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|
*************************************************************************
* This program is to compare two protein structures and identify the
* best superposition that has the highest TM-score. Input structures
* must be in the PDB format. By default, TM-score is normalized by
* the second protein. Users can obtain a brief instruction by simply
* running the program without arguments. For comments/suggestions,
* please contact email: zhng@umich.edu.
*
* Reference:
* Yang Zhang, Jeffrey Skolnick, Proteins, 2004 57:702-10.
*
* Permission to use, copy, modify, and distribute this program for
* any purpose, with or without fee, is hereby granted, provided that
* the notices on the head, the reference information, and this
* copyright notice appear in all copies or substantial portions of
* the Software. It is provided "as is" without express or implied
* warranty.
******************* Updating history ************************************
* 2005/10/19: the program was reformed so that the score values.
* are not dependent on the specific compilers.
* 2006/06/20: selected 'A' if there is altLoc when reading PDB file.
* 2007/02/05: fixed a bug with length<15 in TMscore_32.
* 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
* 2007/12/06: GDT-HA score was added, fixed a bug for reading PDB.
* 2010/08/02: A new RMSD matrix was used and obsolete statement removed.
* 2011/01/03: The length of pdb file names were extended to 500.
* 2011/01/30: An open source license is attached to the program.
* 2012/05/07: Improved RMSD calculation subroutine which speeds up
* TM-score program by 30%.
* 2012/06/05: Added option '-l L' which calculates TM-score (and maxsub
* and GDT scores) normalized by a specific length 'L'.
* 2012/12/17: Added 'TM.sup_atm' to superpose full-atom structures.
* The former superposition is for CA-trace only.
* 2013/05/08: Update TM-score so that it can read all alternate location
* indicators and residue insertions.
* 2013/05/11: Fix a bug in array overflow.
* 2016/03/23: Extended the program to allow calculating TM-score for for
* complex structure comparisons, where multiple-chains are
* merged into a single chain. Chain ID is now included in
* the output files.
* 2019/07/08: Enabled TM-score to support both PDB and mmCIF formats,
* and updated structure reading which makes program faster.
* 2019/08/18: Fixed multiple bugs associated with mmCIF formats.
* 2019/08/22: added output scripts for pymol, C++ version was included.
*************************************************************************
c 1 2 3 4 5 6 7 !
c 3456789012345678901234567890123456789012345678901234567890123456789012345678
program TMscore
PARAMETER(nmax=5000) !maximum number of residues
PARAMETER(namax=50000) !maximum of atoms
common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax)
common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB
common/para/d,d0,d0_fix
common/align/n_ali,iA(nmax),iB(nmax)
common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score
dimension k_ali(nmax),k_ali0(nmax)
character*500 fnam,pdb(100),outname,xxx_p,xxx_pdb
character*3 aa(-1:20),seqA(nmax),seqB(nmax),aanam,ss(2,nmax)
character*500 s,du
character*1 chA(nmax),chB(nmax),ch(nmax)
character*1 chain1(namax),chain2(namax)
character seq1A(nmax),seq1B(nmax),ali(nmax),du1,du3,du4*2
character sequenceA(nmax),sequenceB(nmax),sequenceM(nmax)
character ins1(nmax),ins2(nmax),ains1(namax),ains2(namax)
dimension L_ini(100),iq(nmax)
common/scores/score,score_maxsub,score_fix,score10
common/GDT/n_GDT05,n_GDT1,n_GDT2,n_GDT4,n_GDT8
double precision score,score_max,score_fix,score_fix_max
double precision score_maxsub,score10
dimension xa(nmax),ya(nmax),za(nmax)
dimension x2(2,nmax),y2(2,nmax),z2(2,nmax)
character*10 aa1,ra1,aa2,ra2,du2
integer mm(2,nmax)
dimension nres1(2,nmax,32:122),nres2(2,nmax,32:122,32:122) !number of atoms
character*5 atom1(50) !atom name
dimension m12(2,nmax)
ccc mmCIF
character*500 ctmp(1000),ent(nmax),mn(nmax)
character*500 ch_t,ent_t,mn_t
character*20 Aatom(2,namax)
character Agroup(2,namax)*6
character Ares(2,namax)*3,Aalt(2,namax)
character Ains(2,namax),Ach(2,namax),Aent(2,namax)
character Cins(2,nmax)
integer Aatomi(2,namax),Aresi(2,namax)
dimension iform(10),xx(2,namax),yy(2,namax),zz(2,namax),nL(2)
ccc
ccc RMSD:
double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)
double precision u(3,3),t(3),rms,drms !armsd is real
data w /nmax*1.0/
ccc
double precision u2(3,3),t2(3) !for output
data aa/ 'BCK','GLY','ALA','SER','CYS',
& 'VAL','THR','ILE','PRO','MET',
& 'ASP','ASN','LEU','LYS','GLU',
& 'GLN','ARG','HIS','PHE','TYR',
& 'TRP','CYX'/
character*1 slc(-1:20)
data slc/'X','G','A','S','C',
& 'V','T','I','P','M',
& 'D','N','L','K','E',
& 'Q','R','H','F','Y',
& 'W','C'/
*****instructions ----------------->
call getarg(1,fnam)
if(fnam.eq.' '.or.fnam.eq.'?'.or.fnam.eq.'-h')then
write(*,*)
write(*,*)'Brief instruction for running TM-score program:'
write(*,*)'(For detail: Zhang & Skolnick, Proteins, 2004',
& ' 57:702-10)'
write(*,*)
write(*,*)'1. Run TM-score to compare ''model'' and ',
& '''native'':'
write(*,*)' >TMscore model native'
write(*,*)
write(*,*)'2. Run TM-score to compare two complex structures',
& ' with multiple chains'
write(*,*)' (Compare all chains with the same chain',
& ' identifier)'
write(*,*)' >TMscore -c model native'
write(*,*)
write(*,*)'3. TM-score normalized with an assigned scale d0',
& ' e.g. 5 A:'
write(*,*)' >TMscore model native -d 5'
write(*,*)
write(*,*)'4. TM-score normalized by a specific length, ',
& 'e.g. 120 AA:'
write(*,*)' >TMscore model native -l 120'
write(*,*)
write(*,*)'5. TM-score with superposition output, e.g. ',
& '''TM.sup'':'
write(*,*)' >TMscore model native -o TM.sup'
write(*,*)' To view superimposed CA-traces by rasmol ',
& 'or pymol:'
write(*,*)' >rasmol -script TM.sup'
write(*,*)' >pymol -d @TM.sup.pml'
write(*,*)' To view superimposed atomic models:'
write(*,*)' >rasmol -script TM.sup_atm'
write(*,*)' >pymol -d @TM.sup_atm.pml'
write(*,*)
goto 9999
endif
******* options ----------->
m_out=-1
m_fix=-1
m_len=-1
narg=iargc()
i=0
j=0
m_complex=0
115 continue
i=i+1
call getarg(i,fnam)
if(fnam.eq.'-o')then
m_out=1
i=i+1
call getarg(i,outname)
elseif(fnam.eq.'-d')then
m_fix=1
i=i+1
call getarg(i,fnam)
read(fnam,*)d0_fix
elseif(fnam.eq.'-c')then
m_complex=1
elseif(fnam.eq.'-l')then
m_len=1
i=i+1
call getarg(i,fnam)
read(fnam,*)l0_fix
else
j=j+1
pdb(j)=fnam
endif
if(i.lt.narg)goto 115
**********decide file format (PDB or mmCIF) ------------------->
do j=1,2
iform(j)=0 !format of pdb(j)
open(unit=10,file=pdb(j),status='old')
do while(iform(j).eq.0)
read(10,*)s
if(s(1:6).eq.'HEADER'.or.s(1:4).eq.'ATOM'.or.
