ 302 continue\r
+ 300 continue !for shift\r
+ 333 continue !for initial length, L_ali/M\r
+\r
+******** return the final rotation ****************\r
+ LL=0\r
+ do i=1,ka0\r
+ m=k_ali0(i) !record of the best alignment\r
+ r_1(1,i)=xa(iA(m))\r
+ r_1(2,i)=ya(iA(m))\r
+ r_1(3,i)=za(iA(m))\r
+ r_2(1,i)=xb(iB(m))\r
+ r_2(2,i)=yb(iB(m))\r
+ r_2(3,i)=zb(iB(m))\r
+ LL=LL+1\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ do j=1,nseqA\r
+ x1(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ TM=score_max\r
+\r
+c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ END\r
+\r
+*************************************************************************\r
+*************************************************************************\r
+* This is a subroutine to compare two structures and find the \r
+* superposition that has the maximum TM-score.\r
+*\r
+* L1--Length of the first structure\r
+* (x1(i),y1(i),z1(i))--coordinates of i'th residue at the first structure\r
+* n1(i)--Residue sequence number of i'th residue at the first structure\r
+* L2--Length of the second structure\r
+* (x2(i),y2(i),z2(i))--coordinates of i'th residue at the second structure\r
+* n2(i)--Residue sequence number of i'th residue at the second structure\r
+* TM--TM-score of the comparison\r
+* Rcomm--RMSD of two structures in the common aligned residues\r
+* Lcomm--Length of the common aligned regions\r
+*\r
+* Note: \r
+* 1, Always put native as the second structure, by which TM-score\r
+* is normalized.\r
+* 2, The returned (x1(i),y1(i),z1(i)) are the rotated structure after\r
+* TM-score superposition.\r
+*************************************************************************\r
+*************************************************************************\r
+*** dis<8, but same search engine\r
+ subroutine TMscore8(dx,L1,x1,y1,z1,n1,L2,x2,y2,z2,n2,\r
+ & TM,Rcomm,Lcomm)\r
+ PARAMETER(nmax=5000)\r
+ common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax)\r
+ common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB\r
+ common/para/d,d0\r
+ common/d0min/d0_min\r
+ common/align/n_ali,iA(nmax),iB(nmax)\r
+ common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score\r
+ dimension k_ali(nmax),k_ali0(nmax)\r
+ dimension L_ini(100),iq(nmax)\r
+ common/scores/score\r
+ double precision score,score_max\r
+ dimension xa(nmax),ya(nmax),za(nmax)\r
+\r
+ dimension x1(nmax),y1(nmax),z1(nmax),n1(nmax)\r
+ dimension x2(nmax),y2(nmax),z2(nmax),n2(nmax)\r
+\r
+ccc RMSD:\r
+ double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)\r
+ double precision u(3,3),t(3),rms,drms !armsd is real\r
+ data w /nmax*1.0/\r
+ccc \r
+\r
+********* convert input data ***************************\r
+* because L1=L2 in this special case---------->\r
+ nseqA=L1\r
+ nseqB=L2\r
+ do i=1,nseqA\r
+ xa(i)=x1(i)\r
+ ya(i)=y1(i)\r
+ za(i)=z1(i)\r
+ nresA(i)=n1(i)\r
+ xb(i)=x2(i)\r
+ yb(i)=y2(i)\r
+ zb(i)=z2(i)\r
+ nresB(i)=n2(i)\r
+ iA(i)=i\r
+ iB(i)=i\r
+ enddo\r
+ n_ali=L1 !number of aligned residues\r
+ Lcomm=L1\r
+\r
+************/////\r
