From dc43e8efe87f863e54a2b8e1a34df8298a26ec6f Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Wed, 14 Aug 2024 12:13:38 +0200
Subject: [PATCH 01/13] on the fly computation of nfle

---
 src/haddock/gear/expandable_parameters.py     | 29 ++++++++----
 src/haddock/gear/prepare_run.py               | 47 +++++++++++++------
 .../modules/refinement/emref/defaults.yaml    |  2 +-
 .../modules/refinement/flexref/defaults.yaml  |  2 +-
 .../modules/refinement/mdref/defaults.yaml    |  2 +-
 5 files changed, 55 insertions(+), 27 deletions(-)

diff --git a/src/haddock/gear/expandable_parameters.py b/src/haddock/gear/expandable_parameters.py
index 71d6e9765..0fddcab5c 100644
--- a/src/haddock/gear/expandable_parameters.py
+++ b/src/haddock/gear/expandable_parameters.py
@@ -109,8 +109,9 @@
 # common error messages
 _emsg_num_differ = (
     "The parameter block {!r} expects "
-    "{} parameters, but {} are present "
-    "in the user configuration file: {}."
+    "{} parameters ({}), but {} are present "
+    "in the user configuration file: {}. "
+    "Parameter(s) {} are missing."
 )
 
 
@@ -249,7 +250,7 @@ def _read_groups_in_user_config(
     extract_params: Callable[..., set[str]],
     _emsg_no_group: str = "Parameter block is not a valid expandable group",
     _emsg_unexpected_params: str = "Unexpected params for group",
-) -> set[str]:
+) -> tuple[set[str], dict[str, int]]:
     """
     Read groups in user config.
 
@@ -279,15 +280,18 @@ def _read_groups_in_user_config(
 
     Returns
     -------
-    set
+    new : set[str]
         A set with the new parameters in the user configuration file
         that are acceptable according to the expandable rules.
+    param_name_counts : dict[str, int]
+        Count of expendable parameter parameter name
     """
     # minimum=1 is used to capture groups with missing parameters
     user_groups = get_user_groups(user_config, minimum=1, reference=False)
     default_group_names = set(group[0] for group in default_groups)
 
     new: set[str] = set()
+    param_name_counts: dict[str, int] = {}
     for (param_name, group_idx), params in user_groups.items():
         if param_name not in default_group_names:
             emsg = _emsg_no_group.format(param_name, group_idx)
@@ -311,35 +315,40 @@ def _read_groups_in_user_config(
         # when num_found > num_expected the error about in `diff` is
         # triggered instead
         if num_found != num_expected:
+            expected_missings = set(expected_params).difference(params)
             emsg = _emsg_num_differ.format(
                 param_name,
                 num_expected,
+                ", ".join(expected_params),
                 num_found,
                 ", ".join(params),
+                ", ".join([f"`{p}`" for p in expected_missings]),
             )
             raise ConfigurationError(emsg)
 
         related_params = extract_params(user_config, param_name, group_idx)
+        # Increment counts for this parameter
+        if related_params:
+            param_name_counts.setdefault(param_name, 0)
+            param_name_counts[param_name] = int(group_idx)
         new.update(related_params)
-
-    return new
+    return new, param_name_counts
 
 
 def read_simplest_expandable(
-    expparams: Iterable[str], config: Iterable[str]
+    config: Iterable[str], expparams: Iterable[str], 
 ) -> set[str]:
     """
     Read expandable parameters from config file of the type `param_1`.
 
     Parameters
     ----------
+    config : dict, dict.keys, set, or alike
+        The user configuration file.
     expparams : dict, dict.keys, set, or alike
         The parameter names that should be considered as expandable.
         Usually, this is a module subdictionary of `type_simplest_ep`.
 
-    config : dict, dict.keys, set, or alike
-        The user configuration file.
-
     Returns
     -------
     set of str
diff --git a/src/haddock/gear/prepare_run.py b/src/haddock/gear/prepare_run.py
index 075d2e548..9fcbdc119 100644
--- a/src/haddock/gear/prepare_run.py
+++ b/src/haddock/gear/prepare_run.py
@@ -1017,25 +1017,44 @@ def get_expandable_parameters(
 def _get_expandable(
     user_config: ParamMap, defaults: ParamMap, module_name: str, max_mols: int
 ) -> set[str]:
-    type_1 = get_single_index_groups(defaults)
-    type_2 = get_multiple_index_groups(defaults)
-    type_4 = get_mol_parameters(defaults)
-
+    # Set parsing vars
     allowed_params: set[str] = set()
-    allowed_params.update(
-        read_single_idx_groups_user_config(user_config, type_1)
-    )  # noqa: E501
-    allowed_params.update(
-        read_multiple_idx_groups_user_config(user_config, type_2)
-    )  # noqa: E501
+    all_counts: dict[str, int] = {}
+    # Read single indexed groups (terminating by `_X`)
+    news_t1, counts_t1 = read_single_idx_groups_user_config(
+        user_config,
+        get_single_index_groups(defaults),
+        )
+    allowed_params.update(news_t1)
+    all_counts.update(counts_t1)
+    # Read multiple indexed groups (terminating by `_X_Y`)
+    news_t2, counts_t2 = read_multiple_idx_groups_user_config(
+        user_config,
+        get_multiple_index_groups(defaults),
+        )
+    allowed_params.update(news_t2)
+    all_counts.update(counts_t2)
 
     with suppress(KeyError):
-        type_3 = type_simplest_ep[get_module_name(module_name)]
-        allowed_params.update(read_simplest_expandable(type_3, user_config))
-
-    _ = read_mol_parameters(user_config, type_4, max_mols=max_mols)
+        news_t3 = read_simplest_expandable(
+            user_config,
+            type_simplest_ep[get_module_name(module_name)],
+            )
+        allowed_params.update(news_t3)
+    # Read molecule paramters (starting by `mol_`)
+    _ = read_mol_parameters(
+        user_config,
+        get_mol_parameters(defaults),
+        max_mols=max_mols,
+        )
     allowed_params.update(_)
 
+    # Add counted parameters to hidden user parameters
+    for param, count in all_counts.items():
+        count_param_name = f"n{param}"
+        if count_param_name in defaults.keys():
+            user_config[count_param_name] = count
+    # Return new set of allowed parameters
     return allowed_params
 
 
diff --git a/src/haddock/modules/refinement/emref/defaults.yaml b/src/haddock/modules/refinement/emref/defaults.yaml
index db7c386c8..f22d107c0 100644
--- a/src/haddock/modules/refinement/emref/defaults.yaml
+++ b/src/haddock/modules/refinement/emref/defaults.yaml
@@ -2096,7 +2096,7 @@ nfle:
     If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables
     and segment ID (segid) in the fle_seg_* variable.
   group: 'flexibility'
-  explevel: expert
+  explevel: hidden
 fle_sta_1:
   default: .nan
   type: integer
diff --git a/src/haddock/modules/refinement/flexref/defaults.yaml b/src/haddock/modules/refinement/flexref/defaults.yaml
index 7989eaa44..f0e1d54fd 100644
--- a/src/haddock/modules/refinement/flexref/defaults.yaml
+++ b/src/haddock/modules/refinement/flexref/defaults.yaml
@@ -2639,7 +2639,7 @@ nfle:
     If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables
     and segment ID (segid) in the fle_seg_* variable.
   group: 'flexibility'
-  explevel: expert
+  explevel: hidden
 fle_sta_1:
   default: .nan
   type: integer
diff --git a/src/haddock/modules/refinement/mdref/defaults.yaml b/src/haddock/modules/refinement/mdref/defaults.yaml
index 8714a22b5..cd2d255d6 100644
--- a/src/haddock/modules/refinement/mdref/defaults.yaml
+++ b/src/haddock/modules/refinement/mdref/defaults.yaml
@@ -2195,7 +2195,7 @@ nfle:
     If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables
     and segment ID (segid) in the fle_seg_* variable.
   group: 'flexibility'
-  explevel: expert
+  explevel: hidden
 fle_sta_1:
   default: .nan
   type: integer

