Enhance flexible definition in config files / defaults.yaml

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"