+* parameters:\r
+*****************\r
+*** d0------------->\r
+ d0=dx\r
+ if(d0.lt.d0_min)d0=d0_min\r
+*** d0_search ----->\r
+ d0_search=d0\r
+ if(d0_search.gt.8)d0_search=8\r
+ if(d0_search.lt.4.5)d0_search=4.5\r
+*** iterative parameters ----->\r
+ n_it=20 !maximum number of iterations\r
+ d_output=5 !for output alignment\r
+ n_init_max=6 !maximum number of L_init\r
+ n_init=0\r
+ L_ini_min=4\r
+ if(n_ali.lt.4)L_ini_min=n_ali\r
+ do i=1,n_init_max-1\r
+ n_init=n_init+1\r
+ L_ini(n_init)=n_ali/2**(n_init-1)\r
+ if(L_ini(n_init).le.L_ini_min)then\r
+ L_ini(n_init)=L_ini_min\r
+ goto 402\r
+ endif\r
+ enddo\r
+ n_init=n_init+1\r
+ L_ini(n_init)=L_ini_min\r
+ 402 continue\r
+\r
+******************************************************************\r
+* find the maximum score starting from local structures superposition\r
+******************************************************************\r
+ score_max=-1 !TM-score\r
+ do 333 i_init=1,n_init\r
+ L_init=L_ini(i_init)\r
+ iL_max=n_ali-L_init+1\r
+ do 300 iL=1,iL_max !on aligned residues, [1,nseqA]\r
+ LL=0\r
+ ka=0\r
+ do i=1,L_init\r
+ k=iL+i-1 ![1,n_ali] common aligned\r
+ r_1(1,i)=xa(iA(k))\r
+ r_1(2,i)=ya(iA(k))\r
+ r_1(3,i)=za(iA(k))\r
+ r_2(1,i)=xb(iB(k))\r
+ r_2(2,i)=yb(iB(k))\r
+ r_2(3,i)=zb(iB(k))\r
+ LL=LL+1\r
+ ka=ka+1\r
+ k_ali(ka)=k\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ if(i_init.eq.1)then !global superposition\r
+ armsd=dsqrt(rms/LL)\r
+ Rcomm=armsd\r
+ endif\r
+ do j=1,nseqA\r
+ xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ d=d0_search-1\r
+ call score_fun8 !init, get scores, n_cut+i_ali(i) for iteration\r
+ if(score_max.lt.score)then\r
+ score_max=score\r
+ ka0=ka\r
+ do i=1,ka0\r
+ k_ali0(i)=k_ali(i)\r
+ enddo\r
+ endif\r
+*** iteration for extending ---------------------------------->\r
+ d=d0_search+1\r
+ do 301 it=1,n_it\r
+ LL=0\r
+ ka=0\r
+ do i=1,n_cut\r
+ m=i_ali(i) ![1,n_ali]\r
+ r_1(1,i)=xa(iA(m))\r
+ r_1(2,i)=ya(iA(m))\r
+ r_1(3,i)=za(iA(m))\r
+ r_2(1,i)=xb(iB(m))\r
+ r_2(2,i)=yb(iB(m))\r
+ r_2(3,i)=zb(iB(m))\r
+ ka=ka+1\r
+ k_ali(ka)=m\r
+ LL=LL+1\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ do j=1,nseqA\r
+ xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ call score_fun8 !get scores, n_cut+i_ali(i) for iteration\r
+ if(score_max.lt.score)then\r
+ score_max=score\r
+ ka0=ka\r
+ do i=1,ka\r
+ k_ali0(i)=k_ali(i)\r
+ enddo\r
+ endif\r
+ if(it.eq.n_it)goto 302\r
+ if(n_cut.eq.ka)then\r
+ neq=0\r
+ do i=1,n_cut\r
+ if(i_ali(i).eq.k_ali(i))neq=neq+1\r
+ enddo\r
+ if(n_cut.eq.neq)goto 302\r
+ endif\r
+ 301 continue !for iteration\r
+ 302 continue\r
+ 300 continue !for shift\r
+ 333 continue !for initial length, L_ali/M\r
+\r
+******** return the final rotation ****************\r
+ LL=0\r
+ do i=1,ka0\r
+ m=k_ali0(i) !record of the best alignment\r
+ r_1(1,i)=xa(iA(m))\r
+ r_1(2,i)=ya(iA(m))\r
+ r_1(3,i)=za(iA(m))\r
+ r_2(1,i)=xb(iB(m))\r
+ r_2(2,i)=yb(iB(m))\r
+ r_2(3,i)=zb(iB(m))\r
+ LL=LL+1\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ do j=1,nseqA\r