From 2a4100db9085a31c2f51e1784996a695ffc2e68e Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Wed, 14 Aug 2024 12:16:39 +0200
Subject: [PATCH 02/13] removing nfle parameter from examples

---
 .../docking-flexref-protein-glycan-full.cfg                  | 1 -
 .../docking-flexref-protein-glycan-test.cfg                  | 1 -
 .../docking-protein-peptide-cltsel-full.cfg                  | 2 --
 .../docking-protein-peptide/docking-protein-peptide-full.cfg | 2 --
 .../docking-protein-peptide-mdref-full.cfg                   | 2 --
 .../docking-protein-peptide-mdref-test.cfg                   | 2 --
 .../docking-protein-peptide/docking-protein-peptide-test.cfg | 5 +++--
 7 files changed, 3 insertions(+), 12 deletions(-)

diff --git a/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg b/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg
index 446b65d7e..e2db10af4 100644
--- a/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg
+++ b/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg
@@ -43,7 +43,6 @@ mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
 # give full flexibilit to the glycan
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 4
 fle_seg_1 = "B"
diff --git a/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg b/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
index 7fc02c3ff..9900453b2 100644
--- a/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
+++ b/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
@@ -39,7 +39,6 @@ mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
 # give full flexibilit to the glycan
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 4
 fle_seg_1 = "B"
diff --git a/examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg b/examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg
index 3e6f2e3f6..0fe0e8f6d 100644
--- a/examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg
+++ b/examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg
@@ -51,7 +51,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
@@ -72,7 +71,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
diff --git a/examples/docking-protein-peptide/docking-protein-peptide-full.cfg b/examples/docking-protein-peptide/docking-protein-peptide-full.cfg
index 08e0c49de..45b23459a 100644
--- a/examples/docking-protein-peptide/docking-protein-peptide-full.cfg
+++ b/examples/docking-protein-peptide/docking-protein-peptide-full.cfg
@@ -45,7 +45,6 @@ select = 400
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
@@ -65,7 +64,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
diff --git a/examples/docking-protein-peptide/docking-protein-peptide-mdref-full.cfg b/examples/docking-protein-peptide/docking-protein-peptide-mdref-full.cfg
index ce095acbe..064d8363f 100644
--- a/examples/docking-protein-peptide/docking-protein-peptide-mdref-full.cfg
+++ b/examples/docking-protein-peptide/docking-protein-peptide-mdref-full.cfg
@@ -45,7 +45,6 @@ select = 400
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
@@ -65,7 +64,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
diff --git a/examples/docking-protein-peptide/docking-protein-peptide-mdref-test.cfg b/examples/docking-protein-peptide/docking-protein-peptide-mdref-test.cfg
index 4da16060b..7571f8fb5 100644
--- a/examples/docking-protein-peptide/docking-protein-peptide-mdref-test.cfg
+++ b/examples/docking-protein-peptide/docking-protein-peptide-mdref-test.cfg
@@ -39,7 +39,6 @@ select = 5
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
@@ -60,7 +59,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
diff --git a/examples/docking-protein-peptide/docking-protein-peptide-test.cfg b/examples/docking-protein-peptide/docking-protein-peptide-test.cfg
index 6c819ee2e..9b1b8a80b 100644
--- a/examples/docking-protein-peptide/docking-protein-peptide-test.cfg
+++ b/examples/docking-protein-peptide/docking-protein-peptide-test.cfg
@@ -39,13 +39,15 @@ select = 5
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-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"
+#nseg1 = 2
+#seg_sta_1_1 = 1
+#seg_end_1_1 = 5
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"
@@ -63,7 +65,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"

From f95161b4675ef34c43c71a0602018c262e642dc7 Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Wed, 14 Aug 2024 12:19:58 +0200
Subject: [PATCH 03/13] removing commented lines

---
 .../docking-protein-peptide/docking-protein-peptide-test.cfg   | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/examples/docking-protein-peptide/docking-protein-peptide-test.cfg b/examples/docking-protein-peptide/docking-protein-peptide-test.cfg
index 9b1b8a80b..672ae43ba 100644
--- a/examples/docking-protein-peptide/docking-protein-peptide-test.cfg
+++ b/examples/docking-protein-peptide/docking-protein-peptide-test.cfg
@@ -45,9 +45,6 @@ fle_seg_1 = "B"
 fle_sta_2 = 6
 fle_end_2 = 11
 fle_seg_2 = "B"
-#nseg1 = 2
-#seg_sta_1_1 = 1
-#seg_end_1_1 = 5
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"

From 48582b0734f0141b3201e48e96d9203871b25182 Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 09:53:21 +0200
Subject: [PATCH 04/13] add new tests for counts checks

---
 src/haddock/gear/expandable_parameters.py |   2 +-
 tests/test_gear_expandable_parameters.py  | 117 ++++++++++++++++++----
 2 files changed, 101 insertions(+), 18 deletions(-)

diff --git a/src/haddock/gear/expandable_parameters.py b/src/haddock/gear/expandable_parameters.py
index 0fddcab5c..db41380ad 100644
--- a/src/haddock/gear/expandable_parameters.py
+++ b/src/haddock/gear/expandable_parameters.py
@@ -330,7 +330,7 @@ def _read_groups_in_user_config(
         # Increment counts for this parameter
         if related_params:
             param_name_counts.setdefault(param_name, 0)
-            param_name_counts[param_name] = int(group_idx)
+            param_name_counts[param_name] += 1
         new.update(related_params)
     return new, param_name_counts
 
diff --git a/tests/test_gear_expandable_parameters.py b/tests/test_gear_expandable_parameters.py
index 559f83c77..be3173ca9 100644
--- a/tests/test_gear_expandable_parameters.py
+++ b/tests/test_gear_expandable_parameters.py
@@ -1,6 +1,6 @@
 """Test expandable parameter modules."""
-import importlib
 
+import importlib
 import pytest
 
 from haddock.core.exceptions import ConfigurationError
@@ -423,7 +423,7 @@ def test_read_single_idx_groups_user_config(
         expected,
         ):
     """Test read single index groups in user config."""
-    result = read_single_idx_groups_user_config(user_config, default_groups)
+    result, _ = read_single_idx_groups_user_config(user_config, default_groups)
     assert result == expected
 
 
@@ -431,32 +431,115 @@ def test_read_single_idx_groups_user_config(
     "user_config,default_groups,expected",
     [
         (
-            {"param_other_1", "param_else_1",
-             "param_other_2", "param_else_2",
-             "param_1",
-             "param_sam_1_1", "param_frodo_1_1",
-             "param_sam_1_2", "param_frodo_1_2",
-             "param_sam_2_1", "param_frodo_2_1",
-             },
-            {("param1", "1"): {"sam", "frodo"},
-             ("param2", "1"): {"sam", "frodo"}},
-            {"param_frodo_1_1", "param_sam_1_1",
-             "param_frodo_1_2", "param_sam_1_2",
-             "param_sam_2_1", "param_frodo_2_1",
-             },
+            # user_config
+            {
+                "param_other_1", "param_else_1",  # param 1
+                "param_other_2", "param_else_2",  # param 2
+                "param_1",  # not a single index group
+                "param_other_1_1",  # multiple index group
+                },
+            # default_groups
+            {
+                ("param", "1"): {"other", "else"},
+                },
+            # expected
+            {
+                "param": 2,
+                },
             ),
         ]
     )
-def test_read_multiple_idx_groups_user_config(
+def test_read_single_idx_groups_user_config_count(
         user_config,
         default_groups,
         expected,
         ):
     """Test read single index groups in user config."""
-    result = read_multiple_idx_groups_user_config(user_config, default_groups)
+    _, counts = read_single_idx_groups_user_config(user_config, default_groups)
+    assert counts == expected
+
+
+@pytest.mark.parametrize(
+    "user_config,default_groups,expected",
+    [
+        (
+            # user_config
+            {
+                # single index ones should NOT be considered
+                "param_other_1", "param_else_1",
+                "param_other_2", "param_else_2",
+                "param_1",
+                # multiple index ones should be considered
+                "param_sam_1_1", "param_frodo_1_1",
+                "param_sam_1_2", "param_frodo_1_2",
+                "param_sam_2_1", "param_frodo_2_1",
+                },
+            # default_groups
+            {
+                ("param1", "1"): {"sam", "frodo"},
+                ("param2", "1"): {"sam", "frodo"},
+                },
+            # expected
+            {
+                "param_frodo_1_1", "param_sam_1_1",
+                "param_frodo_1_2", "param_sam_1_2",
+                "param_sam_2_1", "param_frodo_2_1",
+                },
+            ),
+        ]
+    )
+def test_read_multiple_idx_groups_user_config(
+        user_config,
+        default_groups,
+        expected,
+        ):
+    """Test read multiple index groups in user config."""
+    result, _ = read_multiple_idx_groups_user_config(
+        user_config, default_groups,
+        )
     assert result == expected
 