& s(1:6).eq.'REMARK')then
iform(j)=1 !PDB format
elseif(s(1:4).eq.'data'.or.s(1:1).eq.'#'.or.
& s(1:5).eq.'loop_')then
iform(j)=2 !mmCIF format
endif
enddo
if(iform(j).eq.0)then
write(*,*)'error: file must in PDB or mmCIF format!'
endif
close(10)
enddo
*******^^^^ format is decided ^^^^^^^^^^^^^^^^^^^^^^^^^^
c write(*,*)'m_complex=',m_complex
cccccccccRead data from CA file ---------------->
c we only need to read following (keep first chain, keep only one altLoc):
c x,y,z2(ic,i)----(x,y,z)
c mm(2,nmax)---residue order number, for gapless threading
c ss(2,nmax)---residue name ('GLY') for seq_ID calculation and output
c Cins(ic,i)---insertion
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
do 1001 ic=1,2 !ic=1,2 for file1 and file2
i=0
open(unit=10,file=pdb(ic),status='old')
if(iform(ic).eq.1)then !file in PDB format------->
do while (.true.) !start do-while ---------->
read(10,'(A500)',end=1013) s
if(i.gt.0)then
if(m_complex.eq.0)then
if(s(1:3).eq.'TER'.or.s(1:3).eq.'MOD'.
& or.s(1:3).eq.'END')then
goto 1013 !only read the first chain
endif
else
*** skip model_number >=2 ----------->
if(s(1:5).eq.'MODEL')then
read(s,*)du,model_num
if(model_num.gt.1)then
do while(.true.)
read(10,'(A500)',end=1013) s
if(s(1:6).eq.'ENDMDL')goto 1014
enddo
endif
endif
*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
endif
endif
if(s(1:4).eq.'ATOM')then !read 'ATOM' =======>
read(s(13:16),*)du4 !will remove space before 'CA'
if(du4.eq.'CA')then !read 'CA' ---------->
du1=s(27:27) !residue insertion tag
*******remove repeated altLoc atoms (this does not care inserted residues) -------->
mk=1
if(s(17:17).ne.' ')then !with Alternate atom
read(s(23:26),*)i8 !res ID
if(nres1(ic,i8,ichar(du1)).ge.1)then !since CA, cannot be >1
mk=-1 !this residue was already read, skip it
endif
endif
c^^^^^^^^^altLoc checked (mk.ne.1 will be skipped) ^^^^^^^^^
if(mk.eq.1)then !mk=1 ------------>
i=i+1
read(s,'(a6,I5,a6,A3,a1,A1,I4,A1,a3,3F8.3)') !variable include space, different from read(*,*)
& du,itmp,du,aanam,du,ch(i),mm(ic,i),
& Cins(ic,i),du,x2(ic,i),y2(ic,i),z2(ic,i)
***
i8=mm(ic,i)
nres1(ic,i8,ichar(du1))=
& nres1(ic,i8,ichar(du1))+1 !nres1 only for check altLoc
***
ss(ic,i)=aanam !residue name, 'GLY', for seq_ID
if(i.ge.nmax)goto 1013
endif !<-----mk=1
endif !<---- read 'CA'
endif !<==== read 'ATOM'
1014 continue
enddo !<----end do-while
else !<----mmCIF format,if(iform(1).eq.2)
in=0 !number of entries
do while (.true.) !start do-while ---------->
read(10,'(A500)',end=1013) s
if(i.gt.0)then !skip unuseful read to save time, suppose '#' appear before complex completed
if(s(1:1).eq.'#'.or.s(1:5).eq.'loop_'.or.
& s(1:6).eq.'HETATM')goto 1013
endif
if(s(1:11).eq.'_atom_site.')then
in=in+1
read(s,*)du
if(du.eq.'_atom_site.label_atom_id')i_atom=in !CA,O, no need
if(du.eq.'_atom_site.label_alt_id')i_alt=in !'.',A,B
if(du.eq.'_atom_site.label_comp_id')i_res=in !GLY,LEU
if(du.eq.'_atom_site.label_asym_id')i_ch=in !A,B
if(du.eq.'_atom_site.auth_asym_id')i_ch=in !A,B, using later one
if(du.eq.'_atom_site.label_entity_id')i_ent=in !1,2,a,b
if(du.eq.'_atom_site.label_seq_id')i_resi=in !1,2,3,
if(du.eq.'_atom_site.auth_seq_id')i_resi=in !1,2,3, identical to PDB res
if(du.eq.'_atom_site.pdbx_PDB_ins_code')i_ins=in !A,?
if(du.eq.'_atom_site.Cartn_x')i_x=in !x, 1.234
if(du.eq.'_atom_site.Cartn_y')i_y=in !y, 1.234
if(du.eq.'_atom_site.Cartn_z')i_z=in !z, 1.234
if(du.eq.'_atom_site.pdbx_PDB_model_num')i_mn=in !model number, 1,2,3
endif
if(s(1:4).eq.'ATOM')then !read 'ATOM' =======>
read(s,*)(ctmp(j),j=1,in) !no space before characters
if(ctmp(i_atom).eq.'CA')then !read 'CA' ---------->
if(i.gt.0)then
if(m_complex.eq.0)then !monomer
if(i_mn.gt.1)then !sometimes it may have no i_mn
read(ctmp(i_mn),*)mn_t
if(mn_t.ne.mn(i)) goto 1013 !only read first model
endif
read(ctmp(i_ch),*)ch_t
if(ch_t.ne.ch(i)) goto 1013 !only read first chain
read(ctmp(i_ent),*)ent_t
if(ent_t.ne.ent(i)) goto 1013 !only read first entity
else !dimer
if(i_mn.gt.1)then !sometimes it may have no i_mn
read(ctmp(i_mn),*)mn_t
if(mn_t.ne.mn(i)) goto 1016 !only read first model
endif
endif
endif
*******remove repeated altLoc atoms (this does not care inserted residues) -------->
mk=1
du1=ctmp(i_ins) !read insertion tag
if(ctmp(i_alt).ne.'.')then !with Alternate atom
read(ctmp(i_resi),*)i8 !res ID
if(nres1(ic,i8,ichar(du1)).ge.1)then !since CA, cannot be >1
mk=-1 !this residue was already read, skip it
endif
endif
c^^^^^^^^^altLoc checked (mk.ne.1 will be skipped) ^^^^^^^^^
if(mk.eq.1)then !mk=1 ------------>
i=i+1
read(ctmp(i_ch),*)ch(i) !for check other chain
read(ctmp(i_ent),*)ent(i) !for check other entity
read(ctmp(i_mn),*)mn(i) !for check model number
***
read(ctmp(i_x),*)x2(ic,i)
read(ctmp(i_y),*)y2(ic,i)
read(ctmp(i_z),*)z2(ic,i)
read(ctmp(i_resi),*)mm(ic,i) !residue order, 4,5,6
read(ctmp(i_ins),*)Cins(ic,i) !residue insertion, A, ?