+ x1(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ TM=score_max\r
+\r
+c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ END\r
+\r
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc\r
+c 1, collect those residues with dis<d;\r
+c 2, calculate score_GDT, score_maxsub, score_TM\r
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc\r
+ subroutine score_fun8\r
+ PARAMETER(nmax=5000)\r
+\r
+ common/stru/xa(nmax),ya(nmax),za(nmax),xb(nmax),yb(nmax),zb(nmax)\r
+ common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB\r
+ common/para/d,d0\r
+ common/align/n_ali,iA(nmax),iB(nmax)\r
+ common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score\r
+ common/scores/score\r
+ double precision score,score_max\r
+ common/d8/d8\r
+\r
+ d_tmp=d\r
+ 21 n_cut=0 !number of residue-pairs dis<d, for iteration\r
+ score_sum=0 !TMscore\r
+ do k=1,n_ali\r
+ i=iA(k) ![1,nseqA] reoder number of structureA\r
+ j=iB(k) ![1,nseqB]\r
+ dis=sqrt((xa(i)-xb(j))**2+(ya(i)-yb(j))**2+(za(i)-zb(j))**2)\r
+ if(dis.lt.d_tmp)then\r
+ n_cut=n_cut+1\r
+ i_ali(n_cut)=k ![1,n_ali], mark the residue-pairs in dis<d\r
+ endif\r
+ if(dis.le.d8)then\r
+ score_sum=score_sum+1/(1+(dis/d0)**2)\r
+ endif\r
+ enddo\r
+ if(n_cut.lt.3.and.n_ali.gt.3)then\r
+ d_tmp=d_tmp+.5\r
+ goto 21\r
+ endif\r
+ score=score_sum/float(nseqB) !TM-score\r
+\r
+ return\r
+ end\r
+\r
+*************************************************************************\r
+*************************************************************************\r
+* This is a subroutine to compare two structures and find the \r
+* superposition that has the maximum TM-score.\r
+*\r
+* L1--Length of the first structure\r
+* (x1(i),y1(i),z1(i))--coordinates of i'th residue at the first structure\r
+* n1(i)--Residue sequence number of i'th residue at the first structure\r
+* L2--Length of the second structure\r
+* (x2(i),y2(i),z2(i))--coordinates of i'th residue at the second structure\r
+* n2(i)--Residue sequence number of i'th residue at the second structure\r
+* TM--TM-score of the comparison\r
+* Rcomm--RMSD of two structures in the common aligned residues\r
+* Lcomm--Length of the common aligned regions\r
+*\r
+* Note: \r
+* 1, Always put native as the second structure, by which TM-score\r
+* is normalized.\r
+* 2, The returned (x1(i),y1(i),z1(i)) are the rotated structure after\r
+* TM-score superposition.\r
+*************************************************************************\r
+*************************************************************************\r
+*** normal TM-score:\r
+ subroutine TMscore(dx,L1,x1,y1,z1,n1,L2,x2,y2,z2,n2,\r
+ & TM,Rcomm,Lcomm)\r
+ PARAMETER(nmax=5000)\r
+ common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax)\r
+ common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB\r
+ common/para/d,d0\r
+ common/d0min/d0_min\r
+ common/align/n_ali,iA(nmax),iB(nmax)\r
+ common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score\r
+ dimension k_ali(nmax),k_ali0(nmax)\r
+ dimension L_ini(100),iq(nmax)\r
+ common/scores/score\r