 
+@pytest.mark.parametrize(
+    "user_config,default_groups,expected",
+    [
+        (
+            # user_config
+            {
+                # single index ones should NOT be considered
+                "param_other_1", "param_else_1",
+                "param_other_2", "param_else_2",
+                "param_1",
+                # multiple index ones should be considered
+                "param_sam_1_1", "param_frodo_1_1",  # param1 1
+                "param_sam_1_2", "param_frodo_1_2",  # param1 2
+                "param_sam_2_1", "param_frodo_2_1",  # param2 1
+                },
+            # default_groups
+            {
+                ("param1", "1"): {"sam", "frodo"},
+                ("param2", "1"): {"sam", "frodo"},
+                },
+            # expected counts
+            {
+                "param1": 2,
+                "param2": 1,
+                },
+            ),
+        ]
+    )
+def test_read_multiple_idx_groups_user_config_counts(
+        user_config,
+        default_groups,
+        expected,
+        ):
+    """Test counts multiple index groups in user config."""
+    _, counts = read_multiple_idx_groups_user_config(
+        user_config, default_groups,
+        )
+    assert counts == expected
+
+
 @pytest.mark.parametrize(
     "user_config,default_groups",
     [

From 6e7e60ebf89a1287df77d1afea024e33fa0da708 Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 11:10:27 +0200
Subject: [PATCH 05/13] also update symmetry parameters / cns code

---
 .../docking-protein-homotrimer-full.cfg       |  6 ----
 .../docking-protein-homotrimer-test.cfg       |  8 +-----
 .../modules/refinement/emref/cns/emref.cns    | 12 ++++----
 .../refinement/emref/cns/symmultimer.cns      | 12 ++++----
 .../modules/refinement/emref/defaults.yaml    | 28 +++++++++----------
 .../refinement/flexref/cns/check-homomers.cns | 12 ++++----
 .../refinement/flexref/cns/flexref.cns        | 12 ++++----
 .../refinement/flexref/cns/symmultimer.cns    | 12 ++++----
 .../modules/refinement/flexref/defaults.yaml  | 28 +++++++++----------
 .../modules/refinement/mdref/cns/mdref.cns    | 12 ++++----
 .../refinement/mdref/cns/symmultimer.cns      | 12 ++++----
 .../modules/refinement/mdref/defaults.yaml    | 28 +++++++++----------
 .../sampling/rigidbody/cns/check-homomers.cns | 12 ++++----
 .../sampling/rigidbody/cns/randomairs.cns     |  4 +--
 .../sampling/rigidbody/cns/rigidbody.cns      | 24 ++++++++--------
 .../sampling/rigidbody/cns/symmultimer.cns    | 12 ++++----
 .../modules/sampling/rigidbody/defaults.yaml  | 16 +++++------
 17 files changed, 119 insertions(+), 131 deletions(-)

diff --git a/examples/docking-protein-homotrimer/docking-protein-homotrimer-full.cfg b/examples/docking-protein-homotrimer/docking-protein-homotrimer-full.cfg
index cb519bef4..511f316cb 100644
--- a/examples/docking-protein-homotrimer/docking-protein-homotrimer-full.cfg
+++ b/examples/docking-protein-homotrimer/docking-protein-homotrimer-full.cfg
@@ -41,7 +41,6 @@ ambig_fname = "data/1qu9_whiscy_air.tbl"
 sampling = 2000
 # Define CNS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -56,7 +55,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -79,7 +77,6 @@ tolerance = 5
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -94,7 +91,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -113,7 +109,6 @@ tolerance = 5
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -128,7 +123,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
diff --git a/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg b/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg
index 2be4416c8..33980d886 100644
--- a/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg
+++ b/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg
@@ -36,8 +36,7 @@ ambig_fname = "data/1qu9_whiscy_air.tbl"
 sampling = 20
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
-ncs_sta1_1=2
+ncs_sta1_1=1
 ncs_end1_1=128
 ncs_seg1_1="A"
 ncs_sta2_1=2
@@ -51,7 +50,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -74,7 +72,6 @@ tolerance = 20
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -89,7 +86,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -108,7 +104,6 @@ tolerance = 20
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -123,7 +118,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
diff --git a/src/haddock/modules/refinement/emref/cns/emref.cns b/src/haddock/modules/refinement/emref/cns/emref.cns
index 60f72c296..76006e293 100644
--- a/src/haddock/modules/refinement/emref/cns/emref.cns
+++ b/src/haddock/modules/refinement/emref/cns/emref.cns
@@ -64,12 +64,12 @@ evaluate ($data.numncs = $numncs)
 ! Symmetry restraints
 evaluate ($data.ksym = $ksym)
 evaluate ($Data.flags.sym = $sym_on)
-evaluate ($data.numc2sym = $numc2sym)
-evaluate ($data.numc3sym = $numc3sym)
-evaluate ($data.nums3sym = $nums3sym)
-evaluate ($data.numc4sym = $numc4sym)
-evaluate ($data.numc5sym = $numc5sym)
-evaluate ($data.numc6sym = $numc6sym)
+evaluate ($data.nc2sym = $nc2sym)
+evaluate ($data.nc3sym = $nc3sym)
+evaluate ($data.ns3sym = $ns3sym)
+evaluate ($data.nc4sym = $nc4sym)
+evaluate ($data.nc5sym = $nc5sym)
+evaluate ($data.nc6sym = $nc6sym)
 
