From 0b7678445cf520311a261fea95faa035e1abeb80 Mon Sep 17 00:00:00 2001
From: joaomcteixeira <joaomcteixeira@gmail.com>
Date: Wed, 24 Nov 2021 10:18:10 +0100
Subject: [PATCH] corrects ambig_fname var names

---
 src/haddock/modules/refinement/emref/__init__.py   | 8 ++++----
 src/haddock/modules/refinement/flexref/__init__.py | 8 ++++----
 src/haddock/modules/refinement/mdref/__init__.py   | 8 ++++----
 src/haddock/modules/sampling/gdock/__init__.py     | 2 +-
 src/haddock/modules/sampling/gdock/defaults.cfg    | 2 +-
 src/haddock/modules/sampling/rigidbody/__init__.py | 8 ++++----
 6 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/haddock/modules/refinement/emref/__init__.py b/src/haddock/modules/refinement/emref/__init__.py
index d9bf053ca..816417b41 100644
--- a/src/haddock/modules/refinement/emref/__init__.py
+++ b/src/haddock/modules/refinement/emref/__init__.py
@@ -26,7 +26,7 @@ def generate_emref(
         step_path,
         recipe_str,
         defaults,
-        ambig=None,
+        ambig_fname=None,
         ):
     """Generate the .inp file that will run the docking."""
     # prepare the CNS header that will read the input
@@ -45,8 +45,8 @@ def generate_emref(
 
     input_str = prepare_multiple_input([pdb], psf_list)
 
-    if ambig:
-        ambig_str = load_ambig(ambig)
+    if ambig_fname:
+        ambig_str = load_ambig(ambig_fname)
     else:
         ambig_str = ""
 
@@ -110,7 +110,7 @@ def run(self, **params):
                 self.path,
                 self.recipe_str,
                 self.params,
-                ambig=self.params.get('ambig', None),
+                ambig_fname=self.params['ambig_fname'],
                 )
 
             out_file = self.path / f"emref_{idx}.out"
diff --git a/src/haddock/modules/refinement/flexref/__init__.py b/src/haddock/modules/refinement/flexref/__init__.py
index 35b09c54f..da96be08e 100644
--- a/src/haddock/modules/refinement/flexref/__init__.py
+++ b/src/haddock/modules/refinement/flexref/__init__.py
@@ -26,7 +26,7 @@ def generate_flexref(
         step_path,
         recipe_str,
         defaults,
-        ambig=None,
+        ambig_fname=None,
         ):
     """Generate the .inp file that will run the docking."""
     # prepare the CNS header that will read the input
@@ -48,8 +48,8 @@ def generate_flexref(
 
     input_str = prepare_multiple_input([pdb], psf_list)
 
-    if ambig:
-        ambig_str = load_ambig(ambig)
+    if ambig_fname:
+        ambig_str = load_ambig(ambig_fname)
     else:
         ambig_str = ""
 
@@ -108,7 +108,7 @@ def run(self, **params):
                 self.path,
                 self.recipe_str,
                 self.params,
-                ambig=self.params.get('ambig', None),
+                ambig_fname=self.params['ambig_fname'],
                 )
 
             out_file = self.path / f"flexref_{idx}.out"
diff --git a/src/haddock/modules/refinement/mdref/__init__.py b/src/haddock/modules/refinement/mdref/__init__.py
index 63390c486..ca1e2bd9b 100644
--- a/src/haddock/modules/refinement/mdref/__init__.py
+++ b/src/haddock/modules/refinement/mdref/__init__.py
@@ -26,7 +26,7 @@ def generate_waterref(
         step_path,
         recipe_str,
         defaults,
-        ambig=None,
+        ambig_fname=None,
         ):
     """Generate the .inp file that will run the docking."""
     # prepare the CNS header that will read the input
@@ -45,8 +45,8 @@ def generate_waterref(
 
     input_str = prepare_multiple_input([pdb], psf_list)
 
-    if ambig:
-        ambig_str = load_ambig(ambig)
+    if ambig_fname:
+        ambig_str = load_ambig(ambig_fname)
     else:
         ambig_str = ""
 
@@ -103,7 +103,7 @@ def run(self, **params):
                 self.path,
                 self.recipe_str,
                 self.params,
-                ambig=self.params.get('ambig', None),
+                ambig_fname=self.params['ambig_fname'],
                 )
 
             out_file = self.path / f"waterref_{idx}.out"
diff --git a/src/haddock/modules/sampling/gdock/__init__.py b/src/haddock/modules/sampling/gdock/__init__.py
index af41147db..bea499e6f 100644
--- a/src/haddock/modules/sampling/gdock/__init__.py
+++ b/src/haddock/modules/sampling/gdock/__init__.py
@@ -93,7 +93,7 @@ def run(self, **params):
             input[chain] = chain_pdb
 
         # convert ambig to list
-        ambig_dic = ambig2dic(self.params.get('ambig', None))
+        ambig_dic = ambig2dic(self.params['ambig_fname'])
 
         input_toml = '' + os.linesep
         input_toml += '[main]' + os.linesep
diff --git a/src/haddock/modules/sampling/gdock/defaults.cfg b/src/haddock/modules/sampling/gdock/defaults.cfg
index 340ba9a25..ad52a6dd2 100644
--- a/src/haddock/modules/sampling/gdock/defaults.cfg
+++ b/src/haddock/modules/sampling/gdock/defaults.cfg
@@ -1 +1 @@
-ambig = ""
+ambig_fname = ""
diff --git a/src/haddock/modules/sampling/rigidbody/__init__.py b/src/haddock/modules/sampling/rigidbody/__init__.py
index 69558ad03..ff1604bda 100644
--- a/src/haddock/modules/sampling/rigidbody/__init__.py
+++ b/src/haddock/modules/sampling/rigidbody/__init__.py
@@ -26,7 +26,7 @@ def generate_docking(
         step_path,
         recipe_str,
         defaults,
-        ambig=None,
+        ambig_fname=None,
         ):
     """Generate the .inp file that will run the docking."""
     # prepare the CNS header that will read the input
@@ -49,8 +49,8 @@ def generate_docking(
 
     input_str = prepare_multiple_input(pdb_list, psf_list)
 
-    if ambig:
-        ambig_str = load_ambig(ambig)
+    if ambig_fname:
+        ambig_str = load_ambig(ambig_fname)
     else:
         ambig_str = ""
 
@@ -116,7 +116,7 @@ def run(self, **params):
                 self.path,
                 self.recipe_str,
                 self.params,
-                ambig=self.params.get('ambig', None),
+                ambig_fname=self.params['ambig_fname'],
                 )
 
             out_file = self.path / f"rigidbody_{idx}.out"