+ double precision score,score_max\r
+ dimension xa(nmax),ya(nmax),za(nmax)\r
+\r
+ dimension x1(nmax),y1(nmax),z1(nmax),n1(nmax)\r
+ dimension x2(nmax),y2(nmax),z2(nmax),n2(nmax)\r
+\r
+ccc RMSD:\r
+ double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)\r
+ double precision u(3,3),t(3),rms,drms !armsd is real\r
+ data w /nmax*1.0/\r
+ccc \r
+\r
+********* convert input data ***************************\r
+* because L1=L2 in this special case---------->\r
+ nseqA=L1\r
+ nseqB=L2\r
+ do i=1,nseqA\r
+ xa(i)=x1(i)\r
+ ya(i)=y1(i)\r
+ za(i)=z1(i)\r
+ nresA(i)=n1(i)\r
+ xb(i)=x2(i)\r
+ yb(i)=y2(i)\r
+ zb(i)=z2(i)\r
+ nresB(i)=n2(i)\r
+ iA(i)=i\r
+ iB(i)=i\r
+ enddo\r
+ n_ali=L1 !number of aligned residues\r
+ Lcomm=L1\r
+\r
+************/////\r
+* parameters:\r
+*****************\r
+*** d0------------->\r
+c d0=1.24*(nseqB-15)**(1.0/3.0)-1.8\r
+ d0=dx\r
+ if(d0.lt.d0_min)d0=d0_min\r
+*** d0_search ----->\r
+ d0_search=d0\r
+ if(d0_search.gt.8)d0_search=8\r
+ if(d0_search.lt.4.5)d0_search=4.5\r
+*** iterative parameters ----->\r
+ n_it=20 !maximum number of iterations\r
+ d_output=5 !for output alignment\r
+ n_init_max=6 !maximum number of L_init\r
+ n_init=0\r
+ L_ini_min=4\r
+ if(n_ali.lt.4)L_ini_min=n_ali\r
+ do i=1,n_init_max-1\r
+ n_init=n_init+1\r
+ L_ini(n_init)=n_ali/2**(n_init-1)\r
+ if(L_ini(n_init).le.L_ini_min)then\r
+ L_ini(n_init)=L_ini_min\r
+ goto 402\r
+ endif\r
+ enddo\r
+ n_init=n_init+1\r
+ L_ini(n_init)=L_ini_min\r
+ 402 continue\r
+\r
+******************************************************************\r
+* find the maximum score starting from local structures superposition\r
+******************************************************************\r
+ score_max=-1 !TM-score\r
+ do 333 i_init=1,n_init\r
+ L_init=L_ini(i_init)\r
+ iL_max=n_ali-L_init+1\r
+ do 300 iL=1,iL_max !on aligned residues, [1,nseqA]\r
+ LL=0\r
+ ka=0\r
+ do i=1,L_init\r
+ k=iL+i-1 ![1,n_ali] common aligned\r
+ r_1(1,i)=xa(iA(k))\r
+ r_1(2,i)=ya(iA(k))\r
+ r_1(3,i)=za(iA(k))\r
+ r_2(1,i)=xb(iB(k))\r
+ r_2(2,i)=yb(iB(k))\r
+ r_2(3,i)=zb(iB(k))\r
+ LL=LL+1\r
+ ka=ka+1\r
+ k_ali(ka)=k\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ if(i_init.eq.1)then !global superposition\r
+ armsd=dsqrt(rms/LL)\r
+ Rcomm=armsd\r
+ endif\r
+ do j=1,nseqA\r
+ xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ d=d0_search-1\r
+ call score_fun !init, get scores, n_cut+i_ali(i) for iteration\r
+ if(score_max.lt.score)then\r
+ score_max=score\r
+ ka0=ka\r
+ do i=1,ka0\r
+ k_ali0(i)=k_ali(i)\r
+ enddo\r
+ endif\r
+*** iteration for extending ---------------------------------->\r
+ d=d0_search+1\r
+ do 301 it=1,n_it\r
+ LL=0\r
+ ka=0\r
+ do i=1,n_cut\r
+ m=i_ali(i) ![1,n_ali]\r
+ r_1(1,i)=xa(iA(m))\r
+ r_1(2,i)=ya(iA(m))\r
+ r_1(3,i)=za(iA(m))\r
+ r_2(1,i)=xb(iB(m))\r
+ r_2(2,i)=yb(iB(m))\r
+ r_2(3,i)=zb(iB(m))\r
+ ka=ka+1\r
+ k_ali(ka)=m\r
+ LL=LL+1\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ do j=1,nseqA\r
+ xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ call score_fun !get scores, n_cut+i_ali(i) for iteration\r
