[med-svn] [Git][med-team/tm-align][master] 7 commits: New upstream version 20190822+dfsg

Steffen Möller gitlab at salsa.debian.org
Tue Dec 17 16:24:43 GMT 2019



Steffen Möller pushed to branch master at Debian Med / tm-align


Commits:
d52100bb by Steffen Moeller at 2019-12-17T16:22:56Z
New upstream version 20190822+dfsg
- - - - -
f263aaa5 by Steffen Moeller at 2019-12-17T16:22:56Z
routine-update: New upstream version

- - - - -
d32d9f2d by Steffen Moeller at 2019-12-17T16:22:57Z
Update upstream source from tag 'upstream/20190822+dfsg'

Update to upstream version '20190822+dfsg'
with Debian dir 44cca8428d9d6fee22f988e451383d60c9676e79
- - - - -
98ec0516 by Steffen Moeller at 2019-12-17T16:22:59Z
routine-update: Standards-Version: 4.4.1

- - - - -
cf9b30ab by Steffen Moeller at 2019-12-17T16:23:07Z
Use secure URI in Homepage field.

Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.

- - - - -
77eab05e by Steffen Moeller at 2019-12-17T16:23:09Z
Remove obsolete fields Contact, Name from debian/upstream/metadata.
- - - - -
36a80839 by Steffen Moeller at 2019-12-17T16:23:20Z
routine-update: Ready to upload to unstable

- - - - -


7 changed files:

- + TMalign.cpp
- TMalign.f
- + TMscore.cpp
- TMscore.f
- debian/changelog
- debian/control
- debian/upstream/metadata


Changes:

=====================================
TMalign.cpp
=====================================
The diff for this file was not included because it is too large.

=====================================
TMalign.f
=====================================
@@ -77,6 +77,8 @@
 *     2017/07/08: Added one iteration in initial4 to avoid asymmetric alignment
 *     2019/07/08: Enable TM-align to support both PDB and mmCIF formats, and
 *                 fixed a bug on file output
+*     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 !
@@ -102,7 +104,7 @@ c 3456789012345678901234567890123456789012345678901234567890123456789012345678
       character*500 fnam,pdb(100),outname,falign,fmatrix
       character*3 aa(-1:20),aanam,ss(2,nmax)
       character*500 s,du,dum1,dum2
-      character*504 outnameall_tmp,outnameall
+      character*504 xxx,xxx_p,xxx_pdb
       character aseq1(nmax2),aseq2(nmax2),aseq3(nmax2)
       character*8 version
       character*5000 s1         !maximum length of protein is 5000
@@ -113,11 +115,13 @@ ccc   mmCIF
       character*20 Aatom(2,90000)
       character Agroup(2,90000)*6
       character Ares(2,90000)*3,Aalt(2,90000)
-      character Ains(2,9000),Ach(2,90000),Aent(2,90000)
+      character Ains(2,90000),Aent(2,90000)
       character Cins(2,nmax),Cch(2)
-
+      character*2 Ach(2,90000),chid(2,90000)
+      
       integer Aatomi(2,90000),Aresi(2,90000),n_cut(2)
-      dimension iform(10),xx(2,90000),yy(2,90000),zz(2,90000),nL(2)
+      dimension iform(10),xx(2,90000),yy(2,90000),zz(2,90000)
+      dimension nL(2),nLCA(2)
 ccc
       
       dimension m1(nmax),m2(nmax),m12(2,nmax)
@@ -179,20 +183,25 @@ ccc
      &        '''TM.sup_all'' and ''TM.sup_atm'':'
          write(*,*)'   >TMalign chain_1.pdb chain_2.pdb -o TM.sup'
          write(*,*)'      To view superimposed C-alpha traces of',
-     &        ' aligned regions by rasmol:'
+     &        ' aligned regions by rasmol or pymol:'
          write(*,*)'        >rasmol -script TM.sup'
+         write(*,*)'        >pymol -d @TM.sup.pml'
          write(*,*)'      To view superimposed C-alpha traces of',
      &        ' all regions:'
          write(*,*)'        >rasmol -script TM.sup_all'
+         write(*,*)'        >pymol -d @TM.sup_all.pml'
          write(*,*)'      To view superimposed full-atom structures of',
      &        ' aligned regions:'
          write(*,*)'        >rasmol -script TM.sup_atm'
+         write(*,*)'        >pymol -d @TM.sup_atm.pml'
          write(*,*)'      To view superimposed full-atom structures of',
      &        ' all regions:'
          write(*,*)'        >rasmol -script TM.sup_all_atm'
+         write(*,*)'        >pymol -d @TM.sup_all_atm.pml'
          write(*,*)'      To view superimposed full-atom structures of',
      &        ' all regions with ligands:'
          write(*,*)'        >rasmol -script TM.sup_all_atm_lig'
+         write(*,*)'        >pymol -d @TM.sup_all_atm_lig.pml'
          write(*,*)
          write(*,*)'4. There are two TM-scores reported. You ',
      &        'should use the one normalized by'
@@ -214,7 +223,7 @@ ccc
          goto 9999
       endif
       
