think I fixed the pdbfixer issue, adding print statement to debug modeller
@@ -876,7 +876,7 @@ def apply_pdbfixer(input_file_path, output_file_path, directives):
raise ValueError("'ph' must be a floating-point number: found '{}'".format(value))
return pH
- pH = process_tool_directive('ph', dispatch_pH, None, yields_value=True)
+ pH = process_tool_directive(directives, 'ph', dispatch_pH, None, yields_value=True)
def add_missing_residues(value):
if value == 'yes':
@@ -997,7 +997,7 @@ def apply_modeller(input_file_path, output_file_path, directives):
mutations = value['mutations']
# Check that double mutants were not specified
if len(mutations) > 1:
- raise ValueError("You have specified a double mutant, which is not supported by modeller")
+ raise ValueError("You have specified a double mutant, which is not supported by modeller. These mutants are problematic:{}".format(mutations))
# Convert mutations to PDBFixer format
if mutations != 'WT':
modeller_mutations = [generate_pdbfixer_mutation_code(*decompose_mutation(mutation))
