forgot to load parameter and topology files. silence modeller log output
@@ -975,10 +975,19 @@ def apply_modeller(input_file_path, output_file_path, directives):
raise ImportError('Modeller and license must be installed to use this feature.')
directives = copy.deepcopy(directives)
+
+ # Silence unecessart output to the log files
+ modeller.log.none()
+
+ # Create modeller environment and point it to the PDB file
env = modeller.environ()
atom_files_directory = os.path.dirname(input_file_path)
atom_file_name = os.path.basename(input_file_path)
+ # Read in topology and parameter files
+ env.libs.topology.read(file='$(LIB)/top_heav.lib')
+ env.libs.parameters.read(file='$(LIB)/par.lib')
+
env.io.atom_files_directory = [atom_files_directory]
alignment = modeller.alignment(env)
model = modeller.model(env, file=atom_file_name)