 !Dihedral angle energy term:
 evaluate ($data.flags.dihed = true)
diff --git a/src/haddock/modules/refinement/emref/cns/symmultimer.cns b/src/haddock/modules/refinement/emref/cns/symmultimer.cns
index 662bfa630..4bc582995 100644
--- a/src/haddock/modules/refinement/emref/cns/symmultimer.cns
+++ b/src/haddock/modules/refinement/emref/cns/symmultimer.cns
@@ -18,7 +18,7 @@ if ($Data.flags.sym eq true) then
     ! Define C2 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc2sym) loop c2symloop
+    while ($ncount < $data.nc2sym) loop c2symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c2sym_sta1_$ncount)
@@ -65,7 +65,7 @@ if ($Data.flags.sym eq true) then
     ! Define C3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc3sym) loop c3symloop
+    while ($ncount < $data.nc3sym) loop c3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c3sym_sta1_$ncount)
@@ -142,7 +142,7 @@ if ($Data.flags.sym eq true) then
     ! Define S3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.nums3sym) loop s3symloop
+    while ($ncount < $data.ns3sym) loop s3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $s3sym_sta1_$ncount)
@@ -218,7 +218,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc4sym) loop c4symloop
+    while ($ncount < $data.nc4sym) loop c4symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c4sym_sta1_$ncount)
@@ -369,7 +369,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 4)
     eval ($ncount = 0)
-    while ($ncount < $data.numc5sym) loop c5symloop
+    while ($ncount < $data.nc5sym) loop c5symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c5sym_sta1_$ncount)
@@ -482,7 +482,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc6sym) loop c6symloop
+    while ($ncount < $data.nc6sym) loop c6symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c6sym_sta1_$ncount)
diff --git a/src/haddock/modules/refinement/emref/defaults.yaml b/src/haddock/modules/refinement/emref/defaults.yaml
index fdf506336..2b191a935 100644
--- a/src/haddock/modules/refinement/emref/defaults.yaml
+++ b/src/haddock/modules/refinement/emref/defaults.yaml
@@ -237,7 +237,7 @@ symtbl_fname:
   long: Filename of the custom symmetry restraints file. 
   group: 'symmetry'
   explevel: expert
-numc2sym:
+nc2sym:
   default: 0
   type: integer
   min: 0
@@ -248,7 +248,7 @@ numc2sym:
     For each, a pair of segments on which the symmetry restraint is applied will have to be defined.
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c2sym_sta1_1:
   default: .nan
   type: integer
@@ -309,7 +309,7 @@ c2sym_seg2_1:
   long: Segment ID of second C2 segment
   group: 'symmetry'
   explevel: expert
-numc3sym:
+nc3sym:
   default: 0
   type: integer
   min: 0
@@ -320,7 +320,7 @@ numc3sym:
     For each, three segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c3sym_sta1_1:
   default: .nan
   type: integer
@@ -411,7 +411,7 @@ c3sym_seg3_1:
   long: Segment ID of third C3 segment
   group: 'symmetry'
   explevel: expert
-numc4sym:
+nc4sym:
   default: 0
   type: integer
   min: 0
@@ -422,7 +422,7 @@ numc4sym:
     For each, four segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c4sym_sta1_1:
   default: .nan
   type: integer
@@ -543,7 +543,7 @@ c4sym_seg4_1:
   long: Segment ID of fourth C4 segment
   group: 'symmetry'
   explevel: expert
-numc5sym:
+nc5sym:
   default: 0
   type: integer
   min: 0
@@ -554,7 +554,7 @@ numc5sym:
     For each, five segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c5sym_sta1_1:
   default: .nan
   type: integer
@@ -705,7 +705,7 @@ c5sym_seg5_1:
   long: Segment ID of fifth C5 segment
   group: 'symmetry'
   explevel: expert
-numc6sym:
+nc6sym:
   default: 0
   type: integer
   min: 0
@@ -716,7 +716,7 @@ numc6sym:
     For each, six segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c6sym_sta1_1:
   default: .nan
   type: integer
@@ -897,7 +897,7 @@ c6sym_seg6_1:
   long: Segment ID of sixth C6 segment
   group: 'symmetry'
   explevel: expert
-nums3sym:
+ns3sym:
   default: 0
   type: integer
   min: 0
@@ -908,7 +908,7 @@ nums3sym:
     For each, three segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 s3sym_sta1_1:
   default: .nan
   type: integer
@@ -1019,7 +1019,7 @@ kncs:
   long: Force constant for non-crystallographic restraints
   group: 'symmetry'
   explevel: expert
-numncs:
+nncs:
   default: 0
   type: integer
   min: 0
@@ -1029,7 +1029,7 @@ numncs:
   long: Number of non-crystallographic symmetry restraints. For each pairs of segments will have to be defined.
     Note that those must contain exactly the same residues/atom combinations.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 ncs_sta1_1:
   default: .nan
   type: integer
diff --git a/src/haddock/modules/refinement/flexref/cns/check-homomers.cns b/src/haddock/modules/refinement/flexref/cns/check-homomers.cns
index 00a359955..7faf7a4c9 100644
--- a/src/haddock/modules/refinement/flexref/cns/check-homomers.cns
+++ b/src/haddock/modules/refinement/flexref/cns/check-homomers.cns
@@ -22,32 +22,32 @@ while ($ncount < $data.ncomponents) loop checkmol
 end loop checkmol
 
 if ($data.flags.sym eq true) then
-    if ($data.numc2sym > 0) then
+    if ($data.nc2sym > 0) then
         if ($n_moving_mol = 2) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc2sym = 6) then
+    if ($data.nc2sym = 6) then
         if ($n_moving_mol = 4) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc3sym > 0) then
+    if ($data.nc3sym > 0) then
         if ($n_moving_mol = 3) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc4sym > 0) then
+    if ($data.nc4sym > 0) then
         if ($n_moving_mol = 4) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc5sym > 0) then
+    if ($data.nc5sym > 0) then
         if ($n_moving_mol = 5) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc6sym > 0) then
+    if ($data.nc6sym > 0) then
         if ($n_moving_mol = 6) then
             evaluate ($homosymmetry = true)
         end if
diff --git a/src/haddock/modules/refinement/flexref/cns/flexref.cns b/src/haddock/modules/refinement/flexref/cns/flexref.cns
index f5959d7c9..58680ecb6 100644
--- a/src/haddock/modules/refinement/flexref/cns/flexref.cns
+++ b/src/haddock/modules/refinement/flexref/cns/flexref.cns
@@ -123,12 +123,12 @@ evaluate ($data.numncs = $numncs)
 ! Symmetry restraints
 evaluate ($data.ksym = $ksym)
 evaluate ($Data.flags.sym = $sym_on)
-evaluate ($data.numc2sym = $numc2sym)
-evaluate ($data.numc3sym = $numc3sym)
-evaluate ($data.nums3sym = $nums3sym)
-evaluate ($data.numc4sym = $numc4sym)
-evaluate ($data.numc5sym = $numc5sym)
-evaluate ($data.numc6sym = $numc6sym)
+evaluate ($data.nc2sym = $nc2sym)
+evaluate ($data.nc3sym = $nc3sym)
+evaluate ($data.ns3sym = $ns3sym)
+evaluate ($data.nc4sym = $nc4sym)
+evaluate ($data.nc5sym = $nc5sym)
+evaluate ($data.nc6sym = $nc6sym)
 