-      version='20190708'
+      version='20190822'
       if(fnam.eq.'-v')then
          write(*,*)'TM-align Version ',version
          goto 9999
@@ -333,8 +342,8 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
 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,A2,i4,A1,a3,3F8.3)')
-     &                       du,itmp,du,aanam,du,mm(ic,i),
+                        read(s,'(a6,I5,a6,A3,A1,A1,i4,A1,a3,3F8.3)')
+     &                       du,itmp,du,aanam,du,chid(ic,i),mm(ic,i),
      &                       Cins(ic,i),du,
      &                       xa(1,i,ic-1),xa(2,i,ic-1),xa(3,i,ic-1)
 ***   
@@ -363,8 +372,10 @@ c^^^^^^^^^altLoc checked (mk.ne.1 will be skipped) ^^^^^^^^^
                   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
@@ -410,6 +421,7 @@ c^^^^^^^^^altLoc checked (mk.ne.1 will be skipped) ^^^^^^^^^
                         ss(ic,i)=ctmp(i_res) !residue name, 'GLY', for seq_ID
 ***   
                         i8=mm(ic,i)
+                        chid(ic,i)=ch(i)
                         nres1(ic,i8,ichar(du1))=
      &                       nres1(ic,i8,ichar(du1))+1 !nres1 only for check altLoc
 ***   
@@ -802,6 +814,7 @@ 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
+         nLCA(ic)=0             !number of lines with CA in PDB file
          n_cut(ic)=0            !end of first chain, decide to show aaa_all_atm_lig
          open(unit=10,file=pdb(ic),status='old')
          if(iform(ic).eq.1)then !file in PDB format %%%%%%%%%%------->
@@ -845,7 +858,8 @@ 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)),
+                     read(s,'(a6,I5,a1,A4,a1,A3,a1,A1,I4,A1,a3,3F8.3)')
+     &                    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,
@@ -883,8 +897,10 @@ c                     read(Aatom(ic,nL(ic)),*)Aatom(ic,nL(ic)) !remove space bef
                   
                   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
@@ -902,7 +918,8 @@ c                     read(Aatom(ic,nL(ic)),*)Aatom(ic,nL(ic)) !remove space bef
                   endif
 *^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                   
-                  if(n_cut(ic).eq.0.and.nL(ic).gt.0)then !decide n_cut
+                  if(n_cut(ic).eq.0.and.nL(ic).gt.0.and.
+     &                 nLCA(ic).gt.0)then !decide n_cut for mmcif
                      read(ctmp(i_ch),*)ch_t
                      read(ctmp(i_ent),*)ent_t
                      if(ch_t.ne.Ach(ic,nL(ic)).or.ent_t.ne.
@@ -937,6 +954,9 @@ c^^^^^^^^^altLoc checked (mk.ne.1) will be skipped) ^^^^^^^^^
                      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))=' '
+                     if(Aatom(ic,nL(ic)).eq.' CA')then
+                        nLCA(ic)=nLCA(ic)+1 !for deciding n_cut of mmCIF
+                     endif
                      