if(Cins(ic,i).eq.'?')Cins(ic,i)=' '
ss(ic,i)=ctmp(i_res) !residue name, 'GLY', for seq_ID
***
i8=mm(ic,i)
nres1(ic,i8,ichar(du1))=
& nres1(ic,i8,ichar(du1))+1 !nres1 only for check altLoc
***
if(i.ge.nmax)goto 1013
endif !<-----mk=1
endif !<-----read 'CA'
endif !<==== read 'ATOM'
1016 continue !skip model_num >1
enddo !<----end do-while
endif !if(iform(ic).eq.2)
1013 continue
close(10)
c-------convert 'GLY' to 'G', etc ------------>
if(ic.eq.1)then
nseqA=i
do i=1,nseqA
chA(i)=ch(i)
nresA(i)=mm(ic,i)
seqA(i)=ss(ic,i) !GLY
ins1(i)=Cins(1,i)
xa(i)=x2(1,i)
ya(i)=y2(1,i)
za(i)=z2(1,i)
do j=-1,20
if(ss(1,i).eq.aa(j))then
seq1A(i)=slc(j) !G
goto 121
endif
enddo
seq1A(i)=slc(-1)
121 continue
enddo
else
nseqB=i
do i=1,nseqB
chB(i)=ch(i)
nresB(i)=mm(ic,i)
seqB(i)=ss(ic,i) !'GLY'
ins2(i)=Cins(2,i)
xb(i)=x2(2,i)
yb(i)=y2(2,i)
zb(i)=z2(2,i)
do j=-1,20
if(ss(2,i).eq.aa(j))then
seq1B(i)=slc(j) !'G'
goto 122
endif
enddo
seq1B(i)=slc(-1)
122 continue
enddo
endif
1001 continue !ic=1,2 for file1 and file2
c^^^^^^^^^^^^^read input files completed ^^^^^^^^^^^^^^^^^^^^^^
c do i=1,nseqA
c write(*,*)i,xa(i),seqA(i)
c enddo
c do i=1,nseqB
c write(*,*)i,xb(i),seqB(i)
c enddo
******************************************************************
* pickup the aligned residues:
******************************************************************
if(m_complex.eq.0)then !monomer
k=0
do i=1,nseqA
do j=1,nseqB
if(nresA(i).eq.nresB(j))then
if(ins1(i).eq.ins2(j))then
k=k+1
iA(k)=i
iB(k)=j
goto 205
endif
endif
enddo
205 continue
enddo
else !complex
k=0
do i=1,nseqA
do j=1,nseqB
if(nresA(i).eq.nresB(j).and.chA(i).eq.chB(j))then
if(ins1(i).eq.ins2(j))then !Residue_insertion_code
k=k+1
iA(k)=i
iB(k)=j
goto 206
endif
endif
enddo
206 continue
enddo
endif
n_ali=k !number of aligned residues
if(n_ali.lt.1)then
write(*,*)'There is no common residues in the input structures'
goto 9999
endif
c do i=1,n_ali
c write(*,*)i,iA(i),iB(i)
c enddo
******************************************************************
* check the residue serial numbers ------------->
if(m_complex.eq.0)then
nA_repeat=0
do i=1,nseqA
do j=i+1,nseqA
if(nresA(i).eq.nresA(j))then
if(ins1(i).eq.ins1(j))then
nA_repeat=nA_repeat+1
endif
endif
enddo
enddo
if(nA_repeat.gt.0)then
write(*,380)nA_repeat
endif
380 format('Warning: TMscore calculation can be wrong because ',
& 'there are ',I3,' residues with the serial number same ',
& 'as others in first Chain. Please modify the PDB file ',
& 'and rerun the program!!')
nB_repeat=0
do i=1,nseqB
do j=i+1,nseqB
if(nresB(i).eq.nresB(j))then
if(ins2(i).eq.ins2(j))then
nB_repeat=nB_repeat+1
endif
endif
enddo
enddo
if(nB_repeat.gt.0)then
write(*,381)nB_repeat
endif
381 format('Warning: TMscore calculation can be wrong because ',
& 'there are ',I3,' residues with the serial number same ',
& 'as others in second Chain. Please modify the PDB file ',
& 'and rerun the program!!')
endif
************/////
* parameters:
*****************
*** d0------------->
if(nseqB.gt.15)then
d0=1.24*(nseqB-15)**(1.0/3.0)-1.8
else
d0=0.5
endif
if(m_len.eq.1)then
d0=1.24*(l0_fix-15)**(1.0/3.0)-1.8
endif
if(d0.lt.0.5)d0=0.5
if(m_fix.eq.1)d0=d0_fix
*** d0_search ----->
d0_search=d0
if(d0_search.gt.8)d0_search=8
if(d0_search.lt.4.5)d0_search=4.5
*** iterative parameters ----->
n_it=20 !maximum number of iterations
d_output=5 !for output alignment
if(m_fix.eq.1)d_output=d0_fix
n_init_max=6 !maximum number of L_init
n_init=0
L_ini_min=4
if(n_ali.lt.4)L_ini_min=n_ali
do i=1,n_init_max-1
n_init=n_init+1
L_ini(n_init)=n_ali/2**(n_init-1)
if(L_ini(n_init).le.L_ini_min)then
L_ini(n_init)=L_ini_min
goto 402
endif
enddo
n_init=n_init+1
L_ini(n_init)=L_ini_min
402 continue
******************************************************************
* find the maximum score starting from local structures superposition
******************************************************************
score_max=-1 !TM-score
score_maxsub_max=-1 !MaxSub-score
score10_max=-1 !TM-score10
n_GDT05_max=-1 !number of residues<0.5
n_GDT1_max=-1 !number of residues<1
n_GDT2_max=-1 !number of residues<2
n_GDT4_max=-1 !number of residues<4
n_GDT8_max=-1 !number of residues<8
do 333 i_init=1,n_init
L_init=L_ini(i_init)
iL_max=n_ali-L_init+1
do 300 iL=1,iL_max !on aligned residues, [1,nseqA]
LL=0
ka=0
do i=1,L_init
k=iL+i-1 ![1,n_ali] common aligned
r_1(1,i)=xa(iA(k))
r_1(2,i)=ya(iA(k))
r_1(3,i)=za(iA(k))
r_2(1,i)=xb(iB(k))
r_2(2,i)=yb(iB(k))
r_2(3,i)=zb(iB(k))
ka=ka+1
k_ali(ka)=k
LL=LL+1
enddo
if(i_init.eq.1)then !global superposition
call u3b(w,r_1,r_2,LL,2,rms,u,t,ier) !0:rmsd; 1:u,t; 2:rmsd,u,t
armsd=dsqrt(rms/LL)
rmsd_ali=armsd
else
call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2
endif
do j=1,nseqA
xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)
yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
enddo
d=d0_search-1
call score_fun !init, get scores, n_cut+i_ali(i) for iteration
if(score_max.lt.score)then
score_max=score
ka0=ka
do i=1,ka0
k_ali0(i)=k_ali(i)
enddo
endif
if(score10_max.lt.score10)score10_max=score10
if(score_maxsub_max.lt.score_maxsub)score_maxsub_max=
& score_maxsub
if(n_GDT05_max.lt.n_GDT05)n_GDT05_max=n_GDT05
if(n_GDT1_max.lt.n_GDT1)n_GDT1_max=n_GDT1
if(n_GDT2_max.lt.n_GDT2)n_GDT2_max=n_GDT2
if(n_GDT4_max.lt.n_GDT4)n_GDT4_max=n_GDT4
if(n_GDT8_max.lt.n_GDT8)n_GDT8_max=n_GDT8
*** iteration for extending ---------------------------------->
d=d0_search+1
do 301 it=1,n_it
LL=0
ka=0
do i=1,n_cut
m=i_ali(i) ![1,n_ali]
r_1(1,i)=xa(iA(m))
r_1(2,i)=ya(iA(m))
r_1(3,i)=za(iA(m))
r_2(1,i)=xb(iB(m))
r_2(2,i)=yb(iB(m))
r_2(3,i)=zb(iB(m))
ka=ka+1
k_ali(ka)=m
LL=LL+1
enddo
