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Commit 2febd66a authored by Valerio Mariani's avatar Valerio Mariani
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Updated tm tools and parsing scripts

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modules/bindings/pymod/tmtools.py
+ 2
− 2
View file @ 2febd66a
......@@ -63,8 +63,8 @@ def _ParseTmAlign(lines):
tf2[4], tf3[2], tf3[3], tf3[4])
tf=geom.Mat4(rot)
tf.PasteTranslation(geom.Vec3(tf1[1], tf2[1], tf3[1]))
seq1 = seq.CreateSequence("1",lines[20].strip())
seq2 = seq.CreateSequence("2",lines[22].strip())
seq1 = seq.CreateSequence("1",lines[26].strip())
seq2 = seq.CreateSequence("2",lines[28].strip())
alignment = seq.CreateAlignment()
alignment.AddSequence(seq2)
alignment.AddSequence(seq1)
......
modules/bindings/src/tmalign.f
+ 453
− 649
View file @ 2febd66a
This diff is collapsed.
modules/bindings/src/tmscore.f
+ 280
− 247
View file @ 2febd66a
*************************************************************************
* This program is to compare two protein structures and identify the
* best superposition that has the maximum TM-score. The program can
* be freely copied or modified.
* For comments, please email to: yzhang@ku.edu
*
* 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
* 2005/10/19: the program was reformed so that the score values.
* are not dependent on the specific compilers.
* 2006/06/20: select 'A' if there is altLoc when reading PDB file
* 2007/02/05: fix a bug with length<15 in TMscore_32
* 2007/02/27: rotation matrix from Chain-1 to Chain-2 is added
* 2007/12/06: GDT-HA score is added, fixed a bug for reading PDB
* 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.
*************************************************************************
program TMscore
......@@ -26,9 +37,9 @@
common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score
dimension k_ali(nmax),k_ali0(nmax)
character*100 fnam,pdb(100),outname
character*500 fnam,pdb(100),outname
character*3 aa(-1:20),seqA(nmax),seqB(nmax)
character*100 s,du
character*500 s,du
character seq1A(nmax),seq1B(nmax),ali(nmax)
character sequenceA(nmax),sequenceB(nmax),sequenceM(nmax)
......@@ -62,19 +73,22 @@ ccc
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(*,*)'1. Run TM-score to compare ''model'' and ''native',
& ':'
write(*,*)' >TMscore model native'
write(*,*)
write(*,*)'2. Run TM-score with an assigned d0, e.g. 5 Angstroms:'
write(*,*)' TMscore model native -d 5'
write(*,*)'2. Run TM-score with an assigned d0, e.g. 5',
& ' Angstroms:'
write(*,*)' >TMscore model native -d 5'
write(*,*)
write(*,*)'3. Run TM-score with superposition output, e.g. ',
& '''TM.sup'':'
write(*,*)' TMscore model native -o TM.sup'
write(*,*)
write(*,*)'4, To view the superimposed structures by rasmol:'
write(*,*)' rasmol -script TM.sup'
write(*,*)' >TMscore model native -o TM.sup'
write(*,*)' To view the superimposed structures by rasmol:'
write(*,*)' >rasmol -script TM.sup'
write(*,*)
goto 9999
endif
......@@ -314,7 +328,6 @@ c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
303 format(i5,i5,i5,f17.14,f17.14,i5,f7.3)
if(it.eq.n_it)goto 302
if(n_cut.eq.ka)then
neq=0
......@@ -337,17 +350,17 @@ c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
& '************************'
write(*,*)'* TM-SCORE ',
& ' *'
write(*,*)'* A scoring function to assess the quality of protein',
& ' structure predictions *'
write(*,*)'* A scoring function to assess the similarity of prot',
& 'ein structures *'
write(*,*)'* Based on statistics: ',
& ' *'