 !Electrostatics:
 evaluate ($Data.flags.dihed =$dihedflag)
diff --git a/src/haddock/modules/refinement/flexref/cns/symmultimer.cns b/src/haddock/modules/refinement/flexref/cns/symmultimer.cns
index 662bfa630..4bc582995 100644
--- a/src/haddock/modules/refinement/flexref/cns/symmultimer.cns
+++ b/src/haddock/modules/refinement/flexref/cns/symmultimer.cns
@@ -18,7 +18,7 @@ if ($Data.flags.sym eq true) then
     ! Define C2 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc2sym) loop c2symloop
+    while ($ncount < $data.nc2sym) loop c2symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c2sym_sta1_$ncount)
@@ -65,7 +65,7 @@ if ($Data.flags.sym eq true) then
     ! Define C3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc3sym) loop c3symloop
+    while ($ncount < $data.nc3sym) loop c3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c3sym_sta1_$ncount)
@@ -142,7 +142,7 @@ if ($Data.flags.sym eq true) then
     ! Define S3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.nums3sym) loop s3symloop
+    while ($ncount < $data.ns3sym) loop s3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $s3sym_sta1_$ncount)
@@ -218,7 +218,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc4sym) loop c4symloop
+    while ($ncount < $data.nc4sym) loop c4symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c4sym_sta1_$ncount)
@@ -369,7 +369,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 4)
     eval ($ncount = 0)
-    while ($ncount < $data.numc5sym) loop c5symloop
+    while ($ncount < $data.nc5sym) loop c5symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c5sym_sta1_$ncount)
@@ -482,7 +482,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc6sym) loop c6symloop
+    while ($ncount < $data.nc6sym) loop c6symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c6sym_sta1_$ncount)
diff --git a/src/haddock/modules/refinement/flexref/defaults.yaml b/src/haddock/modules/refinement/flexref/defaults.yaml
index 592412d5d..a4a2fbbf5 100644
--- a/src/haddock/modules/refinement/flexref/defaults.yaml
+++ b/src/haddock/modules/refinement/flexref/defaults.yaml
@@ -574,7 +574,7 @@ symtbl_fname:
   long: Filename of the custom symmetry restraints file. 
   group: 'symmetry'
   explevel: expert
-numc2sym:
+nc2sym:
   default: 0
   type: integer
   min: 0
@@ -585,7 +585,7 @@ numc2sym:
     For each, a pair of segments on which the symmetry restraint is applied will have to be defined.
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c2sym_sta1_1:
   default: .nan
   type: integer
@@ -646,7 +646,7 @@ c2sym_seg2_1:
   long: Segment ID of second C2 segment
   group: 'symmetry'
   explevel: expert
-numc3sym:
+nc3sym:
   default: 0
   type: integer
   min: 0
@@ -657,7 +657,7 @@ numc3sym:
     For each, three segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c3sym_sta1_1:
   default: .nan
   type: integer
@@ -748,7 +748,7 @@ c3sym_seg3_1:
   long: Segment ID of third C3 segment
   group: 'symmetry'
   explevel: expert
-numc4sym:
+nc4sym:
   default: 0
   type: integer
   min: 0
@@ -759,7 +759,7 @@ numc4sym:
     For each, four segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c4sym_sta1_1:
   default: .nan
   type: integer
@@ -880,7 +880,7 @@ c4sym_seg4_1:
   long: Segment ID of fourth C4 segment
   group: 'symmetry'
   explevel: expert
-numc5sym:
+nc5sym:
   default: 0
   type: integer
   min: 0
@@ -891,7 +891,7 @@ numc5sym:
     For each, five segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c5sym_sta1_1:
   default: .nan
   type: integer
@@ -1042,7 +1042,7 @@ c5sym_seg5_1:
   long: Segment ID of fifth C5 segment
   group: 'symmetry'
   explevel: expert
-numc6sym:
+nc6sym:
   default: 0
   type: integer
   min: 0
@@ -1053,7 +1053,7 @@ numc6sym:
     For each, six segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c6sym_sta1_1:
   default: .nan
   type: integer
@@ -1234,7 +1234,7 @@ c6sym_seg6_1:
   long: Segment ID of sixth C6 segment
   group: 'symmetry'
   explevel: expert
-nums3sym:
+ns3sym:
   default: 0
   type: integer
   min: 0
@@ -1245,7 +1245,7 @@ nums3sym:
     For each, three segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 s3sym_sta1_1:
   default: .nan
   type: integer
@@ -1356,7 +1356,7 @@ kncs:
   long: Force constant for non-crystallographic restraints
   group: 'symmetry'
   explevel: expert
-numncs:
+nncs:
   default: 0
   type: integer
   min: 0
@@ -1366,7 +1366,7 @@ numncs:
   long: Number of non-crystallographic symmetry restraints. For each pairs of segments will have to be defined.
     Note that those must contain exactly the same residues/atom combinations.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 ncs_sta1_1:
   default: .nan
   type: integer
diff --git a/src/haddock/modules/refinement/mdref/cns/mdref.cns b/src/haddock/modules/refinement/mdref/cns/mdref.cns
index 0419ac3cf..f6e023011 100644
--- a/src/haddock/modules/refinement/mdref/cns/mdref.cns
+++ b/src/haddock/modules/refinement/mdref/cns/mdref.cns
@@ -72,12 +72,12 @@ evaluate ($data.numncs = $numncs)
 ! Symmetry restraints
 evaluate ($data.ksym = $ksym)
 evaluate ($Data.flags.sym = $sym_on)
-evaluate ($data.numc2sym = $numc2sym)
-evaluate ($data.numc3sym = $numc3sym)
-evaluate ($data.nums3sym = $nums3sym)
-evaluate ($data.numc4sym = $numc4sym)
-evaluate ($data.numc5sym = $numc5sym)
-evaluate ($data.numc6sym = $numc6sym)
+evaluate ($data.nc2sym = $nc2sym)
+evaluate ($data.nc3sym = $nc3sym)
+evaluate ($data.ns3sym = $ns3sym)
+evaluate ($data.nc4sym = $nc4sym)
+evaluate ($data.nc5sym = $nc5sym)
+evaluate ($data.nc6sym = $nc6sym)
 
 !Electrostatics:
 evaluate ($Data.flags.dihed =$dihedflag)
diff --git a/src/haddock/modules/refinement/mdref/cns/symmultimer.cns b/src/haddock/modules/refinement/mdref/cns/symmultimer.cns
index 662bfa630..4bc582995 100644
--- a/src/haddock/modules/refinement/mdref/cns/symmultimer.cns
+++ b/src/haddock/modules/refinement/mdref/cns/symmultimer.cns
@@ -18,7 +18,7 @@ if ($Data.flags.sym eq true) then
     ! Define C2 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc2sym) loop c2symloop
+    while ($ncount < $data.nc2sym) loop c2symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c2sym_sta1_$ncount)
@@ -65,7 +65,7 @@ if ($Data.flags.sym eq true) then
     ! Define C3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc3sym) loop c3symloop
+    while ($ncount < $data.nc3sym) loop c3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c3sym_sta1_$ncount)
@@ -142,7 +142,7 @@ if ($Data.flags.sym eq true) then
     ! Define S3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.nums3sym) loop s3symloop
+    while ($ncount < $data.ns3sym) loop s3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $s3sym_sta1_$ncount)
@@ -218,7 +218,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc4sym) loop c4symloop
+    while ($ncount < $data.nc4sym) loop c4symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c4sym_sta1_$ncount)
@@ -369,7 +369,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 4)
     eval ($ncount = 0)
-    while ($ncount < $data.numc5sym) loop c5symloop
+    while ($ncount < $data.nc5sym) loop c5symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c5sym_sta1_$ncount)
@@ -482,7 +482,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc6sym) loop c6symloop
+    while ($ncount < $data.nc6sym) loop c6symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c6sym_sta1_$ncount)
diff --git a/src/haddock/modules/refinement/mdref/defaults.yaml b/src/haddock/modules/refinement/mdref/defaults.yaml
index 18f27a8fb..2cb795de7 100644
--- a/src/haddock/modules/refinement/mdref/defaults.yaml
+++ b/src/haddock/modules/refinement/mdref/defaults.yaml
@@ -276,7 +276,7 @@ symtbl_fname:
   long: Filename of the custom symmetry restraints file. 
   group: 'symmetry'
   explevel: expert
-numc2sym:
+nc2sym:
   default: 0
   type: integer
   min: 0
@@ -287,7 +287,7 @@ numc2sym:
     For each, a pair of segments on which the symmetry restraint is applied will have to be defined.
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c2sym_sta1_1:
   default: .nan
   type: integer
@@ -348,7 +348,7 @@ c2sym_seg2_1:
   long: Segment ID of second C2 segment
   group: 'symmetry'
   explevel: expert
-numc3sym:
+nc3sym:
   default: 0
   type: integer
   min: 0
@@ -359,7 +359,7 @@ numc3sym:
     For each, three segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c3sym_sta1_1:
   default: .nan
   type: integer
@@ -450,7 +450,7 @@ c3sym_seg3_1:
   long: Segment ID of third C3 segment
   group: 'symmetry'
   explevel: expert
-numc4sym:
+nc4sym:
   default: 0
   type: integer
   min: 0
@@ -461,7 +461,7 @@ numc4sym:
     For each, four segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c4sym_sta1_1:
   default: .nan
   type: integer
@@ -582,7 +582,7 @@ c4sym_seg4_1:
   long: Segment ID of fourth C4 segment
   group: 'symmetry'
   explevel: expert
-numc5sym:
+nc5sym:
   default: 0
   type: integer
   min: 0
@@ -593,7 +593,7 @@ numc5sym:
     For each, five segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c5sym_sta1_1:
   default: .nan
   type: integer
@@ -744,7 +744,7 @@ c5sym_seg5_1:
   long: Segment ID of fifth C5 segment
   group: 'symmetry'
   explevel: expert
-numc6sym:
+nc6sym:
   default: 0
   type: integer
   min: 0
@@ -755,7 +755,7 @@ numc6sym:
     For each, six segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 c6sym_sta1_1:
   default: .nan
   type: integer
@@ -936,7 +936,7 @@ c6sym_seg6_1:
   long: Segment ID of sixth C6 segment
   group: 'symmetry'
   explevel: expert
-nums3sym:
+ns3sym:
   default: 0
   type: integer
   min: 0
@@ -947,7 +947,7 @@ nums3sym:
     For each, three segments on which the symmetry restraint is applied will have to be defined. 
     Those must all have the same length.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 s3sym_sta1_1:
   default: .nan
   type: integer
@@ -1058,7 +1058,7 @@ kncs:
   long: Force constant for non-crystallographic restraints
   group: 'symmetry'
   explevel: expert
-numncs:
+nncs:
   default: 0
   type: integer
   min: 0
@@ -1068,7 +1068,7 @@ numncs:
   long: Number of non-crystallographic symmetry restraints. For each pairs of segments will have to be defined.
     Note that those must contain exactly the same residues/atom combinations.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 ncs_sta1_1:
   default: .nan
   type: integer
diff --git a/src/haddock/modules/sampling/rigidbody/cns/check-homomers.cns b/src/haddock/modules/sampling/rigidbody/cns/check-homomers.cns
index 00a359955..7faf7a4c9 100644
--- a/src/haddock/modules/sampling/rigidbody/cns/check-homomers.cns
+++ b/src/haddock/modules/sampling/rigidbody/cns/check-homomers.cns
@@ -22,32 +22,32 @@ while ($ncount < $data.ncomponents) loop checkmol
 end loop checkmol
 