call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2
do j=1,nseqA
xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)
yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
enddo
call score_fun !get scores, n_cut+i_ali(i) for iteration
if(score_max.lt.score)then
score_max=score
ka0=ka
do i=1,ka
k_ali0(i)=k_ali(i)
enddo
endif
if(score10_max.lt.score10)score10_max=score10
if(score_maxsub_max.lt.score_maxsub)score_maxsub_max
& =score_maxsub
if(n_GDT05_max.lt.n_GDT05)n_GDT05_max=n_GDT05
if(n_GDT1_max.lt.n_GDT1)n_GDT1_max=n_GDT1
if(n_GDT2_max.lt.n_GDT2)n_GDT2_max=n_GDT2
if(n_GDT4_max.lt.n_GDT4)n_GDT4_max=n_GDT4
if(n_GDT8_max.lt.n_GDT8)n_GDT8_max=n_GDT8
if(it.eq.n_it)goto 302
if(n_cut.eq.ka)then
neq=0
do i=1,n_cut
if(i_ali(i).eq.k_ali(i))neq=neq+1
enddo
if(n_cut.eq.neq)goto 302
endif
301 continue !for iteration
302 continue
300 continue !for shift
333 continue !for initial length, L_ali/M
ratio=1
if(m_len.gt.0)then
ratio=float(nseqB)/float(l0_fix)
endif
******************************************************************
* Output
******************************************************************
*** output TM-scale ---------------------------->
write(*,*)
write(*,*)'*****************************************************',
& '************************'
write(*,*)'* TM-SCORE ',
& ' *'
write(*,*)'* A scoring function to assess the similarity of prot',
& 'ein structures *'
write(*,*)'* Based on statistics: ',
& ' *'
write(*,*)'* 0.0 < TM-score < 0.17, random structural simi',
& 'larity *'
write(*,*)'* 0.5 < TM-score < 1.00, in about the same fold',
& ' *'
write(*,*)'* Reference: Yang Zhang and Jeffrey Skolnick, ',
& 'Proteins 2004 57: 702-710 *'
write(*,*)'* For comments, please email to: zhng@umich.edu ',
& ' *'
write(*,*)'*****************************************************',
& '************************'
write(*,*)
write(*,501)pdb(1),nseqA
501 format('Structure1: ',A10,' Length= ',I4)
if(m_len.eq.1)then
write(*,411)pdb(2),nseqB
write(*,412)l0_fix
else
write(*,502)pdb(2),nseqB
endif
411 format('Structure2: ',A10,' Length= ',I4)
412 format('TM-score is notmalized by ',I4)
502 format('Structure2: ',A10,' Length= ',I4,
& ' (by which all scores are normalized)')
write(*,503)n_ali
503 format('Number of residues in common= ',I4)
write(*,513)rmsd_ali
513 format('RMSD of the common residues= ',F8.3)
write(*,*)
if(m_len.eq.1)then
score_max=score_max*float(nseqB)/float(l0_fix)
endif
write(*,504)score_max,d0
504 format('TM-score = ',f6.4,' (d0=',f5.2,')')
write(*,505)score_maxsub_max*ratio
505 format('MaxSub-score= ',f6.4,' (d0= 3.50)')
score_GDT=(n_GDT1_max+n_GDT2_max+n_GDT4_max+n_GDT8_max)
& /float(4*nseqB)
write(*,506)score_GDT*ratio,n_GDT1_max/float(nseqB)*ratio,
& n_GDT2_max/float(nseqB)*ratio,n_GDT4_max/float(nseqB)*ratio,
& n_GDT8_max/float(nseqB)*ratio
506 format('GDT-TS-score= ',f6.4,' %(d<1)=',f6.4,' %(d<2)=',f6.4,
$ ' %(d<4)=',f6.4,' %(d<8)=',f6.4)
score_GDT_HA=(n_GDT05_max+n_GDT1_max+n_GDT2_max+n_GDT4_max)
& /float(4*nseqB)
write(*,507)score_GDT_HA*ratio,n_GDT05_max/float(nseqB)*ratio,
& n_GDT1_max/float(nseqB)*ratio,n_GDT2_max/float(nseqB)*ratio,
& n_GDT4_max/float(nseqB)*ratio
507 format('GDT-HA-score= ',f6.4,' %(d<0.5)=',f6.4,' %(d<1)=',f6.4,
$ ' %(d<2)=',f6.4,' %(d<4)=',f6.4)
write(*,*)
*** recall and output the superposition of maxiumum TM-score:
LL=0
do i=1,ka0
m=k_ali0(i) !record of the best alignment
r_1(1,i)=xa(iA(m))
r_1(2,i)=ya(iA(m))
r_1(3,i)=za(iA(m))
r_2(1,i)=xb(iB(m))
r_2(2,i)=yb(iB(m))
r_2(3,i)=zb(iB(m))
LL=LL+1
enddo
call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2
do j=1,nseqA
xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)
yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
enddo
********* extract rotation matrix ------------>
write(*,*)'-------- rotation matrix to rotate Chain-1 to ',
& 'Chain-2 ------'
write(*,*)'i t(i) u(i,1) u(i,2) ',
& ' u(i,3)'
do i=1,3
write(*,304)i,t(i),u(i,1),u(i,2),u(i,3)
enddo
c do j=1,nseqA
c xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)
c yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
c zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
c write(*,*)j,xt(j),yt(j),zt(j)
c enddo
write(*,*)
304 format(I2,f18.10,f15.10,f15.10,f15.10)
********* rmsd in superposed regions --------------->
d=d_output !for output
call score_fun() !give i_ali(i), score_max=score now
******* for output ---------->
if(m_out.eq.1)then
do i=1,3
t2(i)=t(i)
do j=1,3
u2(i,j)=u(i,j)
enddo
enddo
endif
*******************************
*** record aligned residues by i=[1,nseqA], for sequenceM()------------>
do i=1,nseqA
iq(i)=0
enddo
do i=1,n_cut
j=iA(i_ali(i)) ![1,nseqA]
k=iB(i_ali(i)) ![1,nseqB]
dis=sqrt((xt(j)-xb(k))**2+(yt(j)-yb(k))**2+(zt(j)-zb(k))**2)
c write(*,*)i,j,k,dis,d_output,'1--'
if(dis.lt.d_output)then
iq(j)=1
endif
enddo
*******************************************************************
*** output aligned sequences
if(m_complex.eq.0)then
k=0
i=1
j=1
800 continue
if(i.gt.nseqA.and.j.gt.nseqB)goto 802
if(i.gt.nseqA.and.j.le.nseqB)then
k=k+1
sequenceA(k)='-'
sequenceB(k)=seq1B(j)
sequenceM(k)=' '
j=j+1
goto 800
endif
if(i.le.nseqA.and.j.gt.nseqB)then
k=k+1
sequenceA(k)=seq1A(i)
sequenceB(k)='-'
sequenceM(k)=' '
i=i+1
goto 800
endif
if(nresA(i).eq.nresB(j))then
k=k+1
sequenceA(k)=seq1A(i)
sequenceB(k)=seq1B(j)
if(iq(i).eq.1)then
sequenceM(k)=':'
else
sequenceM(k)=' '
endif
i=i+1
j=j+1
goto 800
elseif(nresA(i).lt.nresB(j))then
k=k+1
sequenceA(k)=seq1A(i)
sequenceB(k)='-'
sequenceM(k)=' '
i=i+1
goto 800
elseif(nresB(j).lt.nresA(i))then
k=k+1
sequenceA(k)='-'
sequenceB(k)=seq1B(j)
sequenceM(k)=' '
j=j+1
goto 800
endif
802 continue
else
k=0
i=1 !
