Enhance flexible definition in config files / defaults.yaml

docs/examples.md

@@ -62,7 +62,7 @@ A protein-glycan docking example making use of the knowledge of the binding site
 
 1) 1000 rigidbody docking models, RMSD clustering to select 50 clusters, flexible refinement of the top 5 models of each cluster, final RMSD clustering for cluster-based scoring ([docking-protein-glycan-full.cfg](../examples/docking-protein-glycan/docking-protein-glycan-full.cfg)). The RMSD clustering assumes a good knowledge of the interface, as the user has to define the residues involved in the binding site by means of the resdic_ parameter.
 2) 1000 rigidbody docking models, interface-ligand-RMSD (`ilrmsd`) clustering to select 50 clusters, flexible refinement of the top 5 models of each cluster, final ilRMSD clustering for cluster-based scoring ([docking-protein-glycan-ilrmsd-full.cfg](../examples/docking-protein-glycan/docking-protein-glycan-ilrmsd-full.cfg)). The interface-ligand-RMSD clustering is a more general approach, as it does not require the user to define the residues involved in the binding site. The interface is automatically defined by the residues involved in the protein-glycan interaction in the input models.
-3) 500 flexible docking runs + final RMSD clustering for cluster-based scoring [docking-flexref-protein-glycan-full.cfg](../examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg). In this case, the rigidbody docking is skipped and the docking is performed at the flexible refinement level. In this case the flexible refinement has more steps than usual (`mdsteps_rigid = 5000`, `mdsteps_cool1 = 5000` and so on) and the glycan is defined as fully flexible (`nfle2 = 1` and associated parameters).
+3) 500 flexible docking runs + final RMSD clustering for cluster-based scoring [docking-flexref-protein-glycan-full.cfg](../examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg). In this case, the rigidbody docking is skipped and the docking is performed at the flexible refinement level. In this case the flexible refinement has more steps than usual (`mdsteps_rigid = 5000`, `mdsteps_cool1 = 5000` and so on) and the glycan is defined as fully flexible (`fle_sta_1`, `fle_end_1`, `fle_seg_1`).
 
 __Note__ the modified weight of the van der Waals energy term for the scoring of the rigidbody docking models (`w_vdw = 1.0`), as in the [protein-ligand example](#docking-protein-ligand).
 
@@ -113,7 +113,7 @@ Three different workflows are illustrated:
 2) 3000 rigidbody docking models, selection of top400 and flexible refinement + final refinement in explicit solvent (water) of those ([docking-protein-peptide-mdref-full.cfg](../examples/docking-protein-peptide/docking-protein-peptide-mdref-full.cfg)
 3) 3000 rigidbody docking models, FCC clustering and selection of max 20 models per cluster followed by flexible refinement and EM ([docking-protein-peptide-cltsel-full.cfg](../examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg)).
 
-__Note__ how the peptide is defined as fully flexible for the refinement phase (`nfle2 = 1` and associated parameters) and dihedral angle restraints are automatically defined to maintain secondary structure elements (`ssdihed = "alphabeta"`)
+__Note__ how the peptide is defined as fully flexible for the refinement phase (`fle_sta_1`, `fle_end_1`, `fle_seg_1`) and dihedral angle restraints are automatically defined to maintain secondary structure elements (`ssdihed = "alphabeta"`)
 
 The `caprieval` module is called at various stages during the workflow to assess the quality of the models with respect to the known reference structure.
 

examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg

@@ -43,9 +43,10 @@ mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
 # give full flexibilit to the glycan
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 4
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 4
+fle_seg_1 = "B"
 
 [caprieval]
 reference_fname = "data/target.pdb" 

examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg

@@ -39,9 +39,10 @@ mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
 # give full flexibilit to the glycan
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 4
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 4
+fle_seg_1 = "B"
 