                      read(ctmp(i_res),*)Ares(ic,nL(ic))
                      read(ctmp(i_ch),*)Ach(ic,nL(ic)) !for check other chain
@@ -968,8 +988,6 @@ c     if(Aalt(ic,nL(ic)).eq.'.')Aalt(ic,nL(ic))=' '
          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)
-
 ********** mark aligned residues --------------->
       do i=1,n8_al
          m12(1,i)=m1(i)
@@ -983,15 +1001,29 @@ c*********************************************************************
 c************* Step-2: output structures for Rasmol ******************
 c*********************************************************************
       do 1019 ip=1,5
-         if(ip.eq.1) outnameall=outname(1:len_trim(outname)) !'aaa', aligned CA
-         if(ip.eq.2) outnameall=outname(1:len_trim(outname))//'_all' !'aaa_all', all CA
-         if(ip.eq.3) outnameall=outname(1:len_trim(outname))//'_atm' !'aaa_atm', all aligned atoms
-         if(ip.eq.4) outnameall=outname(1:len_trim(outname))
-     &        //'_all_atm'      !'aaa_all_atm', all atoms
-         if(ip.eq.5) outnameall=outname(1:len_trim(outname))
-     &        //'_all_atm_lig'  !'aaa_all_atm_lig', all atom + ligand
+         if(ip.eq.1) xxx=outname(1:len_trim(outname)) !'aaa', aligned CA
+         if(ip.eq.2) xxx=outname(1:len_trim(outname))//'_all' !'aaa_all', all CA
+         if(ip.eq.3) xxx=outname(1:len_trim(outname))//'_atm' !'aaa_atm', all aligned atoms
+         if(ip.eq.4) xxx=outname(1:len_trim(outname))//'_all_atm' !'aaa_all_atm', all atoms
+         if(ip.eq.5) xxx=outname(1:len_trim(outname))//'_all_atm_lig' !'aaa_all_atm_lig', atom+ligand
+         OPEN(unit=10,file=xxx,status='unknown')
+         
+*************for pymol preset ------>
+         xxx_p=xxx(1:len_trim(xxx))//'.pml' !for pymol script
+         xxx_pdb=xxx(1:len_trim(xxx))//'.pdb' !for pymol pdb
+         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 sphere_scale, 0.25'
+         write(11,'(A)')'set stick_radius, 0.3'
+*^^^^^^^^^ pymol preset complete ^^^^^^^^^^^^^^^^^^^
          
-         OPEN(unit=10,file=outnameall,status='unknown')
 ***   script:
          if(ip.eq.1.or.ip.eq.2)then !'aaa','aaa_all'
             write(10,'(A)')'load inline'
@@ -1010,6 +1042,9 @@ c*********************************************************************
                endif
             enddo
             write(10,'(A)')'select all'
+            
+            write(11,'(A)')'show sticks, chain A'
+            write(11,'(A)')'show sticks, chain B'
          elseif(ip.eq.3.or.ip.eq.4)then !'aaa_atm', 'aaa_all_atm'
             write(10,'(A)')'load inline'
             write(10,'(A)')'select *A'
@@ -1018,6 +1053,9 @@ c*********************************************************************
             write(10,'(A)')'color red'
             write(10,'(A)')'select all'
             write(10,'(A)')'cartoon'
+            
+            write(11,'(A)')'show cartoon, chain A'
+            write(11,'(A)')'show cartoon, chain B'
          else                   !'aaa_all_atm_lig
             write(10,'(A)')'load inline'
             write(10,'(A)')'select all'
@@ -1031,6 +1069,11 @@ c*********************************************************************
             write(10,'(A)')'select solvent'
             write(10,'(A)')'spacefill 0.25'
             write(10,'(A)')'select all'
+            
+            write(11,'(A)')'show cartoon, chain A'
+            write(11,'(A)')'show cartoon, chain B'
+            write(11,'(A)')'show stick, HETATM'
+            write(11,'(A)')'show spheres, solvent'
          endif
          write(10,'(A)')'exit'
          write(10,903)version
@@ -1045,11 +1088,11 @@ c------------output coordinates ----------->
             else                !na=5001-10000
                na=5000          !for CONECT
             endif
-c            write(*,*)'ip=',ip,'ic=',ic,nL(ic)
-
+            
             if(n_cut(ic).eq.0)then
                n_cut(ic)=nL(ic) !there is no cut
             endif
+            
             do i=1,nL(ic)
 c---------- decide if we should output this line ------------>
                mk=0
@@ -1057,8 +1100,8 @@ c---------- decide if we should output this line ------------>
                   if(i.le.n_cut(ic))then
                      if(Aatom(ic,i).eq.' CA')then
                         do j=1,n8_al
-                           if(Aresi(ic,i).eq.mm(ic,m12(ic,j)))then
-                              if(Ains(ic,i).eq.Cins(ic,m12(ic,j)))then
+                           if(Aresi(ic,i).eq.mm(ic,m12(ic,j)))then !residue order
+                              if(Ains(ic,i).eq.Cins(ic,m12(ic,j)))then !residue insertion
                                  mk=1
                                  goto 120 !each line output once
                               endif
@@ -1072,28 +1115,33 @@ c---------- decide if we should output this line ------------>
                         mk=1
                      endif
                   endif
-               elseif(ip.eq.3)then !'aaa_atm', all aligned atoms
+               elseif(ip.eq.3)then !'aaa_atm', all aligned protein atoms
                   if(i.le.n_cut(ic))then
                      do j=1,n8_al
-                        if(Aresi(ic,i).eq.mm(ic,m12(ic,j)))then
-                           if(Ains(ic,i).eq.Cins(ic,m12(ic,j)))then
-                              mk=1
-                              goto 120 !each line output once
+                        if(Ach(ic,i).eq.chid(ic,m12(ic,j)))then ! residue order (e.g. 100)
+                           if(Aresi(ic,i).eq.mm(ic,m12(ic,j)))then ! residue order (e.g. 100)
+                              if(Ains(ic,i).eq.Cins(ic,m12(ic,j)))then !resi insertion (eg, A)
+                                 mk=1
+                                 goto 120 !each line output once
+                              endif
                            endif
                         endif
                      enddo
                   endif
-               elseif(ip.eq.4)then !'aaa_all_atm', all atoms
-                  if(i.le.n_cut(ic))then
+               elseif(ip.eq.4)then !'aaa_all_atm', all protein atoms
+                  if(Ach(ic,i).eq.chid(ic,1))then ! residue order (e.g. 100)
+                     if(i.le.n_cut(ic))then
+                        mk=1
+                     endif
+                  endif
+               elseif(ip.eq.5)then !'aaa_all_atm_lig', first chain and all ligands
+                  if(i.le.n_cut(ic).or.Agroup(ic,i).eq.'HETATM')then
                      mk=1
                   endif
-               elseif(ip.eq.5)then !'aaa_all_atm_lig', all atoms and ligands
-                  mk=1
                endif
  120           continue
 