j=1
803 continue
if(i.gt.nseqA.and.j.gt.nseqB)goto 804
if(i.gt.nseqA.and.j.le.nseqB)then
k=k+1
sequenceA(k)='-'
sequenceB(k)=seq1B(j)
sequenceM(k)=' '
j=j+1
goto 803
endif
if(i.le.nseqA.and.j.gt.nseqB)then
k=k+1
sequenceA(k)=seq1A(i)
sequenceB(k)='-'
sequenceM(k)=' '
i=i+1
goto 803
endif
if(chA(i).ne.chB(j))then
kk=0 !check if chA(i) match later chains
do i2=j,nseqB
if(chA(i).eq.chB(i2))then
kk=kk+1
endif
enddo
if(kk.eq.0)then !chA(i) is not matched
k=k+1
sequenceA(k)=seq1A(i)
sequenceB(k)='-'
sequenceM(k)=' '
i=i+1
goto 803
endif
kk=0 !check if chB(j) match later chains
do i1=i,nseqA
if(chA(i1).eq.chB(j))then
kk=kk+1
endif
enddo
if(kk.eq.0)then !chB(j) is not matched
k=k+1
sequenceA(k)='-'
sequenceB(k)=seq1B(j)
sequenceM(k)=' '
j=j+1
goto 803
endif
write(*,*)'Chains in complexes have crossed order, ',
& 'therefore, no alignment is output'
stop
else
if(nresA(i).eq.nresB(j))then
k=k+1
sequenceA(k)=seq1A(i)
sequenceB(k)=seq1B(j)
if(iq(i).eq.1)then
sequenceM(k)=':'
else
sequenceM(k)=' '
endif
i=i+1
j=j+1
goto 803
elseif(nresA(i).lt.nresB(j))then
k=k+1
sequenceA(k)=seq1A(i)
sequenceB(k)='-'
sequenceM(k)=' '
i=i+1
goto 803
elseif(nresB(j).lt.nresA(i))then
k=k+1
sequenceA(k)='-'
sequenceB(k)=seq1B(j)
sequenceM(k)=' '
j=j+1
goto 803
endif
endif
804 continue
endif
ccc RMSD (d<5.0)-------->
LL=0
do i=1,n_cut
m=i_ali(i) ![1,nseqA]
r_1(1,i)=xa(iA(m))
r_1(2,i)=ya(iA(m))
r_1(3,i)=za(iA(m))
r_2(1,i)=xb(iB(m))
r_2(2,i)=yb(iB(m))
r_2(3,i)=zb(iB(m))
LL=LL+1
enddo
call u3b(w,r_1,r_2,LL,0,rms,u,t,ier)
armsd=dsqrt(rms/LL)
rmsd=armsd
write(*,600)d_output,n_cut,rmsd
600 format('Superposition in the TM-score: Length(d<',f3.1,
$ ')=',i3,' RMSD=',f6.2)
write(*,603)d_output
603 format('(":" denotes the residue pairs of distance < ',f3.1,
& ' Angstrom)')
write(*,601)(sequenceA(i),i=1,k)
write(*,601)(sequenceM(i),i=1,k)
write(*,601)(sequenceB(i),i=1,k)
write(*,602)(mod(i,10),i=1,k)
601 format(2000A1)
602 format(2000I1)
write(*,*)
c^^^^^^^^^^screen output is done ^^^^^^^^^^^^^^^^^^^^^^^^^^
if(m_out.ne.1)then
stop
endif
*******************************************************
* output alignment structure for Rasmal review *
*******************************************************
c*****************************************************************
c************* Step-1: read all-atom structures ******************
c*****************************************************************
do 1002 ic=1,2 !ic=1,2 for file1 and file2
nL(ic)=0 !number of lines in PDB file
open(unit=10,file=pdb(ic),status='old')
if(iform(ic).eq.1)then !file in PDB format %%%%%%%%%%------->
do while (.true.)
read(10,'(A500)',end=1015) s
if(nL(ic).gt.0)then !decide n_cut
if(m_complex.eq.0)then
if(s(1:3).eq.'TER'.or.s(1:3).eq.'MOD'.
& or.s(1:3).eq.'END')then
goto 1015 !no ligand allowed
endif
else
*** skip model_number >=2 ----------->
if(s(1:5).eq.'MODEL')then
read(s,*)du,model_num
if(model_num.gt.1)then
do while(.true.)
read(10,'(A500)',end=1015) s
if(s(1:6).eq.'ENDMDL')goto 1017
enddo
endif
endif
*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
endif
endif
if(s(1:6).eq.'ATOM ')then !read ATOM ====>
*******remove repeated altLoc atoms -------->
mk=1
du1=s(27:27) !read insertion tag
du3=s(22:22) !chain ID
if(s(17:17).ne.' ')then !with Alternate atom
du2=s(13:16) !atom ID
read(s(23:26),*)i8 !res ID
do i1=1,nres2(ic,i8,ichar(du1),ichar(du3)) !#of atoms for res_insert
if(du2.eq.atom1(i1))then !such atom was already read
mk=-1
endif
enddo
endif
c^^^^^^^^^altLoc checked (mk.ne.1) will be skipped) ^^^^^^^^^
if(mk.eq.1)then !mk=1--------->
nL(ic)=nL(ic)+1
read(s,8999)Agroup(ic,nL(ic)),Aatomi(ic,nL(ic)),
& du,Aatom(ic,nL(ic)),Aalt(ic,nL(ic)),
& Ares(ic,nL(ic)),du,Ach(ic,nL(ic)),
& Aresi(ic,nL(ic)),Ains(ic,nL(ic)),du,
& xx(ic,nL(ic)),yy(ic,nL(ic)),zz(ic,nL(ic))
***
i8=Aresi(ic,nL(ic))
if(nres2(ic,i8,ichar(du1),ichar(du3)).lt.50)then
nres2(ic,i8,ichar(du1),ichar(du3))=
& nres2(ic,i8,ichar(du1),ichar(du3))+1 !#of atoms for res_ins
atom1(nres2(ic,i8,ichar(du1),ichar(du3)))=
& Aatom(ic,nL(ic)) !atom ID
endif
***
if(nL(ic).ge.namax)goto 1015
endif !<------mk=1
endif !<======read ATOM
1017 continue
enddo !<--- do while
else !<----mmCIF format,if(iform(1).eq.2) %%%%%%%%%%%%%%%%
in=0 !number of entries
do while (.true.) !start do-while ---------->
read(10,'(A500)',end=1015) s
if(nL(ic).gt.0)then !skip unuseful read to save time
if(s(1:1).eq.'#'.or.s(1:5).eq.'loop_')goto 1015
endif
if(s(1:11).eq.'_atom_site.')then
in=in+1
read(s,*)du
if(du.eq.'_atom_site.group_PDB')i_group=in !'ATOM','HETATM'
if(du.eq.'_atom_site.id')i_atomi=in !1,2,3,4
if(du.eq.'_atom_site.type_symbol')i_type=in !N,C,O
if(du.eq.'_atom_site.label_atom_id')i_atom=in !CA,O
if(du.eq.'_atom_site.label_alt_id')i_alt=in !'.',A,B
if(du.eq.'_atom_site.label_comp_id')i_res=in !GLY,LEU
if(du.eq.'_atom_site.label_asym_id')i_ch=in !A,B
if(du.eq.'_atom_site.auth_asym_id')i_ch=in !A,B, using later one
if(du.eq.'_atom_site.label_entity_id')i_ent=in !1,2,a,b
if(du.eq.'_atom_site.label_seq_id')i_resi=in !1,2,3
if(du.eq.'_atom_site.auth_seq_id')i_resi=in !1,2,3, identical to PDB res
if(du.eq.'_atom_site.pdbx_PDB_ins_code')i_ins=in !A,?
