Addressing issue #919

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"

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

@@ -39,49 +39,21 @@ 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)