********>Bugfix 2:
Author:  Terry Lang
Date:  July 23, 2006 (updated August 2, 2006)

Program:  dock

Description:  Heavy atom RMSD printed after calculation is complete but was not being caluculated properly.  Numerator was being divided by number of atoms in entire molecule instead of just the heavy atoms.  Fix also involved reading vdw parameter file whenever RMSD is calculated.  Corrections to the test directory files are included.

Fix:  Make the following changes to the files src/dock/dock.cpp, srd/dock/library_file.cpp, install/test/ligand_io/io1.dockin, install/test/ligand_io/io2.dockin, install/test/ligand_io/io4.dockin, install/test/ligand_io/io1.dockout.save, install/test/ligand_io/io2.dockout.save, and install/test/ligand_io/io4.dockout.save  

Index: install/test/ligand_io/io1.dockin
===================================================================
RCS file: /usr/local/cvsroot/dock6/install/test/ligand_io/io1.dockin,v
retrieving revision 1.4
diff -c -r1.4 io1.dockin
*** install/test/ligand_io/io1.dockin	7 Jun 2006 09:34:49 -0000	1.4
--- install/test/ligand_io/io1.dockin	3 Aug 2006 00:39:42 -0000
***************
*** 15,17 ****
--- 15,21 ----
  flexible_ligand                                              no
  bump_filter                                                  no
  score_molecules                                              no
+ atom_model                                                   all
+ vdw_defn_file                                                ../../../parameters/vdw_AMBER_parm99.defn
+ flex_defn_file                                               ../../../parameters/flex.defn
+ flex_drive_file                                              ../../../parameters/flex_drive.tbl
Index: install/test/ligand_io/io1.dockout.save
===================================================================
RCS file: /usr/local/cvsroot/dock6/install/test/ligand_io/io1.dockout.save,v
retrieving revision 1.5
diff -c -r1.5 io1.dockout.save
*** install/test/ligand_io/io1.dockout.save	7 Jun 2006 09:34:49 -0000	1.5
--- install/test/ligand_io/io1.dockout.save	3 Aug 2006 00:39:42 -0000
***************
*** 40,45 ****
--- 40,52 ----
  Master Score Parameters
  ------------------------------------------------------------------------------------------
  score_molecules                                              no
+ 
+ Atom Typing Parameters
+ ------------------------------------------------------------------------------------------
+ atom_model                                                   all
+ vdw_defn_file                                                ../../../parameters/vdw_AMBER_parm99.defn
+ flex_defn_file                                               ../../../parameters/flex.defn
+ flex_drive_file                                              ../../../parameters/flex_drive.tbl
  ------------------------------------------------------------------------------------------
  
  Initializing Library File Routines...
Index: install/test/ligand_io/io2.dockin
===================================================================
RCS file: /usr/local/cvsroot/dock6/install/test/ligand_io/io2.dockin,v
retrieving revision 1.4
diff -c -r1.4 io2.dockin
*** install/test/ligand_io/io2.dockin	7 Jun 2006 09:34:49 -0000	1.4
--- install/test/ligand_io/io2.dockin	3 Aug 2006 00:39:42 -0000
***************
*** 15,17 ****
--- 15,21 ----
  flexible_ligand                                              no
  bump_filter                                                  no
  score_molecules                                              no
+ atom_model                                                   all
+ vdw_defn_file                                                ../../../parameters/vdw_AMBER_parm99.defn
+ flex_defn_file                                               ../../../parameters/flex.defn
+ flex_drive_file                                              ../../../parameters/flex_drive.tbl
Index: install/test/ligand_io/io2.dockout.save
===================================================================
RCS file: /usr/local/cvsroot/dock6/install/test/ligand_io/io2.dockout.save,v
retrieving revision 1.5
diff -c -r1.5 io2.dockout.save
*** install/test/ligand_io/io2.dockout.save	7 Jun 2006 09:34:49 -0000	1.5
--- install/test/ligand_io/io2.dockout.save	3 Aug 2006 00:39:42 -0000
***************
*** 40,45 ****
--- 40,52 ----
  Master Score Parameters
  ------------------------------------------------------------------------------------------
  score_molecules                                              no
+ 
+ Atom Typing Parameters
+ ------------------------------------------------------------------------------------------
+ atom_model                                                   all
+ vdw_defn_file                                                ../../../parameters/vdw_AMBER_parm99.defn
+ flex_defn_file                                               ../../../parameters/flex.defn
+ flex_drive_file                                              ../../../parameters/flex_drive.tbl
  ------------------------------------------------------------------------------------------
  