if(du.eq.'_atom_site.Cartn_x')i_x=in !x, 1.234
if(du.eq.'_atom_site.Cartn_y')i_y=in !y, 1.234
if(du.eq.'_atom_site.Cartn_z')i_z=in !z, 1.234
if(du.eq.'_atom_site.pdbx_PDB_model_num')i_mn=in !model number, 1,2,3
endif
if(s(1:4).eq.'ATOM')then !read 'ATOM' =======>
read(s,*)(ctmp(j),j=1,in)
if(nL(ic).gt.0)then
if(m_complex.eq.0)then !monomer
if(i_mn.gt.1)then !sometimes it may have no i_mn
read(ctmp(i_mn),*)mn_t
if(mn_t.ne.mn(i)) goto 1015 !only read first model
endif
read(ctmp(i_ch),*)ch_t
if(ch_t.ne.Ach(ic,nL(ic))) goto 1015
read(ctmp(i_ent),*)ent_t
if(ent_t.ne.Aent(ic,nL(ic))) goto 1015
else
if(i_mn.gt.1)then !sometimes it may have no i_mn
read(ctmp(i_mn),*)mn_t
if(mn_t.ne.mn(i)) goto 1018 !only read first model
endif
endif
endif
*******remove repeated altLoc atoms -------->
mk=1
du1=ctmp(i_ins) !read insertion tag
du3=ctmp(i_ch) !chain ID
if(ctmp(i_alt).ne.'.')then !with Alternate atom
du2=ctmp(i_atom) !atom ID
read(ctmp(i_resi),*)i8 !res ID
do i1=1,nres2(ic,i8,ichar(du1),ichar(du3)) !#of atoms for res_insert
if(du2.eq.atom1(i1))then !such atom was already read
mk=-1
endif
enddo
endif
c^^^^^^^^^altLoc checked (mk.ne.1) will be skipped) ^^^^^^^^^
if(mk.eq.1)then !mk=1 -------------->
nL(ic)=nL(ic)+1
read(ctmp(i_group),*)Agroup(ic,nL(ic))
read(ctmp(i_atomi),*)Aatomi(ic,nL(ic))
read(ctmp(i_atom),*)Aatom(ic,nL(ic))
********add space before Aatom(ic,nL(ic)) for output ------>
if(Aatom(ic,nL(ic))(4:4).eq.' ')then
Aatom(ic,nL(ic))=' '//Aatom(ic,nL(ic))
endif
c read(ctmp(i_alt),*)Aalt(ic,nL(ic)) ! not used, because we alway use 1 atom for altLoc
c if(Aalt(ic,nL(ic)).eq.'.')Aalt(ic,nL(ic))=' '
read(ctmp(i_res),*)Ares(ic,nL(ic))
read(ctmp(i_ch),*)Ach(ic,nL(ic)) !for check other chain
read(ctmp(i_ent),*)Aent(ic,nL(ic)) !for check other entity
read(ctmp(i_mn),*)mn(i) !for check model number
read(ctmp(i_resi),*)Aresi(ic,nL(ic))
read(ctmp(i_ins),*)Ains(ic,nL(ic))
if(Ains(ic,nL(ic)).eq.'?')Ains(ic,nL(ic))=' '
***
read(ctmp(i_x),*)xx(ic,nL(ic))
read(ctmp(i_y),*)yy(ic,nL(ic))
read(ctmp(i_z),*)zz(ic,nL(ic))
***
i8=Aresi(ic,nL(ic))
if(nres2(ic,i8,ichar(du1),ichar(du3)).lt.50)then
nres2(ic,i8,ichar(du1),ichar(du3))=
& nres2(ic,i8,ichar(du1),ichar(du3))+1 !#of atoms for res_ins
atom1(nres2(ic,i8,ichar(du1),ichar(du3)))=
& Aatom(ic,nL(ic)) !atom ID
endif
***
if(nL(ic).ge.namax)goto 1015
endif !<---- mk=1
endif !<==== read 'ATOM'
1018 continue
enddo !<----end do-while
endif !<----mmCIF format,if(iform(1).eq.2) %%%%%%%%%
1015 continue
close(10)
1002 continue !ic=1,2 for file1 and file2
8999 format(a6,I5,a1,A4,a1,A3,a1,A1,I4,A1,a3,3F8.3)
c**************************************************************
c************* Step-2: output 'aaa' (CA only) ***************
c**************************************************************
OPEN(unit=7,file=outname,status='unknown') !pdb1.aln + pdb2.aln
*************for pymol preset ------>
xxx_p=outname(1:len_trim(outname))//'.pml' !for pymol script
xxx_pdb=outname(1:len_trim(outname))//'.pdb' !for pymol script
OPEN(unit=11,file=xxx_p,status='unknown')
OPEN(unit=12,file=xxx_pdb,status='unknown')
write(11,'(A,A)')'load ',xxx_pdb(1:len_trim(xxx_pdb))
write(11,'(A)')'hide all'
write(11,'(A)')'bg_color white'
write(11,'(A)')'color blue, chain A'
write(11,'(A)')'color red, chain B'
write(11,'(A)')'set transparency=0.2'
write(11,'(A)')'set stick_radius, 0.3'
write(11,'(A)')'show sticks, chain A'
write(11,'(A)')'show sticks, chain B'
*^^^^^^^^^ pymol preset complete ^^^^^^^^^^^^^^^^^^^
900 format(A)
901 format('select atomno= ',I5)
902 format('select atomno= ',I5)
write(7,900)'load inline'
write(7,900)'select atomno<50001'
write(7,900)'wireframe .45'
write(7,900)'select atomno>50000'
write(7,900)'wireframe .15'
write(7,900)'select all'
write(7,900)'color white' !all above atoms are white
do i=1,n_cut
write(7,901)iA(i_ali(i))
write(7,900)'color red'
write(7,902)50000+iB(i_ali(i))
write(7,900)'color red'
enddo
write(7,900)'select all'
write(7,900)'exit'
write(7,514)rmsd_ali
514 format('REMARK RMSD of the common residues=',F8.3)
write(7,515)score_max,d0
515 format('REMARK TM-score=',f6.4,' (d0=',f5.2,')')
do i=1,nseqA
write(7,1236)i,seqA(i),chA(i),nresA(i),ins1(i),
& xt(i),yt(i),zt(i)
write(12,1236)i,seqA(i),'A',nresA(i),ins1(i),
& xt(i),yt(i),zt(i)
enddo
write(7,1238)
write(12,1238)
do i=2,nseqA
write(7,1239)i-1,i
write(12,1239)i-1,i
enddo
do i=1,nseqB
write(7,1236)50000+i,seqB(i),chB(i),nresB(i),ins2(i),
& xb(i),yb(i),zb(i)
write(12,1236)50000+i,seqB(i),'B',nresB(i),ins2(i),
& xb(i),yb(i),zb(i)
enddo
write(7,1238)
write(12,1238)
do i=2,nseqB
write(7,1239)50000+i-1,50000+i
write(12,1239)50000+i-1,50000+i
enddo
close(7)
close(11)
close(12)
1236 format('ATOM ',i5,' CA ',A3,' ',A1,I4,A1,3X,3F8.3)
1238 format('TER')
1239 format('CONECT',I5,I5)