+ if(score_max.lt.score)then\r
+ score_max=score\r
+ ka0=ka\r
+ do i=1,ka\r
+ k_ali0(i)=k_ali(i)\r
+ enddo\r
+ endif\r
+ if(it.eq.n_it)goto 302\r
+ if(n_cut.eq.ka)then\r
+ neq=0\r
+ do i=1,n_cut\r
+ if(i_ali(i).eq.k_ali(i))neq=neq+1\r
+ enddo\r
+ if(n_cut.eq.neq)goto 302\r
+ endif\r
+ 301 continue !for iteration\r
+ 302 continue\r
+ 300 continue !for shift\r
+ 333 continue !for initial length, L_ali/M\r
+\r
+******** return the final rotation ****************\r
+ LL=0\r
+ do i=1,ka0\r
+ m=k_ali0(i) !record of the best alignment\r
+ r_1(1,i)=xa(iA(m))\r
+ r_1(2,i)=ya(iA(m))\r
+ r_1(3,i)=za(iA(m))\r
+ r_2(1,i)=xb(iB(m))\r
+ r_2(2,i)=yb(iB(m))\r
+ r_2(3,i)=zb(iB(m))\r
+ LL=LL+1\r
+ enddo\r
+ call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2\r
+ do j=1,nseqA\r
+ x1(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)\r
+ y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)\r
+ z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)\r
+ enddo\r
+ TM=score_max\r
+\r
+c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ END\r
+\r
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc\r
+c 1, collect those residues with dis<d;\r
+c 2, calculate score_GDT, score_maxsub, score_TM\r
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc\r
+ subroutine score_fun\r
+ PARAMETER(nmax=5000)\r
+\r
+ common/stru/xa(nmax),ya(nmax),za(nmax),xb(nmax),yb(nmax),zb(nmax)\r
+ common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB\r
+ common/para/d,d0\r
+ common/align/n_ali,iA(nmax),iB(nmax)\r
+ common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score\r
+ common/scores/score\r
+ double precision score\r
+\r
+ d_tmp=d\r
+ 21 n_cut=0 !number of residue-pairs dis<d, for iteration\r
+ score_sum=0 !TMscore\r
+ do k=1,n_ali\r
+ i=iA(k) ![1,nseqA] reoder number of structureA\r
+ j=iB(k) ![1,nseqB]\r
+ dis=sqrt((xa(i)-xb(j))**2+(ya(i)-yb(j))**2+(za(i)-zb(j))**2)\r
+ if(dis.lt.d_tmp)then\r
+ n_cut=n_cut+1\r
+ i_ali(n_cut)=k ![1,n_ali], mark the residue-pairs in dis<d\r
+ endif\r
+ score_sum=score_sum+1/(1+(dis/d0)**2)\r
+ enddo\r
+ if(n_cut.lt.3.and.n_ali.gt.3)then\r
+ d_tmp=d_tmp+.5\r
+ goto 21\r
+ endif\r
+ score=score_sum/float(nseqB) !TM-score\r
+\r
+ return\r
+ end\r
+\r
+********************************************************************\r
+* Dynamic programming for alignment.\r
+* Input: score(i,j), and gap_open\r
+* Output: invmap(j)\r
+* \r
+* Please note this subroutine is not a correct implementation of \r
+* the N-W dynamic programming because the score tracks back only \r
+* one layer of the matrix. This code was exploited in TM-align \r
+* because it is about 1.5 times faster than a complete N-W code\r
+* and does not influence much the final structure alignment result.\r
+********************************************************************\r
+ SUBROUTINE DP(NSEQ1,NSEQ2)\r
+ PARAMETER(nmax=5000)\r
+ LOGICAL*1 DIR\r
+ common/dpc/score(nmax,nmax),gap_open,invmap(nmax)\r
+ dimension DIR(0:nmax,0:nmax),VAL(0:nmax,0:nmax)\r
+ REAL H,V\r
+ \r
+*** initialize the matrix:\r