write(*,*)'* 0.0 < TM-score < 0.17, Random predictions ',
& ' *'
write(*,*)'* 0.4 < TM-score < 1.00, Meaningful predictions',
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: yzhang@ku.edu ',
write(*,*)'* For comments, please email to: zhng@umich.edu ',
& ' *'
write(*,*)'*****************************************************',
& '************************'
......@@ -648,240 +661,260 @@ 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)
integer ip(9), ip2312(4), i, j, k, l, m1, m, ier, n, mode
double precision w(1), x(3, 1), y(3, 1), u(3, 3), t(3), rms, sigma
double precision r(3, 3), xc(3), yc(3), wc, a(3, 3), b(3, 3), e0,
&e(3), e1, e2, e3, d, spur, det, cof, h, g, cth, sth, sqrth, p, tol
&, rr(6), rr1, rr2, rr3, rr4, rr5, rr6, ss(6), ss1, ss2, ss3, ss4,
&ss5, ss6, zero, one, two, three, sqrt3
equivalence (rr(1), rr1), (rr(2), rr2), (rr(3), rr3), (rr(4), rr4)
&, (rr(5), rr5), (rr(6), rr6), (ss(1), ss1), (ss(2), ss2), (ss(3),
&ss3), (ss(4), ss4), (ss(5), ss5), (ss(6), ss6), (e(1), e1), (e(2)
&, e2), (e(3), e3)
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 sqrt3, tol, zero
data sqrt3 / 1.73205080756888d+00 /
data tol / 1.0d-2 /
data zero / 0.0d+00 /
data one / 1.0d+00 /
data two / 2.0d+00 /
data three / 3.0d+00 /
data ip / 1, 2, 4, 2, 3, 5, 4, 5, 6 /
data ip2312 / 2, 3, 1, 2 /
c 156 "rms.for"
wc = zero
rms = 0.0
rms = zero
e0 = zero
do 1 i = 1, 3
xc(i) = zero
yc(i) = zero
t(i) = 0.0
do 1 j = 1, 3
d = zero
if (i .eq. j) d = one
u(i,j) = d
a(i,j) = d
1 r(i,j) = 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
c**** DETERMINE CENTROIDS OF BOTH VECTOR SETS X AND Y
c 170 "rms.for"
if (n .lt. 1) return
c 172 "rms.for"
if( n .lt. 1 ) return
ier = -2
do 2 m = 1, n
if (w(m) .lt. 0.0) return
wc = wc + w(m)
do 2 i = 1, 3
xc(i) = xc(i) + (w(m) * x(i,m))
2 yc(i) = yc(i) + (w(m) * y(i,m))
if (wc .le. zero) return
do 3 i = 1, 3
xc(i) = xc(i) / wc
c**** DETERMINE CORRELATION MATRIX R BETWEEN VECTOR SETS Y AND X
c 182 "rms.for"
3 yc(i) = yc(i) / wc
c 184 "rms.for"
do 4 m = 1, n
do 4 i = 1, 3
e0 = e0 + (w(m) * (((x(i,m) - xc(i)) ** 2) + ((y(i,m) - yc(i)) **
&2)))
c 187 "rms.for"
d = w(m) * (y(i,m) - yc(i))
do 4 j = 1, 3
c**** CALCULATE DETERMINANT OF R(I,J)
c 189 "rms.for"
4 r(i,j) = r(i,j) + (d * (x(j,m) - xc(j)))
c 191 "rms.for"
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))))
c**** FORM UPPER TRIANGLE OF TRANSPOSED(R)*R
c 194 "rms.for"
do m=1, n
if( w(m) .lt. 0.0 ) return
wc = wc + w(m)
do i=1, 3
xc(i) = xc(i) + w(m)*x(i,m)
yc(i) = yc(i) + w(m)*y(i,m)
end do
end do
if( wc .le. zero ) return
do i=1, 3
xc(i) = xc(i) / wc
yc(i) = yc(i) / wc
end do
do m=1, n
do i=1, 3
e0=e0+w(m)*((x(i,m)-xc(i))**2+(y(i,m)-yc(i))**2)
d = w(m) * ( y(i,m) - yc(i) )
do j=1, 3
r(i,j) = r(i,j) + d*( x(j,m) - xc(j) )
end do
end do
end do
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
c 196 "rms.for"
m = 0
do 5 j = 1, 3
do 5 i = 1, j
m = m + 1
c***************** EIGENVALUES *****************************************
c**** FORM CHARACTERISTIC CUBIC X**3-3*SPUR*X**2+3*COF*X-DET=0
c 200 "rms.for"
5 rr(m) = ((r(1,i) * r(1,j)) + (r(2,i) * r(2,j))) + (r(3,i) * r(3,j)
&)
c 203 "rms.for"
spur = ((rr1 + rr3) + rr6) / three
cof = ((((((rr3 * rr6) - (rr5 * rr5)) + (rr1 * rr6)) - (rr4 * rr4)
&) + (rr1 * rr3)) - (rr2 * rr2)) / three
c 205 "rms.for"
det = det * det
do 6 i = 1, 3
6 e(i) = spur
c**** REDUCE CUBIC TO STANDARD FORM Y**3-3HY+2G=0 BY PUTTING X=Y+SPUR
c 208 "rms.for"
if (spur .le. zero) goto 40
c 210 "rms.for"
d = spur * spur
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
c**** SOLVE CUBIC. ROOTS ARE E1,E2,E3 IN DECREASING ORDER