c**************************************************************
c************* Step-3: output 'aaa_atm' (all-atom) ***********
c**************************************************************
outname=outname(1:len_trim(outname))//'_atm'
OPEN(unit=7,file=outname,status='unknown') !pdb1.aln + pdb2.aln
*************for pymol preset ------>
xxx_p=outname(1:len_trim(outname))//'.pml' !for pymol script
xxx_pdb=outname(1:len_trim(outname))//'.pdb' !for pymol script
OPEN(unit=11,file=xxx_p,status='unknown')
OPEN(unit=12,file=xxx_pdb,status='unknown')
write(11,'(A,A)')'load ',xxx_pdb(1:len_trim(xxx_pdb))
write(11,'(A)')'hide all'
write(11,'(A)')'bg_color white'
write(11,'(A)')'color blue, chain A'
write(11,'(A)')'color red, chain B'
write(11,'(A)')'set transparency=0.2'
write(11,'(A)')'set stick_radius, 0.3'
write(11,'(A)')'show cartoon, chain A'
write(11,'(A)')'show cartoon, chain B'
*^^^^^^^^^ pymol preset complete ^^^^^^^^^^^^^^^^^^^
write(7,900)'load inline'
write(7,900)'select atomno<50001'
write(7,900)'color blue'
write(7,900)'select atomno>50000'
write(7,900)'color red'
write(7,900)'select all'
write(7,900)'cartoon'
write(7,900)'exit'
write(7,514)rmsd_ali
write(7,515)score_max,d0
*** chain1:
do i=1,nL(1)
ax=t2(1)+u2(1,1)*xx(1,i)+u2(1,2)*yy(1,i)+u2(1,3)*zz(1,i)
ay=t2(2)+u2(2,1)*xx(1,i)+u2(2,2)*yy(1,i)+u2(2,3)*zz(1,i)
az=t2(3)+u2(3,1)*xx(1,i)+u2(3,2)*yy(1,i)+u2(3,3)*zz(1,i)
write(7,8888)i,Aatom(1,i),Ares(1,i),Ach(1,i),
& Aresi(1,i),Ains(1,i),ax,ay,az
write(12,8888)i,Aatom(1,i),Ares(1,i),'A',
& Aresi(1,i),Ains(1,i),ax,ay,az
enddo
write(7,1238) !TER
write(12,1238) !TER
*** chain2:
do i=1,nL(2)
write(7,8888)50000+i,Aatom(2,i),Ares(2,i),Ach(2,i),
& Aresi(2,i),Ains(2,i),xx(2,i),yy(2,i),zz(2,i)
write(12,8888)50000+i,Aatom(2,i),Ares(2,i),'B',
& Aresi(2,i),Ains(2,i),xx(2,i),yy(2,i),zz(2,i)
enddo
write(7,1238) !TER
write(12,1238) !TER
close(7)
close(11)
close(12)
8888 format('ATOM ',I5,1x,A4,1x,A3,' ',A1,I4,A1,3x,3F8.3)
*^^^^^^^^^^^^^^^^^^ output finished ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9999 END
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c 1, collect those residues with dis<d;
c 2, calculate score_GDT, score_maxsub, score_TM
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
subroutine score_fun
PARAMETER(nmax=5000)
common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax)
common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB
common/para/d,d0,d0_fix
common/align/n_ali,iA(nmax),iB(nmax)
common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score
common/scores/score,score_maxsub,score_fix,score10
common/GDT/n_GDT05,n_GDT1,n_GDT2,n_GDT4,n_GDT8
double precision score,score_max,score_fix,score_fix_max
double precision score_maxsub,score10
d_tmp=d
21 n_cut=0 !number of residue-pairs dis<d, for iteration
n_GDT05=0 !for GDT-score, # of dis<0.5
n_GDT1=0 !for GDT-score, # of dis<1
n_GDT2=0 !for GDT-score, # of dis<2
n_GDT4=0 !for GDT-score, # of dis<4
n_GDT8=0 !for GDT-score, # of dis<8
score_maxsub_sum=0 !Maxsub-score
score_sum=0 !TMscore
score_sum10=0 !TMscore10
do k=1,n_ali
i=iA(k) ![1,nseqA] reoder number of structureA
j=iB(k) ![1,nseqB]
dis=sqrt((xt(i)-xb(j))**2+(yt(i)-yb(j))**2+(zt(i)-zb(j))**2)
*** for iteration:
if(dis.lt.d_tmp)then
n_cut=n_cut+1
i_ali(n_cut)=k ![1,n_ali], mark the residue-pairs in dis<d
endif
*** for GDT-score:
if(dis.le.8)then
n_GDT8=n_GDT8+1
if(dis.le.4)then
n_GDT4=n_GDT4+1
if(dis.le.2)then
n_GDT2=n_GDT2+1
if(dis.le.1)then
n_GDT1=n_GDT1+1
if(dis.le.0.5)then
n_GDT05=n_GDT05+1
endif
endif
endif
endif
endif
*** for MAXsub-score:
if(dis.lt.3.5)then
score_maxsub_sum=score_maxsub_sum+1/(1+(dis/3.5)**2)
endif
*** for TM-score:
score_sum=score_sum+1/(1+(dis/d0)**2)
*** for TM-score10:
if(dis.lt.10)then
score_sum10=score_sum10+1/(1+(dis/d0)**2)
endif
enddo
if(n_cut.lt.3.and.n_ali.gt.3)then
d_tmp=d_tmp+.5
goto 21
endif
score_maxsub=score_maxsub_sum/float(nseqB) !MAXsub-score
score=score_sum/float(nseqB) !TM-score
score10=score_sum10/float(nseqB) !TM-score10
return
end
cccccccccccccccc Calculate sum of (r_d-r_m)^2 cccccccccccccccccccccccccc
c w - w(m) is weight for atom pair c m (given)
c x - x(i,m) are coordinates of atom c m in set x (given)
c y - y(i,m) are coordinates of atom c m in set y (given)
c n - n is number of atom pairs (given)
c mode - 0:calculate rms only (given,short)
c 1:calculate u,t only (given,medium)
c 2:calculate rms,u,t (given,longer)
c rms - sum of w*(ux+t-y)**2 over all atom pairs (result)
c u - u(i,j) is rotation matrix for best superposition (result)
c t - t(i) is translation vector for best superposition (result)
c ier - 0: a unique optimal superposition has been determined(result)
c -1: superposition is not unique but optimal
c -2: no result obtained because of negative weights w
c or all weights equal to zero.