+ val(0,0)=0\r
+ do i=1,nseq1\r
+ dir(i,0)=.false.\r
+ val(i,0)=0\r
+ enddo\r
+ do j=1,nseq2\r
+ dir(0,j)=.false.\r
+ val(0,j)=0\r
+ invmap(j)=-1\r
+ enddo\r
+\r
+*** decide matrix and path:\r
+ DO j=1,NSEQ2\r
+ DO i=1,NSEQ1\r
+ D=VAL(i-1,j-1)+SCORE(i,j)\r
+ H=VAL(i-1,j)\r
+ if(DIR(i-1,j))H=H+GAP_OPEN\r
+ V=VAL(i,j-1)\r
+ if(DIR(i,j-1))V=V+GAP_OPEN\r
+ \r
+ IF((D.GE.H).AND.(D.GE.V)) THEN\r
+ DIR(I,J)=.true.\r
+ VAL(i,j)=D\r
+ ELSE\r
+ DIR(I,J)=.false.\r
+ if(V.GE.H)then\r
+ val(i,j)=v\r
+ else\r
+ val(i,j)=h\r
+ end if\r
+ ENDIF\r
+ ENDDO\r
+ ENDDO\r
+ \r
+*** extract the alignment:\r
+ i=NSEQ1\r
+ j=NSEQ2\r
+ DO WHILE((i.GT.0).AND.(j.GT.0))\r
+ IF(DIR(i,j))THEN\r
+ invmap(j)=i\r
+ i=i-1\r
+ j=j-1\r
+ ELSE\r
+ H=VAL(i-1,j)\r
+ if(DIR(i-1,j))H=H+GAP_OPEN\r
+ V=VAL(i,j-1)\r
+ if(DIR(i,j-1))V=V+GAP_OPEN\r
+ IF(V.GE.H) THEN\r
+ j=j-1\r
+ ELSE\r
+ i=i-1\r
+ ENDIF\r
+ ENDIF\r
+ ENDDO\r
+ \r
+c^^^^^^^^^^^^^^^Dynamical programming done ^^^^^^^^^^^^^^^^^^^\r
+ return\r
+ END\r
+\r
+cccccccccccccccc Calculate sum of (r_d-r_m)^2 cccccccccccccccccccccccccc\r
+c w - w(m) is weight for atom pair c m (given)\r
+c x - x(i,m) are coordinates of atom c m in set x (given)\r
+c y - y(i,m) are coordinates of atom c m in set y (given)\r
+c n - n is number of atom pairs (given)\r
+c mode - 0:calculate rms only (given)\r
+c 1:calculate rms,u,t (takes longer)\r
+c rms - sum of w*(ux+t-y)**2 over all atom pairs (result)\r
+c u - u(i,j) is rotation matrix for best superposition (result)\r
+c t - t(i) is translation vector for best superposition (result)\r
+c ier - 0: a unique optimal superposition has been determined(result)\r
+c -1: superposition is not unique but optimal\r
+c -2: no result obtained because of negative weights w\r
+c or all weights equal to zero.\r
+cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc\r
+ subroutine u3b(w, x, y, n, mode, rms, u, t, ier)\r
+ integer ip(9), ip2312(4), i, j, k, l, m1, m, ier, n, mode\r
+ double precision w(1), x(3, 1), y(3, 1), u(3, 3), t(3), rms, sigma\r
+ double precision r(3, 3), xc(3), yc(3), wc, a(3, 3), b(3, 3), e0, \r
+ &e(3), e1, e2, e3, d, spur, det, cof, h, g, cth, sth, sqrth, p, tol\r
+ &, rr(6), rr1, rr2, rr3, rr4, rr5, rr6, ss(6), ss1, ss2, ss3, ss4, \r
+ &ss5, ss6, zero, one, two, three, sqrt3\r
+ equivalence (rr(1), rr1), (rr(2), rr2), (rr(3), rr3), (rr(4), rr4)\r
+ &, (rr(5), rr5), (rr(6), rr6), (ss(1), ss1), (ss(2), ss2), (ss(3), \r
+ &ss3), (ss(4), ss4), (ss(5), ss5), (ss(6), ss6), (e(1), e1), (e(2)\r
+ &, e2), (e(3), e3)\r
+ data sqrt3 / 1.73205080756888d+00 /\r
+ data tol / 1.0d-2 /\r
+ data zero / 0.0d+00 /\r
+ data one / 1.0d+00 /\r
+ data two / 2.0d+00 /\r
+ data three / 3.0d+00 /\r
+ data ip / 1, 2, 4, 2, 3, 5, 4, 5, 6 /\r
+ data ip2312 / 2, 3, 1, 2 /\r
+c 156 "rms.for"\r
+ wc = zero\r
+ rms = 0.0\r
+ e0 = zero\r
+ do 1 i = 1, 3\r
+ xc(i) = zero\r
+ yc(i) = zero\r
+ t(i) = 0.0\r
+ do 1 j = 1, 3\r
+ d = zero\r
+ if (i .eq. j) d = one\r
+ u(i,j) = d\r
+ a(i,j) = d\r
+ 1 r(i,j) = zero\r
+ ier = -1\r
+c**** DETERMINE CENTROIDS OF BOTH VECTOR SETS X AND Y\r