c 212 "rms.for"
g = (((spur * cof) - det) / two) - (spur * h)
c 214 "rms.for"
if (h .le. zero) goto 8
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) / three
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)
e1 = (spur + cth) + cth
e2 = (spur - cth) + sth
e3 = (spur - cth) - sth
c.....HANDLE SPECIAL CASE OF 3 IDENTICAL ROOTS
c 224 "rms.for"
if (mode) 10, 50, 10
c**************** EIGENVECTORS *****************************************
c 226 "rms.for"
8 if (mode) 30, 50, 30
c 228 "rms.for"
10 do 15 l = 1, 3, 2
d = e(l)
ss1 = ((d - rr3) * (d - rr6)) - (rr5 * rr5)
ss2 = ((d - rr6) * rr2) + (rr4 * rr5)
ss3 = ((d - rr1) * (d - rr6)) - (rr4 * rr4)
ss4 = ((d - rr3) * rr4) + (rr2 * rr5)
ss5 = ((d - rr1) * rr5) + (rr2 * rr4)
ss6 = ((d - rr1) * (d - rr3)) - (rr2 * rr2)
j = 1
if (dabs(ss1) .ge. dabs(ss3)) goto 12
j = 2
if (dabs(ss3) .ge. dabs(ss6)) goto 13
11 j = 3
goto 13
12 if (dabs(ss1) .lt. dabs(ss6)) goto 11
13 d = zero
j = 3 * (j - 1)
do 14 i = 1, 3
k = ip(i + j)
a(i,l) = ss(k)
14 d = d + (ss(k) * ss(k))
if (d .gt. zero) d = one / dsqrt(d)
do 15 i = 1, 3
15 a(i,l) = a(i,l) * d
d = ((a(1,1) * a(1,3)) + (a(2,1) * a(2,3))) + (a(3,1) * a(3,3))
m1 = 3
m = 1
if ((e1 - e2) .gt. (e2 - e3)) goto 16
m1 = 1
m = 3
16 p = zero
do 17 i = 1, 3
a(i,m1) = a(i,m1) - (d * a(i,m))
17 p = p + (a(i,m1) ** 2)
if (p .le. tol) goto 19
p = one / dsqrt(p)
do 18 i = 1, 3
18 a(i,m1) = a(i,m1) * p
goto 21
19 p = one
do 20 i = 1, 3
if (p .lt. dabs(a(i,m))) goto 20
p = dabs(a(i,m))
j = i
20 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
21 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))
c****************** ROTATION MATRIX ************************************
c 282 "rms.for"
a(3,2) = (a(1,3) * a(2,1)) - (a(1,1) * a(2,3))
c 284 "rms.for"
30 do 32 l = 1, 2
d = zero
do 31 i = 1, 3
b(i,l) = ((r(i,1) * a(1,l)) + (r(i,2) * a(2,l))) + (r(i,3) * a(3,l
&))
c 288 "rms.for"
31 d = d + (b(i,l) ** 2)
if (d .gt. zero) d = one / dsqrt(d)
do 32 i = 1, 3
32 b(i,l) = b(i,l) * d
d = ((b(1,1) * b(1,2)) + (b(2,1) * b(2,2))) + (b(3,1) * b(3,2))
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 33 i = 1, 3
b(i,2) = b(i,2) - (d * b(i,1))
33 p = p + (b(i,2) ** 2)
if (p .le. tol) goto 35
p = one / dsqrt(p)
do 34 i = 1, 3
34 b(i,2) = b(i,2) * p
goto 37
35 p = one
do 36 i = 1, 3
if (p .lt. dabs(b(i,1))) goto 36
p = dabs(b(i,1))
j = i
36 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
37 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 39 i = 1, 3
do 39 j = 1, 3
c****************** TRANSLATION VECTOR *********************************
c 320 "rms.for"
39 u(i,j) = ((b(i,1) * a(j,1)) + (b(i,2) * a(j,2))) + (b(i,3) * a(j,3
&))
40 do 41 i = 1, 3
c********************** RMS ERROR **************************************
c 323 "rms.for"
41 t(i) = ((yc(i) - (u(i,1) * xc(1))) - (u(i,2) * xc(2))) - (u(i,3)
& * xc(3))
50 do 51 i = 1, 3
if (e(i) .lt. zero) e(i) = zero
51 e(i) = dsqrt(e(i))
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 (e2 .le. (e1 * 1.0d-05)) ier = -1
d = e3
if (sigma .ge. 0.0) goto 52
d = - d
if ((e2 - e3) .le. (e1 * 1.0d-05)) ier = -1
52 d = (d + e2) + e1
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)
rms = (e0 - d) - d
if (rms .lt. 0.0) rms = 0.0
return
c.....END U3B...........................................................
c----------------------------------------------------------
c THE END
c----------------------------------------------------------
c 338 "rms.for"
end
\ No newline at end of file
if( rms .lt. 0.0 ) rms = 0.0
return
end
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