 if ($data.flags.sym eq true) then
-    if ($data.numc2sym > 0) then
+    if ($data.nc2sym > 0) then
         if ($n_moving_mol = 2) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc2sym = 6) then
+    if ($data.nc2sym = 6) then
         if ($n_moving_mol = 4) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc3sym > 0) then
+    if ($data.nc3sym > 0) then
         if ($n_moving_mol = 3) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc4sym > 0) then
+    if ($data.nc4sym > 0) then
         if ($n_moving_mol = 4) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc5sym > 0) then
+    if ($data.nc5sym > 0) then
         if ($n_moving_mol = 5) then
             evaluate ($homosymmetry = true)
         end if
     end if
-    if ($data.numc6sym > 0) then
+    if ($data.nc6sym > 0) then
         if ($n_moving_mol = 6) then
             evaluate ($homosymmetry = true)
         end if
diff --git a/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns b/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns
index db61f2f26..ce39de650 100644
--- a/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns
+++ b/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns
@@ -102,9 +102,9 @@ while ($nchain1 < $data.ncomponents) loop nloop1
         do (store5 = $nchain1) (segid $prot_segid_$nchain1)
         display RANDOM AIRS SAMPLED FROM ENTIRE SURFACE FOR MOLECULE $nchain1
     else
-        evaluate ($numseg = abs($nrair_$nchain1))
+        evaluate ($nseg = abs($nrair_$nchain1))
         display RANDOM AIRS SAMPLED FROM SEGMENTS FOR MOLECULE $nchain1
-        while ($fcounter < $numseg) loop Xflex
+        while ($fcounter < $nseg) loop Xflex
             evaluate($fcounter=$fcounter + 1)
             do (store5 = $nchain1) ( resid $rair_sta_$nchain1_$fcounter : $rair_end_$nchain1_$fcounter
                                      and segid $prot_segid_$nchain1)
diff --git a/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns b/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns
index 1da4ab5e9..a828552e2 100644
--- a/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns
+++ b/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns
@@ -58,26 +58,26 @@ evaluate ($toppar.par_nonbonded = "OPLSX")
 ! Symmetry restraints
 evaluate ($data.ksym = $ksym)
 evaluate ($Data.flags.sym = $sym_on)
-evaluate ($data.numc2sym = $numc2sym)
-evaluate ($data.numc3sym = $numc3sym)
-evaluate ($data.nums3sym= $nums3sym)
-evaluate ($data.numc4sym = $numc4sym)
-evaluate ($data.numc5sym = $numc5sym)
-evaluate ($data.numc6sym = $numc6sym)
-
-if ( $data.numc2sym eq 6) then
+evaluate ($data.nc2sym = $nc2sym)
+evaluate ($data.nc3sym = $nc3sym)
+evaluate ($data.ns3sym= $ns3sym)
+evaluate ($data.nc4sym = $nc4sym)
+evaluate ($data.nc5sym = $nc5sym)
+evaluate ($data.nc6sym = $nc6sym)
+
+if ( $data.nc2sym eq 6) then
     evaluate ($saprotocol.rotate180 = false)
 end if
-if ( $data.numc3sym ne 0) then
+if ( $data.nc3sym ne 0) then
     evaluate ($saprotocol.rotate180 = false)
 end if
-if ( $data.numc4sym ne 0) then
+if ( $data.nc4sym ne 0) then
     evaluate ($saprotocol.rotate180 = false)
 end if
-if ( $data.numc5sym ne 0) then
+if ( $data.nc5sym ne 0) then
     evaluate ($saprotocol.rotate180 = false)
 end if
-if ( $data.numc6sym ne 0) then
+if ( $data.nc6sym ne 0) then
     evaluate ($saprotocol.rotate180 = false)
 end if
 
diff --git a/src/haddock/modules/sampling/rigidbody/cns/symmultimer.cns b/src/haddock/modules/sampling/rigidbody/cns/symmultimer.cns
index 662bfa630..4bc582995 100644
--- a/src/haddock/modules/sampling/rigidbody/cns/symmultimer.cns
+++ b/src/haddock/modules/sampling/rigidbody/cns/symmultimer.cns
@@ -18,7 +18,7 @@ if ($Data.flags.sym eq true) then
     ! Define C2 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc2sym) loop c2symloop
+    while ($ncount < $data.nc2sym) loop c2symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c2sym_sta1_$ncount)
@@ -65,7 +65,7 @@ if ($Data.flags.sym eq true) then
     ! Define C3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.numc3sym) loop c3symloop
+    while ($ncount < $data.nc3sym) loop c3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c3sym_sta1_$ncount)
@@ -142,7 +142,7 @@ if ($Data.flags.sym eq true) then
     ! Define S3 symmetry restraints for symmetrical multimers
     !
     eval ($ncount = 0)
-    while ($ncount < $data.nums3sym) loop s3symloop
+    while ($ncount < $data.ns3sym) loop s3symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $s3sym_sta1_$ncount)
@@ -218,7 +218,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc4sym) loop c4symloop
+    while ($ncount < $data.nc4sym) loop c4symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c4sym_sta1_$ncount)
@@ -369,7 +369,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 4)
     eval ($ncount = 0)
-    while ($ncount < $data.numc5sym) loop c5symloop
+    while ($ncount < $data.nc5sym) loop c5symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c5sym_sta1_$ncount)
@@ -482,7 +482,7 @@ if ($Data.flags.sym eq true) then
     !
     eval ($istep = 10)
     eval ($ncount = 0)
-    while ($ncount < $data.numc6sym) loop c6symloop
+    while ($ncount < $data.nc6sym) loop c6symloop
 