 [caprieval]
 reference_fname = "data/target.pdb" 

examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg

@@ -51,9 +51,10 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"
@@ -71,9 +72,10 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"

examples/docking-protein-peptide/docking-protein-peptide-full.cfg

@@ -45,9 +45,10 @@ select = 400
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"
@@ -64,9 +65,10 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"

examples/docking-protein-peptide/docking-protein-peptide-mdref-full.cfg

@@ -45,9 +45,10 @@ select = 400
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"
@@ -64,9 +65,10 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"

examples/docking-protein-peptide/docking-protein-peptide-mdref-test.cfg

@@ -39,9 +39,10 @@ select = 5
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"
@@ -59,9 +60,10 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"

examples/docking-protein-peptide/docking-protein-peptide-test.cfg

@@ -39,11 +39,13 @@ select = 5
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 2
-fle_sta_2_1 = 1
-fle_end_2_1 = 5
-fle_sta_2_2 = 6
-fle_end_2_2 = 11
+nfle = 2
+fle_sta_1 = 1
+fle_end_1 = 5
+fle_seg_1 = "B"
+fle_sta_2 = 6
+fle_end_2 = 11
+fle_seg_2 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"
@@ -61,9 +63,10 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 1
-fle_sta_2_1 = 1
-fle_end_2_1 = 11
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 11
+fle_seg_1 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"

examples/peptide-cyclisation/cyclise-peptide-full.cfg

@@ -44,18 +44,20 @@ mdsteps_cool1 = 2000
 mdsteps_cool2 = 4000
 mdsteps_cool3 = 4000
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 # turn off electrostatic
 elecflag = false
 
 [mdref]
 unambig_fname = "data/1sfi_unambig.tbl"
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 
 [caprieval]
 reference_fname = "data/1sfi_peptide-bound.pdb" 
@@ -98,18 +100,20 @@ mdsteps_cool1 = 2000
 mdsteps_cool2 = 4000
 mdsteps_cool3 = 4000
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 # turn off electrostatic
 elecflag = false
 
 [mdref]
 watersteps = 5000
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 
 [caprieval]
 reference_fname = "data/1sfi_peptide-bound.pdb" 

examples/peptide-cyclisation/cyclise-peptide-test.cfg

@@ -41,18 +41,20 @@ mdsteps_cool1 = 2000
 mdsteps_cool2 = 4000
 mdsteps_cool3 = 4000
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 # turn off electrostatic
 elecflag = false
 
 [mdref]
 unambig_fname = "data/1sfi_unambig.tbl"
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 
 [caprieval]
 reference_fname = "data/1sfi_peptide-bound.pdb" 
@@ -92,18 +94,20 @@ mdsteps_cool1 = 2000
 mdsteps_cool2 = 4000
 mdsteps_cool3 = 4000
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 # turn off electrostatic
 elecflag = false
 
 [mdref]
 watersteps = 5000
 # give full flexibilit to the peptide
-nfle1 = 1
-fle_sta_1_1 = 1
-fle_end_1_1 = 99
+nfle = 1
+fle_sta_1 = 1
+fle_end_1 = 99
+fle_seg_1 = "B"
 
 [caprieval]
 reference_fname = "data/1sfi_peptide-bound.pdb" 

src/haddock/modules/refinement/emref/cns/flex_segment_back.cns

@@ -12,7 +12,6 @@
 
 do (store5 = 0) (all)
 do (store6 = 0) (all)
-do (store7 = 0) (all)
 
 !first flexible segments for docking
 evaluate($nchain1 = 0)
@@ -39,49 +38,21 @@ while ($nchain1 < $data.ncomponents) loop nloop1
 end loop nloop1
 