 c^^^^^^^^^^
-c               write(*,*)ip,ic,i,'mk=',mk,n_cut(ic)
                if(mk.eq.1)then  !mk=1----------->
                   if(ic.eq.1)then
                      ax=t(1)+u(1,1)*xx(ic,i)+u(1,2)*yy(ic,i)+
@@ -1107,35 +1155,46 @@ c               write(*,*)ip,ic,i,'mk=',mk,n_cut(ic)
                      ay=yy(ic,i)
                      az=zz(ic,i)
                   endif
-
+                  
 c--------------output (x,y,z) --------------------------------->                  
                   na=na+1       !number of atoms for CONECT
                   if(ip.eq.1.or.ip.eq.2)then !need CONECT
                      write(10,1236)Agroup(ic,i),na,'',
      &                    Aatom(ic,i),'',Ares(ic,i),'',Cch(ic),
+     &                    Aresi(ic,i),Ains(ic,i),'',ax,ay,az
+                     write(12,1236)Agroup(ic,i),na,'',
+     &                    Aatom(ic,i),'',Ares(ic,i),'',Cch(ic),
      &                    Aresi(ic,i),Ains(ic,i),'',ax,ay,az
                   else          !all atoms
                      write(10,1236)Agroup(ic,i),Aatomi(ic,i),'',
      &                    Aatom(ic,i),'',Ares(ic,i),'',Cch(ic),
+     &                    Aresi(ic,i),Ains(ic,i),'',ax,ay,az
+                     write(12,1236)Agroup(ic,i),Aatomi(ic,i),'',
+     &                    Aatom(ic,i),'',Ares(ic,i),'',Cch(ic),
      &                    Aresi(ic,i),Ains(ic,i),'',ax,ay,az
                   endif
                endif            !<----mk=1
             enddo               !do i=1,nL(ic)
 
             write(10,'(A)')'TER' !TER
+            write(12,'(A)')'TER' !TER
             if(ip.eq.1.or.ip.eq.2)then
                if(ic.eq.1)then
                   do i=2,na
                      write(10,'(A6,I5,I5)')'CONECT',i-1,i !CONECT atom numbers
+                     write(12,'(A6,I5,I5)')'CONECT',i-1,i !CONECT atom numbers
                   enddo
                else
                   do i=5002,na
                      write(10,'(A6,I5,I5)')'CONECT',i-1,i !CONECT atom numbers
+                     write(12,'(A6,I5,I5)')'CONECT',i-1,i !CONECT atom numbers
                   enddo
                endif
             endif
          enddo                  !do ic=1,2
          close(10)
+         close(11)
+         close(12)
  1019 continue                  !ip=1,5
 
  902     format('select ',I4,':A,',I4,':B')


=====================================
TMscore.cpp
=====================================
The diff for this file was not included because it is too large.