         eval ($ncount = $ncount + 1)
         evaluate ($i1start = $c6sym_sta1_$ncount)
diff --git a/src/haddock/modules/sampling/rigidbody/defaults.yaml b/src/haddock/modules/sampling/rigidbody/defaults.yaml
index ff3a35dd9..c909b6b41 100644
--- a/src/haddock/modules/sampling/rigidbody/defaults.yaml
+++ b/src/haddock/modules/sampling/rigidbody/defaults.yaml
@@ -956,7 +956,7 @@ symtbl_fname:
   long: Filename of the custom symmetry restraints file. 
   group: 'symmetry'
   explevel: expert
-numc2sym:
+nc2sym:
   default: 0
   type: integer
   min: 0
@@ -1028,7 +1028,7 @@ c2sym_seg2_1:
   long: Segment ID of second C2 segment
   group: 'symmetry'
   explevel: expert
-numc3sym:
+nc3sym:
   default: 0
   type: integer
   min: 0
@@ -1130,7 +1130,7 @@ c3sym_seg3_1:
   long: Segment ID of third C3 segment
   group: 'symmetry'
   explevel: expert
-numc4sym:
+nc4sym:
   default: 0
   type: integer
   min: 0
@@ -1262,7 +1262,7 @@ c4sym_seg4_1:
   long: Segment ID of fourth C4 segment
   group: 'symmetry'
   explevel: expert
-numc5sym:
+nc5sym:
   default: 0
   type: integer
   min: 0
@@ -1424,7 +1424,7 @@ c5sym_seg5_1:
   long: Segment ID of fifth C5 segment
   group: 'symmetry'
   explevel: expert
-numc6sym:
+nc6sym:
   default: 0
   type: integer
   min: 0
@@ -1616,7 +1616,7 @@ c6sym_seg6_1:
   long: Segment ID of sixth C6 segment
   group: 'symmetry'
   explevel: expert
-nums3sym:
+ns3sym:
   default: 0
   type: integer
   min: 0
@@ -1738,7 +1738,7 @@ kncs:
   long: Force constant for non-crystallographic restraints
   group: 'symmetry'
   explevel: expert
-numncs:
+nncs:
   default: 0
   type: integer
   min: 0
@@ -1748,7 +1748,7 @@ numncs:
   long: Number of non-crystallographic symmetry restraints. For each pairs of segments will have to be defined.
     Note that those must contain exactly the same residues/atom combinations.
   group: 'symmetry'
-  explevel: expert
+  explevel: hidden
 ncs_sta1_1:
   default: .nan
   type: integer

From a0d7403184fb317c362bff5ced9750a03fb5892e Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 11:14:33 +0200
Subject: [PATCH 06/13] update numncs in cns files

---
 src/haddock/modules/refinement/emref/cns/emref.cns     | 2 +-
 src/haddock/modules/refinement/flexref/cns/flexref.cns | 2 +-
 src/haddock/modules/refinement/mdref/cns/mdref.cns     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/haddock/modules/refinement/emref/cns/emref.cns b/src/haddock/modules/refinement/emref/cns/emref.cns
index 76006e293..a048bc1d1 100644
--- a/src/haddock/modules/refinement/emref/cns/emref.cns
+++ b/src/haddock/modules/refinement/emref/cns/emref.cns
@@ -59,7 +59,7 @@ evaluate ($data.kcont=$kcont)
 ! NCS restraints
 evaluate ($data.kncs = $kncs)
 evaluate ($Data.flags.ncs = $ncs_on)
-evaluate ($data.numncs = $numncs)
+evaluate ($data.nncs = $nncs)
 
 ! Symmetry restraints
 evaluate ($data.ksym = $ksym)
diff --git a/src/haddock/modules/refinement/flexref/cns/flexref.cns b/src/haddock/modules/refinement/flexref/cns/flexref.cns
index 58680ecb6..4ca0f0c3a 100644
--- a/src/haddock/modules/refinement/flexref/cns/flexref.cns
+++ b/src/haddock/modules/refinement/flexref/cns/flexref.cns
@@ -118,7 +118,7 @@ end if
 ! NCS restraints
 evaluate ($data.kncs = $kncs)
 evaluate ($Data.flags.ncs = $ncs_on)
-evaluate ($data.numncs = $numncs)
+evaluate ($data.nncs = $nncs)
 
 ! Symmetry restraints
 evaluate ($data.ksym = $ksym)
diff --git a/src/haddock/modules/refinement/mdref/cns/mdref.cns b/src/haddock/modules/refinement/mdref/cns/mdref.cns
index f6e023011..4c206f484 100644
--- a/src/haddock/modules/refinement/mdref/cns/mdref.cns
+++ b/src/haddock/modules/refinement/mdref/cns/mdref.cns
@@ -67,7 +67,7 @@ end if
 ! NCS restraints
 evaluate ($data.kncs = $kncs)
 evaluate ($Data.flags.ncs = $ncs_on)
-evaluate ($data.numncs = $numncs)
+evaluate ($data.nncs = $nncs)
 
 ! Symmetry restraints
 evaluate ($data.ksym = $ksym)

From 06a0801adc62988a08c07e80e5d776ce4c4ce8d8 Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 11:30:26 +0200
Subject: [PATCH 07/13] modify parameter name in ncs checks

---
 src/haddock/gear/prepare_run.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/haddock/gear/prepare_run.py b/src/haddock/gear/prepare_run.py
index 1df4e65b2..7c4e6a745 100644
--- a/src/haddock/gear/prepare_run.py
+++ b/src/haddock/gear/prepare_run.py
@@ -799,18 +799,18 @@ def validate_ncs_params(params: dict) -> None:
     # Validate value of `numncs`
     ncs_suffixes = list(groupped_ncs.keys())
     # Case when number of definition do not match
-    if params["numncs"] != len(ncs_suffixes):
+    if params["nncs"] != len(ncs_suffixes):
         msg = (
-            f'Number of NCS restraints (`numncs = {params["numncs"]}`) '
+            f'Number of NCS restraints (`nncs = {params["nncs"]}`) '
             " do not match with the number of defined NCS restraints "
             f"({len(ncs_suffixes)})"
             )
         error_list.append(msg)
     else:
         # Case when numbers do not match
-        if max(ncs_suffixes) != params["numncs"]:
+        if max(ncs_suffixes) != params["nncs"]:
             msg = (
-                f'Number of NCS restraints (`numncs = {params["numncs"]}`) '
+                f'Number of NCS restraints (`nncs = {params["nncs"]}`) '
                 " do not match with the number of defined NCS restraints "
                 f"({', '.join([str(s) for s in ncs_suffixes])})"
                 )

From 4258b99a0a458402b216880b559c12dc7713205f Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 11:33:31 +0200
Subject: [PATCH 08/13] modify numncs parameter in tests

---
 tests/test_gear_prepare_run.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_gear_prepare_run.py b/tests/test_gear_prepare_run.py
index 3e0a74b6f..92bf59f57 100644
--- a/tests/test_gear_prepare_run.py
+++ b/tests/test_gear_prepare_run.py
@@ -38,7 +38,7 @@
 def fixture_proper_ncs_params() -> dict[str, Union[str, int]]:
     return {
         "ncs_on": True,
-        "numncs": 2,
+        "nncs": 2,
         "ncs_sta1_1": 1,
         "ncs_sta2_1": 1,
         "ncs_end1_1": 10,
@@ -469,7 +469,7 @@ def test_validate_ncs_params_different_end(proper_ncs_params):
 def test_validate_ncs_params_wrong_count(proper_ncs_params):
     """Test NCS param error when missmatch in number of ncs defined."""
     # Set wrong number of ncs definition
-    proper_ncs_params["numncs"] = 1
+    proper_ncs_params["nncs"] = 1
     with pytest.raises(ConfigurationError):
         assert validate_ncs_params(proper_ncs_params) is None
 
@@ -486,6 +486,6 @@ def test_validate_ncs_params_wrong_suffix_value(proper_ncs_params):
             proper_ncs_params[k3] = proper_ncs_params[k2]
             # Delete key2
             del proper_ncs_params[k2]
-    # Except error as _3 != (numncs = 2)
+    # Except error as _3 != (nncs = 2)
     with pytest.raises(ConfigurationError):
         assert validate_ncs_params(proper_ncs_params) is None

From 3c1cacdc1112ef2cc77bd1bd784a6c4cf217afb5 Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 12:09:49 +0200
Subject: [PATCH 09/13] fix testing changes...

