[Dock-fans] 6.2 bugfix 1

[Scott Brozell]

http://dock.compbio.ucsf.edu/DOCK_6/bugfixes.htm

********>Bugfix 1:
Author:  Scott Brozell
Date:  May 5, 2008

Program:  dock

Description:  the Amber score distance movable residue selection was
not correct.  This bug was only exercised when a strand had no residues
within the distance cutoff; in that case the whole strand instead of none
of the strand was selected by the generated NAB atom expression.

Fix:  make the following changes to the file src/dock/score_amber.cpp
-------------------------------------------------------------------------
*** src/dock/score_amber.cpp	19 Dec 2007 18:58:06 -0000	1.75
--- src/dock/score_amber.cpp	6 May 2008 00:01:47 -0000	1.77
***************
*** 743,750 ****
  
      // NAB idiom to loop over all atoms
      for( n = 0, sp = (*m)->m_strands; sp; sp = sp->s_next ){
!         residue_numbers.insert( ResiduesPerStrand::value_type(
!             sp->s_strandname, set< Residue_Sequence_Number >() ) );
          for( r = 0; r < sp->s_nresidues; r++ ){
              res = sp->s_residues[ r ];
              for( a = 0; a < res->r_natoms; a++ ){
--- 743,749 ----
  
      // NAB idiom to loop over all atoms
      for( n = 0, sp = (*m)->m_strands; sp; sp = sp->s_next ){
!         set< Residue_Sequence_Number> rsnset;
          for( r = 0; r < sp->s_nresidues; r++ ){
              res = sp->s_residues[ r ];
              for( a = 0; a < res->r_natoms; a++ ){
***************
*** 755,761 ****
                          ap->a_pos[ 2 ] );
                      if ( i->crds.distance_squared( axyz ) <
                          distance_cutoff*distance_cutoff ) {
!                         residue_numbers[sp->s_strandname].insert( r + 1 );
                          ++ n;
                          goto NEXT_RESIDUE;  // exit sphere and atom loops
                      }
--- 754,760 ----
                          ap->a_pos[ 2 ] );
                      if ( i->crds.distance_squared( axyz ) <
                          distance_cutoff*distance_cutoff ) {
!                         rsnset.insert( r + 1 );
                          ++ n;
                          goto NEXT_RESIDUE;  // exit sphere and atom loops
                      }
***************
*** 764,769 ****
--- 763,772 ----
  NEXT_RESIDUE:
          ;  // null statement
          }
+         if ( ! rsnset.empty() ) {
+             residue_numbers.insert( ResiduesPerStrand::value_type(
+                 sp->s_strandname, rsnset ) );
+         }
      }
  
      ostringstream mae;
--------------------------------------------------------------------------

Workaround:  none.