=====================================
TMscore.f
=====================================
@@ -40,6 +40,8 @@
 *                 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 !
@@ -56,7 +58,7 @@ c 3456789012345678901234567890123456789012345678901234567890123456789012345678
       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
+      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)
@@ -86,7 +88,7 @@ ccc   mmCIF
       character*20 Aatom(2,namax)
       character Agroup(2,namax)*6
       character Ares(2,namax)*3,Aalt(2,namax)
-      character Ains(2,9000),Ach(2,namax),Aent(2,namax)
+      character Ains(2,namax),Ach(2,namax),Aent(2,namax)
       character Cins(2,nmax)
 
       integer Aatomi(2,namax),Aresi(2,namax)
@@ -142,10 +144,13 @@ ccc
          write(*,*)'5. TM-score with superposition output, e.g. ',
      &        '''TM.sup'':'
          write(*,*)'   >TMscore model native -o TM.sup'
-         write(*,*)'   To view the superimposed CA-traces by rasmol:'
+         write(*,*)'   To view superimposed CA-traces by rasmol ',
+     &        'or pymol:'
          write(*,*)'      >rasmol -script TM.sup'
-         write(*,*)'   To view superimposed atomic models by rasmol:'
+         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
@@ -284,8 +289,10 @@ c^^^^^^^^^altLoc checked (mk.ne.1 will be skipped) ^^^^^^^^^
                   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.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
@@ -296,7 +303,7 @@ c^^^^^^^^^altLoc checked (mk.ne.1 will be skipped) ^^^^^^^^^
                   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
+                        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
@@ -305,7 +312,7 @@ c^^^^^^^^^altLoc checked (mk.ne.1 will be skipped) ^^^^^^^^^
                            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
+                        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
@@ -1026,13 +1033,13 @@ c^^^^^^^^^altLoc checked (mk.ne.1) will be skipped) ^^^^^^^^^
                   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
@@ -1122,6 +1129,24 @@ 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)
@@ -1146,21 +1171,31 @@ c**************************************************************
  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)
@@ -1169,9 +1204,26 @@ c**************************************************************
 c**************************************************************
 c*************  Step-3: output 'aaa_atm' (all-atom) ***********
 c**************************************************************
-c     outname=trim(outname)//'_atm'
       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'
@@ -1189,18 +1241,26 @@ c     outname=trim(outname)//'_atm'
          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


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+tm-align (20190822+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.4.1
+  * Use secure URI in Homepage field.
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata.
+
+ -- Steffen Moeller <moeller at debian.org>  Tue, 17 Dec 2019 17:23:09 +0100
+
 tm-align (20190708+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -7,10 +7,10 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                gfortran
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/tm-align
 Vcs-Git: https://salsa.debian.org/med-team/tm-align.git
-Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/
+Homepage: https://zhanglab.ccmb.med.umich.edu/TM-align/
 
 Package: tm-align
 Architecture: any


=====================================
debian/upstream/metadata
=====================================
@@ -1,25 +1,23 @@
-Contact: Yang Zhang <zhng at umich.edu>
-Name: TM-align & TM-score
 Reference:
- AUTHOR: Yang Zhang and Jeffrey Skolnick
- TITLE: >
-  TM-align: A protein structure alignment algorithm based on TM-score
- JOURNAL: Nucleic Acids Research
- YEAR: 2005
- PAGES: 2302-2309
- VOLUME: 33
- NUMBER: 7
- URL: http://nar.oxfordjournals.org/content/33/7/2302
- eprint: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf
- ISSN: 1362-4962
- DOI: 10.1093/nar/gki524
- PMID: 15849316
+  AUTHOR: Yang Zhang and Jeffrey Skolnick
+  TITLE: >
+    TM-align: A protein structure alignment algorithm based on TM-score
+  JOURNAL: Nucleic Acids Research
+  YEAR: 2005
+  PAGES: 2302-2309
+  VOLUME: 33
+  NUMBER: 7
+  URL: http://nar.oxfordjournals.org/content/33/7/2302
+  eprint: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf
+  ISSN: 1362-4962
+  DOI: 10.1093/nar/gki524
+  PMID: 15849316
 Registry:
- - Name: OMICtools
-   Entry: OMICS_03646
- - Name: bio.tools
-   Entry: NA
- - Name: SciCrunch
-   Entry: NA
- - Name: conda:bioconda
-   Entry: NA
+- Name: OMICtools
+  Entry: OMICS_03646
+- Name: bio.tools
+  Entry: NA
+- Name: SciCrunch
+  Entry: NA
+- Name: conda:bioconda
+  Entry: NA



View it on GitLab: https://salsa.debian.org/med-team/tm-align/compare/bfdac6eb96922711a91e1bdda69947e6d9e40ff0...36a808393bd838e5a7dd6d1aa1bc0ce373fc2267

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View it on GitLab: https://salsa.debian.org/med-team/tm-align/compare/bfdac6eb96922711a91e1bdda69947e6d9e40ff0...36a808393bd838e5a7dd6d1aa1bc0ce373fc2267
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