+c 170 "rms.for"\r
+ if (n .lt. 1) return \r
+c 172 "rms.for"\r
+ ier = -2\r
+ do 2 m = 1, n\r
+ if (w(m) .lt. 0.0) return \r
+ wc = wc + w(m)\r
+ do 2 i = 1, 3\r
+ xc(i) = xc(i) + (w(m) * x(i,m))\r
+ 2 yc(i) = yc(i) + (w(m) * y(i,m))\r
+ if (wc .le. zero) return \r
+ do 3 i = 1, 3\r
+ xc(i) = xc(i) / wc\r
+c**** DETERMINE CORRELATION MATRIX R BETWEEN VECTOR SETS Y AND X\r
+c 182 "rms.for"\r
+ 3 yc(i) = yc(i) / wc\r
+c 184 "rms.for"\r
+ do 4 m = 1, n\r
+ do 4 i = 1, 3\r
+ e0 = e0 + (w(m) * (((x(i,m) - xc(i)) ** 2) + ((y(i,m) - yc(i)) ** \r
+ &2)))\r
+c 187 "rms.for"\r
+ d = w(m) * (y(i,m) - yc(i))\r
+ do 4 j = 1, 3\r
+c**** CALCULATE DETERMINANT OF R(I,J)\r
+c 189 "rms.for"\r
+ 4 r(i,j) = r(i,j) + (d * (x(j,m) - xc(j)))\r
+c 191 "rms.for"\r
+ det = ((r(1,1) * ((r(2,2) * r(3,3)) - (r(2,3) * r(3,2)))) - (r(1,2\r
+ &) * ((r(2,1) * r(3,3)) - (r(2,3) * r(3,1))))) + (r(1,3) * ((r(2,1)\r
+ & * r(3,2)) - (r(2,2) * r(3,1))))\r
+c**** FORM UPPER TRIANGLE OF TRANSPOSED(R)*R\r
+c 194 "rms.for"\r
+ sigma = det\r
+c 196 "rms.for"\r
+ m = 0\r
+ do 5 j = 1, 3\r
+ do 5 i = 1, j\r
+ m = m + 1\r
+c***************** EIGENVALUES *****************************************\r
+c**** FORM CHARACTERISTIC CUBIC X**3-3*SPUR*X**2+3*COF*X-DET=0\r
+c 200 "rms.for"\r
+ 5 rr(m) = ((r(1,i) * r(1,j)) + (r(2,i) * r(2,j))) + (r(3,i) * r(3,j)\r
+ &)\r
+c 203 "rms.for"\r
+ spur = ((rr1 + rr3) + rr6) / three\r
+ cof = ((((((rr3 * rr6) - (rr5 * rr5)) + (rr1 * rr6)) - (rr4 * rr4)\r
+ &) + (rr1 * rr3)) - (rr2 * rr2)) / three\r
+c 205 "rms.for"\r
+ det = det * det\r
+ do 6 i = 1, 3\r
+ 6 e(i) = spur\r
+c**** REDUCE CUBIC TO STANDARD FORM Y**3-3HY+2G=0 BY PUTTING X=Y+SPUR\r
+c 208 "rms.for"\r
+ if (spur .le. zero) goto 40\r
+c 210 "rms.for"\r
+ d = spur * spur\r
+ h = d - cof\r
+c**** SOLVE CUBIC. ROOTS ARE E1,E2,E3 IN DECREASING ORDER\r
+c 212 "rms.for"\r
+ g = (((spur * cof) - det) / two) - (spur * h)\r
+c 214 "rms.for"\r
+ if (h .le. zero) goto 8\r
+ sqrth = dsqrt(h)\r
+ d = ((h * h) * h) - (g * g)\r
+ if (d .lt. zero) d = zero\r
+ d = datan2(dsqrt(d),- g) / three\r
+ cth = sqrth * dcos(d)\r
+ sth = (sqrth * sqrt3) * dsin(d)\r
+ e1 = (spur + cth) + cth\r
+ e2 = (spur - cth) + sth\r
+ e3 = (spur - cth) - sth\r
+c.....HANDLE SPECIAL CASE OF 3 IDENTICAL ROOTS\r
+c 224 "rms.for"\r
+ if (mode) 10, 50, 10\r
+c**************** EIGENVECTORS *****************************************\r
+c 226 "rms.for"\r
+ 8 if (mode) 30, 50, 30\r
+c 228 "rms.for"\r
+ 10 do 15 l = 1, 3, 2\r
+ d = e(l)\r
+ ss1 = ((d - rr3) * (d - rr6)) - (rr5 * rr5)\r
+ ss2 = ((d - rr6) * rr2) + (rr4 * rr5)\r
+ ss3 = ((d - rr1) * (d - rr6)) - (rr4 * rr4)\r
+ ss4 = ((d - rr3) * rr4) + (rr2 * rr5)\r
+ ss5 = ((d - rr1) * rr5) + (rr2 * rr4)\r
+ ss6 = ((d - rr1) * (d - rr3)) - (rr2 * rr2)\r
+ j = 1\r
+ if (dabs(ss1) .ge. dabs(ss3)) goto 12\r
+ j = 2\r
+ if (dabs(ss3) .ge. dabs(ss6)) goto 13\r
+ 11 j = 3\r
+ goto 13\r
+ 12 if (dabs(ss1) .lt. dabs(ss6)) goto 11\r
+ 13 d = zero\r
+ j = 3 * (j - 1)\r
+ do 14 i = 1, 3\r
+ k = ip(i + j)\r
+ a(i,l) = ss(k)\r