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
subroutine u3b(w, x, y, n, mode, rms, u, t, ier)
double precision w(*), x(3,*), y(3,*)
integer n, mode
double precision rms, u(3,3), t(3)
integer ier
integer i, j, k, l, m1, m
integer ip(9), ip2312(4)
double precision r(3,3), xc(3), yc(3), wc
double precision a(3,3), b(3,3), e(3), rr(6), ss(6)
double precision e0, d, spur, det, cof, h, g
double precision cth, sth, sqrth, p, sigma
double precision c1x, c1y, c1z, c2x, c2y, c2z
double precision s1x, s1y, s1z, s2x, s2y, s2z
double precision sxx, sxy, sxz, syx, syy, syz, szx, szy, szz
double precision sqrt3, tol, zero
data sqrt3 / 1.73205080756888d+00 /
data tol / 1.0d-2 /
data zero / 0.0d+00 /
data ip / 1, 2, 4, 2, 3, 5, 4, 5, 6 /
data ip2312 / 2, 3, 1, 2 /
wc = zero
rms = zero
e0 = zero
s1x = zero
s1y = zero
s1z = zero
s2x = zero
s2y = zero
s2z = zero
sxx = zero
sxy = zero
sxz = zero
syx = zero
syy = zero
syz = zero
szx = zero
szy = zero
szz = zero
do i=1, 3
xc(i) = zero
yc(i) = zero
t(i) = zero
do j=1, 3
r(i,j) = zero
u(i,j) = zero
a(i,j) = zero
if( i .eq. j ) then
u(i,j) = 1.0
a(i,j) = 1.0
end if
end do
end do
ier = -1
if( n .lt. 1 ) return
ier = -2
do m=1, n
c1x=x(1, m)
c1y=x(2, m)
c1z=x(3, m)
c2x=y(1, m)
c2y=y(2, m)
c2z=y(3, m)
s1x = s1x + c1x
s1y = s1y + c1y;
s1z = s1z + c1z;
s2x = s2x + c2x;
s2y = s2y + c2y;
s2z = s2z + c2z;
sxx = sxx + c1x*c2x;
sxy = sxy + c1x*c2y;
sxz = sxz + c1x*c2z;
syx = syx + c1y*c2x;
syy = syy + c1y*c2y;
syz = syz + c1y*c2z;
szx = szx + c1z*c2x;
szy = szy + c1z*c2y;
szz = szz + c1z*c2z;
end do
xc(1) = s1x/n;
xc(2) = s1y/n;
xc(3) = s1z/n;
yc(1) = s2x/n;
yc(2) = s2y/n;
yc(3) = s2z/n;
if(mode.eq.2.or.mode.eq.0) then ! need rmsd
do m=1, n
do i=1, 3
e0 = e0+ (x(i, m)-xc(i))**2 + (y(i, m)-yc(i))**2
end do
end do
endif
r(1, 1) = sxx-s1x*s2x/n;
r(2, 1) = sxy-s1x*s2y/n;
r(3, 1) = sxz-s1x*s2z/n;
r(1, 2) = syx-s1y*s2x/n;
r(2, 2) = syy-s1y*s2y/n;
r(3, 2) = syz-s1y*s2z/n;
r(1, 3) = szx-s1z*s2x/n;
r(2, 3) = szy-s1z*s2y/n;
r(3, 3) = szz-s1z*s2z/n;
det = r(1,1) * ( (r(2,2)*r(3,3)) - (r(2,3)*r(3,2)) )
& - r(1,2) * ( (r(2,1)*r(3,3)) - (r(2,3)*r(3,1)) )
& + r(1,3) * ( (r(2,1)*r(3,2)) - (r(2,2)*r(3,1)) )
sigma = det
m = 0
do j=1, 3
do i=1, j
m = m+1
rr(m) = r(1,i)*r(1,j) + r(2,i)*r(2,j) + r(3,i)*r(3,j)
end do
end do
spur = (rr(1)+rr(3)+rr(6)) / 3.0
cof = (((((rr(3)*rr(6) - rr(5)*rr(5)) + rr(1)*rr(6))
& - rr(4)*rr(4)) + rr(1)*rr(3)) - rr(2)*rr(2)) / 3.0
det = det*det
do i=1, 3
e(i) = spur
end do
if( spur .le. zero ) goto 40
d = spur*spur
h = d - cof
g = (spur*cof - det)/2.0 - spur*h
if( h .le. zero ) then
if( mode .eq. 0 ) then
goto 50
else
goto 30
end if
end if
sqrth = dsqrt(h)
d = h*h*h - g*g
if( d .lt. zero ) d = zero
d = datan2( dsqrt(d), -g ) / 3.0
cth = sqrth * dcos(d)
sth = sqrth*sqrt3*dsin(d)
e(1) = (spur + cth) + cth
e(2) = (spur - cth) + sth
e(3) = (spur - cth) - sth
if( mode .eq. 0 ) then
goto 50
end if
do l=1, 3, 2
d = e(l)
ss(1) = (d-rr(3)) * (d-rr(6)) - rr(5)*rr(5)
ss(2) = (d-rr(6)) * rr(2) + rr(4)*rr(5)
ss(3) = (d-rr(1)) * (d-rr(6)) - rr(4)*rr(4)
ss(4) = (d-rr(3)) * rr(4) + rr(2)*rr(5)
ss(5) = (d-rr(1)) * rr(5) + rr(2)*rr(4)
ss(6) = (d-rr(1)) * (d-rr(3)) - rr(2)*rr(2)
if( dabs(ss(1)) .ge. dabs(ss(3)) ) then
j=1
if( dabs(ss(1)) .lt. dabs(ss(6)) ) j = 3
else if( dabs(ss(3)) .ge. dabs(ss(6)) ) then
j = 2
else
j = 3
end if
d = zero
j = 3 * (j - 1)
do i=1, 3
k = ip(i+j)
a(i,l) = ss(k)
d = d + ss(k)*ss(k)
end do
if( d .gt. zero ) d = 1.0 / dsqrt(d)
do i=1, 3
a(i,l) = a(i,l) * d
end do
end do
d = a(1,1)*a(1,3) + a(2,1)*a(2,3) + a(3,1)*a(3,3)
if ((e(1) - e(2)) .gt. (e(2) - e(3))) then
m1 = 3
m = 1
else
m1 = 1
m = 3
endif
p = zero
do i=1, 3
a(i,m1) = a(i,m1) - d*a(i,m)
p = p + a(i,m1)**2
end do
if( p .le. tol ) then
p = 1.0
do 21 i=1, 3
if (p .lt. dabs(a(i,m))) goto 21
p = dabs( a(i,m) )
j = i
21 continue
k = ip2312(j)
l = ip2312(j+1)
p = dsqrt( a(k,m)**2 + a(l,m)**2 )
if( p .le. tol ) goto 40
a(j,m1) = zero
a(k,m1) = -a(l,m)/p
a(l,m1) = a(k,m)/p
else
p = 1.0 / dsqrt(p)
do i=1, 3
a(i,m1) = a(i,m1)*p
end do
end if
a(1,2) = a(2,3)*a(3,1) - a(2,1)*a(3,3)
a(2,2) = a(3,3)*a(1,1) - a(3,1)*a(1,3)
a(3,2) = a(1,3)*a(2,1) - a(1,1)*a(2,3)
30 do l=1, 2
d = zero
do i=1, 3
b(i,l) = r(i,1)*a(1,l) + r(i,2)*a(2,l) + r(i,3)*a(3,l)
d = d + b(i,l)**2
end do
if( d .gt. zero ) d = 1.0 / dsqrt(d)
do i=1, 3
b(i,l) = b(i,l)*d
end do
end do
d = b(1,1)*b(1,2) + b(2,1)*b(2,2) + b(3,1)*b(3,2)
p = zero
do i=1, 3
b(i,2) = b(i,2) - d*b(i,1)
p = p + b(i,2)**2
end do
if( p .le. tol ) then
p = 1.0
do 22 i=1, 3
if(p.lt.dabs(b(i,1)))goto 22
p = dabs( b(i,1) )
j = i
22 continue
k = ip2312(j)
l = ip2312(j+1)
p = dsqrt( b(k,1)**2 + b(l,1)**2 )
if( p .le. tol ) goto 40
b(j,2) = zero
b(k,2) = -b(l,1)/p
b(l,2) = b(k,1)/p
else
p = 1.0 / dsqrt(p)
do i=1, 3
b(i,2) = b(i,2)*p
end do
end if
b(1,3) = b(2,1)*b(3,2) - b(2,2)*b(3,1)
b(2,3) = b(3,1)*b(1,2) - b(3,2)*b(1,1)
b(3,3) = b(1,1)*b(2,2) - b(1,2)*b(2,1)
do i=1, 3
do j=1, 3
u(i,j) = b(i,1)*a(j,1) + b(i,2)*a(j,2) + b(i,3)*a(j,3)
end do
end do
40 do i=1, 3
t(i) = ((yc(i) - u(i,1)*xc(1)) - u(i,2)*xc(2)) - u(i,3)*xc(3)
end do
50 do i=1, 3
if( e(i) .lt. zero ) e(i) = zero
e(i) = dsqrt( e(i) )
end do
ier = 0
if( e(2) .le. (e(1) * 1.0d-05) ) ier = -1
d = e(3)
if( sigma .lt. 0.0 ) then
d = - d
if( (e(2) - e(3)) .le. (e(1) * 1.0d-05) ) ier = -1
end if
d = (d + e(2)) + e(1)
if(mode .eq. 2.or.mode.eq.0) then ! need rmsd
rms = (e0 - d) - d
if( rms .lt. 0.0 ) rms = 0.0
endif
return
end
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