---
 .../docking-protein-homotrimer-test.cfg                         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg b/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg
index 33980d886..c8dca6e3a 100644
--- a/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg
+++ b/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg
@@ -36,7 +36,7 @@ ambig_fname = "data/1qu9_whiscy_air.tbl"
 sampling = 20
 # Define NCS restraints between molecules
 ncs_on = true
-ncs_sta1_1=1
+ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
 ncs_sta2_1=2

From 7f98b9d9d352e710d5fd7f40305221d8351a23d9 Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 12:10:47 +0200
Subject: [PATCH 10/13] upgrade test_examples_general.py with handling
 functions

---
 tests/test_examples_general.py | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/tests/test_examples_general.py b/tests/test_examples_general.py
index 1a4fd8fdc..cf15af7fe 100644
--- a/tests/test_examples_general.py
+++ b/tests/test_examples_general.py
@@ -73,9 +73,26 @@ def test_integration_examples():
 def test_validate_cfg_files():
     """Test all the examples configuration files are valid."""
     for cfg_file in examples_cfg_files:
+        assert  validate_cfg_file(cfg_file), f"Error detected in {cfg_file}!"
+
+
+def validate_cfg_file(cfg_file: Path) -> bool:
+    """Handeler to validate a configuration file.
+
+    Parameters
+    ----------
+    cfg_file : Path
+        Path to the configuration file to check.
+
+    Returns
+    -------
+    bool
+        True if config file is OK else False
+    """
+    try:
         if cfg_file.name == "params.cfg":
             # skip the params.cfg files as they might be part of old runs
-            continue
+            return True
         config_files = read_config(cfg_file)
         # update default non-mandatory parameters with user params
         params = recursive_dict_update(
@@ -99,4 +116,9 @@ def test_validate_cfg_files():
             reference_parameters=ALL_POSSIBLE_GENERAL_PARAMETERS,
         )
 
-        validate_modules_params(modules_params, 20)
\ No newline at end of file
+        validate_modules_params(modules_params, 20)
+    except Exception as e:
+        print(e)
+        return False
+    else:
+        return True

From fa0cf07bd9827298110394ffa199259f9bb9bfc1 Mon Sep 17 00:00:00 2001
From: VGPReys <v.g.p.reys@uu.nl>
Date: Tue, 17 Sep 2024 12:39:21 +0200
Subject: [PATCH 11/13] reverse changes on randomairs.cns

---
 src/haddock/modules/sampling/rigidbody/cns/randomairs.cns | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns b/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns
index ce39de650..db61f2f26 100644
--- a/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns
+++ b/src/haddock/modules/sampling/rigidbody/cns/randomairs.cns
@@ -102,9 +102,9 @@ while ($nchain1 < $data.ncomponents) loop nloop1
         do (store5 = $nchain1) (segid $prot_segid_$nchain1)
         display RANDOM AIRS SAMPLED FROM ENTIRE SURFACE FOR MOLECULE $nchain1
     else
-        evaluate ($nseg = abs($nrair_$nchain1))
+        evaluate ($numseg = abs($nrair_$nchain1))
         display RANDOM AIRS SAMPLED FROM SEGMENTS FOR MOLECULE $nchain1
-        while ($fcounter < $nseg) loop Xflex
+        while ($fcounter < $numseg) loop Xflex
             evaluate($fcounter=$fcounter + 1)
             do (store5 = $nchain1) ( resid $rair_sta_$nchain1_$fcounter : $rair_end_$nchain1_$fcounter
                                      and segid $prot_segid_$nchain1)

From 128d68d91ca79bb9e9effa12c42aacfab071c6e3 Mon Sep 17 00:00:00 2001
From: Victor Reys <132575181+VGPReys@users.noreply.github.com>
Date: Tue, 17 Sep 2024 13:55:02 +0200
Subject: [PATCH 12/13] Apply typo suggestions from code review

Co-authored-by: Anna Engel <113177776+AljaLEngel@users.noreply.github.com>
---
 .../docking-flexref-protein-glycan-full.cfg                     | 2 +-
 .../docking-flexref-protein-glycan-test.cfg                     | 2 +-
 src/haddock/gear/expandable_parameters.py                       | 2 +-
 tests/test_examples_general.py                                  | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg b/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg
index e2db10af4..5787521ad 100644
--- a/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg
+++ b/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg
@@ -42,7 +42,7 @@ mdsteps_cool1 = 5000
 mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
-# give full flexibilit to the glycan
+# give full flexibility to the glycan
 fle_sta_1 = 1
 fle_end_1 = 4
 fle_seg_1 = "B"
diff --git a/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg b/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
index 9900453b2..86d062148 100644
--- a/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
+++ b/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
@@ -38,7 +38,7 @@ mdsteps_cool1 = 5000
 mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
-# give full flexibilit to the glycan
+# give full flexibility to the glycan
 fle_sta_1 = 1
 fle_end_1 = 4
 fle_seg_1 = "B"
diff --git a/src/haddock/gear/expandable_parameters.py b/src/haddock/gear/expandable_parameters.py
index db41380ad..1676843b1 100644
--- a/src/haddock/gear/expandable_parameters.py
+++ b/src/haddock/gear/expandable_parameters.py
@@ -284,7 +284,7 @@ def _read_groups_in_user_config(
         A set with the new parameters in the user configuration file
         that are acceptable according to the expandable rules.
     param_name_counts : dict[str, int]
-        Count of expendable parameter parameter name
+        Count of expendable parameter parameter names
     """
     # minimum=1 is used to capture groups with missing parameters
     user_groups = get_user_groups(user_config, minimum=1, reference=False)
diff --git a/tests/test_examples_general.py b/tests/test_examples_general.py
index cf15af7fe..975fc0cb3 100644
--- a/tests/test_examples_general.py
+++ b/tests/test_examples_general.py
@@ -73,7 +73,7 @@ def test_integration_examples():
 def test_validate_cfg_files():
     """Test all the examples configuration files are valid."""
     for cfg_file in examples_cfg_files:
-        assert  validate_cfg_file(cfg_file), f"Error detected in {cfg_file}!"
+        assert validate_cfg_file(cfg_file), f"Error detected in {cfg_file}!"
 
 
 def validate_cfg_file(cfg_file: Path) -> bool:

From 4d971fd32582fbe3382087263b2998d04dd343b4 Mon Sep 17 00:00:00 2001
From: Alexandre Bonvin <alexandre.bonvin@gmail.com>
Date: Tue, 17 Sep 2024 14:09:24 +0200
Subject: [PATCH 13/13] Update
 src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns

Co-authored-by: Anna Engel <113177776+AljaLEngel@users.noreply.github.com>
---
 src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns b/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns
index a828552e2..c3ffc1ed3 100644
--- a/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns
+++ b/src/haddock/modules/sampling/rigidbody/cns/rigidbody.cns
@@ -60,7 +60,7 @@ evaluate ($data.ksym = $ksym)
 evaluate ($Data.flags.sym = $sym_on)
 evaluate ($data.nc2sym = $nc2sym)
 evaluate ($data.nc3sym = $nc3sym)
-evaluate ($data.ns3sym= $ns3sym)
+evaluate ($data.ns3sym = $ns3sym)
 evaluate ($data.nc4sym = $nc4sym)
 evaluate ($data.nc5sym = $nc5sym)
 evaluate ($data.nc6sym = $nc6sym)