  Initializing Library File Routines...
Index: install/test/ligand_io/io4.dockin
===================================================================
RCS file: /usr/local/cvsroot/dock6/install/test/ligand_io/io4.dockin,v
retrieving revision 1.4
diff -c -r1.4 io4.dockin
*** install/test/ligand_io/io4.dockin	7 Jun 2006 09:34:49 -0000	1.4
--- install/test/ligand_io/io4.dockin	3 Aug 2006 00:39:42 -0000
***************
*** 15,17 ****
--- 15,21 ----
  flexible_ligand                                              no
  bump_filter                                                  no
  score_molecules                                              no
+ atom_model                                                   all
+ vdw_defn_file                                                ../../../parameters/vdw_AMBER_parm99.defn
+ flex_defn_file                                               ../../../parameters/flex.defn
+ flex_drive_file                                              ../../../parameters/flex_drive.tbl
Index: install/test/ligand_io/io4.dockout.save
===================================================================
RCS file: /usr/local/cvsroot/dock6/install/test/ligand_io/io4.dockout.save,v
retrieving revision 1.5
diff -c -r1.5 io4.dockout.save
*** install/test/ligand_io/io4.dockout.save	7 Jun 2006 09:34:49 -0000	1.5
--- install/test/ligand_io/io4.dockout.save	3 Aug 2006 00:39:42 -0000
***************
*** 40,45 ****
--- 40,52 ----
  Master Score Parameters
  ------------------------------------------------------------------------------------------
  score_molecules                                              no
+ 
+ Atom Typing Parameters
+ ------------------------------------------------------------------------------------------
+ atom_model                                                   all
+ vdw_defn_file                                                ../../../parameters/vdw_AMBER_parm99.defn
+ flex_defn_file                                               ../../../parameters/flex.defn
+ flex_drive_file                                              ../../../parameters/flex_drive.tbl
  ------------------------------------------------------------------------------------------
  
  Initializing Library File Routines...
Index: src/dock/dock.cpp
===================================================================
RCS file: /usr/local/cvsroot/dock6/src/dock/dock.cpp,v
retrieving revision 1.18.2.1
diff -c -r1.18.2.1 dock.cpp
*** src/dock/dock.cpp	2 Aug 2006 21:19:47 -0000	1.18.2.1
--- src/dock/dock.cpp	3 Aug 2006 00:39:43 -0000
***************
*** 84,90 ****
    c_master_score.input_parameters(c_parm);
    c_simplex.input_parameters(c_parm, c_master_conf.flexible_ligand, c_master_score);
    mol.input_parameters(c_parm);
!   if(c_master_conf.use_internal_energy || c_simplex.minimize_ligand || c_orient.orient_ligand || c_bmp_score.bump_filter)
  	c_master_score.read_vdw = true;
    c_typer.input_parameters(c_parm, c_master_score.read_vdw, c_orient.use_chemical_matching);
  
--- 84,90 ----
    c_master_score.input_parameters(c_parm);
    c_simplex.input_parameters(c_parm, c_master_conf.flexible_ligand, c_master_score);
    mol.input_parameters(c_parm);
!   if(c_master_conf.use_internal_energy || c_simplex.minimize_ligand || c_orient.orient_ligand || c_bmp_score.bump_filter || c_library.calc_rmsd)
  	c_master_score.read_vdw = true;
    c_typer.input_parameters(c_parm, c_master_score.read_vdw, c_orient.use_chemical_matching);
  