+ 14 d = d + (ss(k) * ss(k))\r
+ if (d .gt. zero) d = one / dsqrt(d)\r
+ do 15 i = 1, 3\r
+ 15 a(i,l) = a(i,l) * d\r
+ d = ((a(1,1) * a(1,3)) + (a(2,1) * a(2,3))) + (a(3,1) * a(3,3))\r
+ m1 = 3\r
+ m = 1\r
+ if ((e1 - e2) .gt. (e2 - e3)) goto 16\r
+ m1 = 1\r
+ m = 3\r
+ 16 p = zero\r
+ do 17 i = 1, 3\r
+ a(i,m1) = a(i,m1) - (d * a(i,m))\r
+ 17 p = p + (a(i,m1) ** 2)\r
+ if (p .le. tol) goto 19\r
+ p = one / dsqrt(p)\r
+ do 18 i = 1, 3\r
+ 18 a(i,m1) = a(i,m1) * p\r
+ goto 21\r
+ 19 p = one\r
+ do 20 i = 1, 3\r
+ if (p .lt. dabs(a(i,m))) goto 20\r
+ p = dabs(a(i,m))\r
+ j = i\r
+ 20 continue\r
+ k = ip2312(j)\r
+ l = ip2312(j + 1)\r
+ p = dsqrt((a(k,m) ** 2) + (a(l,m) ** 2))\r
+ if (p .le. tol) goto 40\r
+ a(j,m1) = zero\r
+ a(k,m1) = - (a(l,m) / p)\r
+ a(l,m1) = a(k,m) / p\r
+ 21 a(1,2) = (a(2,3) * a(3,1)) - (a(2,1) * a(3,3))\r
+ a(2,2) = (a(3,3) * a(1,1)) - (a(3,1) * a(1,3))\r
+c****************** ROTATION MATRIX ************************************\r
+c 282 "rms.for"\r
+ a(3,2) = (a(1,3) * a(2,1)) - (a(1,1) * a(2,3))\r
+c 284 "rms.for"\r
+ 30 do 32 l = 1, 2\r
+ d = zero\r
+ do 31 i = 1, 3\r
+ b(i,l) = ((r(i,1) * a(1,l)) + (r(i,2) * a(2,l))) + (r(i,3) * a(3,l\r
+ &))\r
+c 288 "rms.for"\r
+ 31 d = d + (b(i,l) ** 2)\r
+ if (d .gt. zero) d = one / dsqrt(d)\r
+ do 32 i = 1, 3\r
+ 32 b(i,l) = b(i,l) * d\r
+ d = ((b(1,1) * b(1,2)) + (b(2,1) * b(2,2))) + (b(3,1) * b(3,2))\r
+ p = zero\r
+ do 33 i = 1, 3\r
+ b(i,2) = b(i,2) - (d * b(i,1))\r
+ 33 p = p + (b(i,2) ** 2)\r
+ if (p .le. tol) goto 35\r
+ p = one / dsqrt(p)\r
+ do 34 i = 1, 3\r
+ 34 b(i,2) = b(i,2) * p\r
+ goto 37\r
+ 35 p = one\r
+ do 36 i = 1, 3\r
+ if (p .lt. dabs(b(i,1))) goto 36\r
+ p = dabs(b(i,1))\r
+ j = i\r
+ 36 continue\r
+ k = ip2312(j)\r
+ l = ip2312(j + 1)\r
+ p = dsqrt((b(k,1) ** 2) + (b(l,1) ** 2))\r
+ if (p .le. tol) goto 40\r
+ b(j,2) = zero\r
+ b(k,2) = - (b(l,1) / p)\r
+ b(l,2) = b(k,1) / p\r
+ 37 b(1,3) = (b(2,1) * b(3,2)) - (b(2,2) * b(3,1))\r
+ b(2,3) = (b(3,1) * b(1,2)) - (b(3,2) * b(1,1))\r
+ b(3,3) = (b(1,1) * b(2,2)) - (b(1,2) * b(2,1))\r
+ do 39 i = 1, 3\r
+ do 39 j = 1, 3\r
+c****************** TRANSLATION VECTOR *********************************\r
+c 320 "rms.for"\r
+ 39 u(i,j) = ((b(i,1) * a(j,1)) + (b(i,2) * a(j,2))) + (b(i,3) * a(j,3\r
+ &))\r
+ 40 do 41 i = 1, 3\r
+c********************** RMS ERROR **************************************\r
+c 323 "rms.for"\r
+ 41 t(i) = ((yc(i) - (u(i,1) * xc(1))) - (u(i,2) * xc(2))) - (u(i,3)\r
+ & * xc(3))\r
+ 50 do 51 i = 1, 3\r
+ if (e(i) .lt. zero) e(i) = zero\r
+ 51 e(i) = dsqrt(e(i))\r
+ ier = 0\r
+ if (e2 .le. (e1 * 1.0d-05)) ier = -1\r
+ d = e3\r
+ if (sigma .ge. 0.0) goto 52\r
+ d = - d\r
+ if ((e2 - e3) .le. (e1 * 1.0d-05)) ier = -1\r
+ 52 d = (d + e2) + e1\r
+ rms = (e0 - d) - d\r
+ if (rms .lt. 0.0) rms = 0.0\r
+ return \r
+c.....END U3B...........................................................\r
+c----------------------------------------------------------\r
+c THE END\r
+c----------------------------------------------------------\r
+c 338 "rms.for"\r
+ end\r
+\r