 !then fully flexible segments for all stages
-evaluate($nchain1 = 0)
-while ($nchain1 < $data.ncomponents) loop nloop2
-    evaluate($nchain1 = $nchain1 + 1)
-    if ($nfle$nchain1 = 0) then
-        display NO FULLY FLEXIBLE SEGMENTS for molecule $nchain1
-    else
-        display FULLY FLEXIBLE SEGMENTS for molecule $nchain1
-        evaluate($nf=0)
-        while ($nf < $nfle$nchain1) loop Xfflex
-            evaluate($nf=$nf + 1)
-            do (store5 = $nchain1) ( resid $fle_sta_$nchain1_$nf : $fle_end_$nchain1_$nf
-                                     and segid $prot_segid_$nchain1 )
-            display FULLY FLEXIBLE SEGMENT NR $nf FROM $fle_sta_$nchain1_$nf TO $fle_end_$nchain1_$nf
-        end loop Xfflex
-    end if
-end loop nloop2
+display NO FLEXIBLE SEGMENTS for all molecule at this stage
+if ($nfle = 0) then
+    display NO FULLY FLEXIBLE SEGMENTS
+else
+    evaluate($nf=0)
+    while ($nf < $nfle) loop Xfflex
+        evaluate($nf=$nf + 1)
+        do (store5 = 1) ( resid $fle_sta_$nf : $fle_end_$nf and segid $fle_seg_$nf )
+            display FULLY FLEXIBLE SEGMENT NR $nf FROM $fle_sta_$nf TO $fle_end_$nf FOR CHAIN $fle_seg_$nf
+    end loop Xfflex
+end if
 
 do (store5 = 21) (resn WAT or resn HOH or resn TIP*)
-evaluate ($nfletot = 0)
-
-! check number of flexible residues per molecule
-evaluate($nchain1 = 0)
-while ($nchain1 < $data.ncomponents) loop nloop3
-    evaluate($nchain1 = $nchain1 + 1)
-    do (store6 = 0) (all)
-    do (store6 = 1) (tag and (attr store5 = $nchain1))
-    show sum (store6) (all)
-    evaluate ($numfle=$result)
-    do (store6 = 0) (all)
-    do (store6 = 1) (tag and segid $prot_segid_$nchain1 and not (attr store5 = $nchain1))
-    show sum (store6) (all)
-    evaluate ($numrig=$result)
-    do (store6 = 0) (all)
-    do (store6 = 1) (tag and segid $prot_segid_$nchain1)
-    show sum (store6) (all)
-    evaluate ($numres=$result)
-    display FLEXIBILITY STATISTIC FOR MOLECULE $nchain1 : Nres=$numres Nrigid=$numrig Nflex=$numfle
-    evaluate ($nfletot = $nfletot + $numfle)
-end loop nloop3
 
 do (store1 = 0) (all)
 do (store1 = 1) ((resn WAT or resn HOH or resn TIP*) and name OH2)
 show sum (store1) ((resn WAT or resn HOH or resn TIP*))
-evaluate ($nfletot = $nfletot + $result)
 
-evaluate ($nfletot = $nfletot + 10)

src/haddock/modules/refinement/emref/cns/flexauto-neighbors.cns

@@ -15,8 +15,6 @@ evaluate ($flcut = 5.0)
 
 do (store5 = $nchain1) (byres (segid $prot_segid_$nchain1 
                                and (not (segid $prot_segid_$nchain1 or resn SHA)) around $flcut))
-do (store7 = $nchain1) (byres (segid $prot_segid_$nchain1 
-                               and (not (segid $prot_segid_$nchain1 or resn SHA)) around $flcut))
 
 do (store6 = 0) (segid $prot_segid_$nchain1)
 for $id in id (tag and attr store5 >0 and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO) and segid $prot_segid_$nchain1) loop flexres1
@@ -30,7 +28,6 @@ for $id in id (tag and attr store5 >0 and not ((resn WAT or resn HOH or resn TIP
 end loop flexres1
 
 do (store5 = store6) (segid $prot_segid_$nchain1)
-do (store7 = store6) (segid $prot_segid_$nchain1)
 
 display THE FOLLOWING RESIDUES HAVE BEEN DEFINED AS FLEXIBLE for molecule $nchain1
 for $id in id (tag and attr store5 >0 and not ((resn WAT or resn HOH or resn TIP*) or resn DMSO) and segid $prot_segid_$nchain1) loop flexres2