Index: src/dock/library_file.cpp
===================================================================
RCS file: /usr/local/cvsroot/dock6/src/dock/library_file.cpp,v
retrieving revision 1.13.2.2
diff -c -r1.13.2.2 library_file.cpp
*** src/dock/library_file.cpp	2 Aug 2006 21:19:47 -0000	1.13.2.2
--- src/dock/library_file.cpp	3 Aug 2006 00:39:43 -0000
***************
*** 1180,1203 ****
  float Library_File::calculate_rmsd(DOCKMol &mol) {
  	float	rmsd;
  	int		i;
! //	int		hcount;
  
  	rmsd = 0.00;
  
  	if(rmsd_reference.num_atoms != mol.num_atoms)
  		return 0.00;
  
! //	hcount = 0;
! 
  	for(i=0;i<mol.num_atoms;i++) {
  		if(mol.amber_at_heavy_flag[i]) {
  			rmsd +=( pow((mol.x[i] - rmsd_reference.x[i]),2) + pow((mol.y[i] - rmsd_reference.y[i]),2) + pow((mol.z[i] - rmsd_reference.z[i]),2) );
! //			hcount++;
  		}
  	}
  
! 	rmsd = rmsd/mol.num_atoms;
! //	rmsd = rmsd/hcount;
  	rmsd = sqrt(rmsd);
  
  	return rmsd;
--- 1180,1202 ----
  float Library_File::calculate_rmsd(DOCKMol &mol) {
  	float	rmsd;
  	int		i;
! 	int		hcount;
  
  	rmsd = 0.00;
  
  	if(rmsd_reference.num_atoms != mol.num_atoms)
  		return 0.00;
  
! 	hcount = 0;
  	for(i=0;i<mol.num_atoms;i++) {
  		if(mol.amber_at_heavy_flag[i]) {
  			rmsd +=( pow((mol.x[i] - rmsd_reference.x[i]),2) + pow((mol.y[i] - rmsd_reference.y[i]),2) + pow((mol.z[i] - rmsd_reference.z[i]),2) );
! 			hcount++;
  		}
  	}
  
! 	//rmsd = rmsd/mol.num_atoms;
! 	rmsd = rmsd/hcount;
  	rmsd = sqrt(rmsd);
  
  	return rmsd;
***************
*** 1208,1231 ****
  float Library_File::calculate_rmsd(DOCKMol &refmol, DOCKMol &mol) {
          float   rmsd;
          int             i;
! //      int             hcount;
  
          rmsd = 0.00;
  
          if(refmol.num_atoms != mol.num_atoms)
                  return 0.00;
  
! //      hcount = 0;
  
          for(i=0;i<mol.num_atoms;i++) {
                  if(mol.amber_at_heavy_flag[i]) {
                          rmsd +=( pow((mol.x[i] - refmol.x[i]),2) + pow((mol.y[i] - refmol.y[i]),2) + pow((mol.z[i] - refmol.z[i]),2) );
! //                      hcount++;
                  }
          }
  
!         rmsd = rmsd/mol.num_atoms;
! //      rmsd = rmsd/hcount;
          rmsd = sqrt(rmsd);
  
          return rmsd;
--- 1207,1230 ----
  float Library_File::calculate_rmsd(DOCKMol &refmol, DOCKMol &mol) {
          float   rmsd;
          int             i;
!         int             hcount;
  
          rmsd = 0.00;
  
          if(refmol.num_atoms != mol.num_atoms)
                  return 0.00;
  
!         hcount = 0;
  
          for(i=0;i<mol.num_atoms;i++) {
                  if(mol.amber_at_heavy_flag[i]) {
                          rmsd +=( pow((mol.x[i] - refmol.x[i]),2) + pow((mol.y[i] - refmol.y[i]),2) + pow((mol.z[i] - refmol.z[i]),2) );
!                       hcount++;
                  }
          }
  
!         //rmsd = rmsd/mol.num_atoms;
!         rmsd = rmsd/hcount;
          rmsd = sqrt(rmsd);
  
          return rmsd;