diff --git a/biobb_chemistry/acpype/acpype_params_ac.py b/biobb_chemistry/acpype/acpype_params_ac.py index 601baa3d..0916c8e1 100755 --- a/biobb_chemistry/acpype/acpype_params_ac.py +++ b/biobb_chemistry/acpype/acpype_params_ac.py @@ -161,6 +161,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) else: + self.tmp_files.extend([self.basename + "." + self.unique_name + ".acpype"]) process_output(self.unique_name, self.basename + "." + self.unique_name + ".acpype", self.remove_tmp, @@ -168,6 +169,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) + self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code @@ -184,6 +186,8 @@ def acpype_params_ac(input_path: str, output_path_frcmod: str, output_path_inpcr output_path_prmtop=output_path_prmtop, properties=properties, **kwargs).launch() + acpype_params_ac.__doc__ = AcpypeParamsAC.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/acpype/acpype_params_cns.py b/biobb_chemistry/acpype/acpype_params_cns.py index 6bd68ed7..f4bbbc65 100755 --- a/biobb_chemistry/acpype/acpype_params_cns.py +++ b/biobb_chemistry/acpype/acpype_params_cns.py @@ -162,6 +162,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) else: + self.tmp_files.extend([self.basename + "." + self.unique_name + ".acpype"]) process_output_cns( self.unique_name, self.basename + "." + self.unique_name + ".acpype", @@ -170,6 +171,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) + self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code @@ -186,6 +188,8 @@ def acpype_params_cns(input_path: str, output_path_par: str, output_path_inp: st output_path_pdb=output_path_pdb, properties=properties, **kwargs).launch() + acpype_params_cns.__doc__ = AcpypeParamsCNS.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/acpype/acpype_params_gmx.py b/biobb_chemistry/acpype/acpype_params_gmx.py index 841f10c8..2749df5c 100755 --- a/biobb_chemistry/acpype/acpype_params_gmx.py +++ b/biobb_chemistry/acpype/acpype_params_gmx.py @@ -157,6 +157,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) else: + self.tmp_files.extend([self.basename + "." + self.unique_name + ".acpype"]) process_output_gmx(self.unique_name, self.basename + "." + self.unique_name + ".acpype", self.remove_tmp, @@ -164,6 +165,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) + self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code @@ -179,6 +181,8 @@ def acpype_params_gmx(input_path: str, output_path_gro: str, output_path_itp: st output_path_top=output_path_top, properties=properties, **kwargs).launch() + acpype_params_gmx.__doc__ = AcpypeParamsGMX.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/acpype/acpype_params_gmx_opls.py b/biobb_chemistry/acpype/acpype_params_gmx_opls.py index c772ee74..5e4af598 100755 --- a/biobb_chemistry/acpype/acpype_params_gmx_opls.py +++ b/biobb_chemistry/acpype/acpype_params_gmx_opls.py @@ -153,6 +153,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) else: + self.tmp_files.extend([self.basename + "." + self.unique_name + ".acpype"]) process_output_gmx(self.unique_name, self.basename + "." + self.unique_name + ".acpype", self.remove_tmp, @@ -160,6 +161,7 @@ def launch(self) -> int: get_default_value(self.__class__.__name__), self.output_files, self.out_log) + self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code @@ -174,6 +176,8 @@ def acpype_params_gmx_opls(input_path: str, output_path_itp: str, output_path_to output_path_top=output_path_top, properties=properties, **kwargs).launch() + acpype_params_gmx_opls.__doc__ = AcpypeParamsGMXOPLS.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/ambertools/reduce_add_hydrogens.py b/biobb_chemistry/ambertools/reduce_add_hydrogens.py index ee031b6f..60ddfa41 100755 --- a/biobb_chemistry/ambertools/reduce_add_hydrogens.py +++ b/biobb_chemistry/ambertools/reduce_add_hydrogens.py @@ -195,9 +195,9 @@ def launch(self) -> int: self.copy_to_host() # remove temporary folder(s) - self.tmp_files.extend([ + '''self.tmp_files.extend([ self.stage_io_dict.get("unique_dir", "") - ]) + ])''' self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) @@ -213,6 +213,8 @@ def reduce_add_hydrogens(input_path: str, output_path: str, properties: Optional output_path=output_path, properties=properties, **kwargs).launch() + reduce_add_hydrogens.__doc__ = ReduceAddHydrogens.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/ambertools/reduce_remove_hydrogens.py b/biobb_chemistry/ambertools/reduce_remove_hydrogens.py index 5bf27817..936e53f6 100755 --- a/biobb_chemistry/ambertools/reduce_remove_hydrogens.py +++ b/biobb_chemistry/ambertools/reduce_remove_hydrogens.py @@ -114,9 +114,9 @@ def launch(self) -> int: self.copy_to_host() # remove temporary folder(s) - self.tmp_files.extend([ + '''self.tmp_files.extend([ self.stage_io_dict.get("unique_dir", "") - ]) + ])''' self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) @@ -132,6 +132,8 @@ def reduce_remove_hydrogens(input_path: str, output_path: str, properties: Optio output_path=output_path, properties=properties, **kwargs).launch() + reduce_remove_hydrogens.__doc__ = ReduceRemoveHydrogens.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/babelm/babel_add_hydrogens.py b/biobb_chemistry/babelm/babel_add_hydrogens.py index 6e274cab..6dca9737 100755 --- a/biobb_chemistry/babelm/babel_add_hydrogens.py +++ b/biobb_chemistry/babelm/babel_add_hydrogens.py @@ -194,7 +194,7 @@ def launch(self) -> int: self.copy_to_host() # remove temporary folder(s) - self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) + # self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) @@ -212,6 +212,8 @@ def babel_add_hydrogens( input_path=input_path, output_path=output_path, properties=properties, **kwargs ).launch() + babel_add_hydrogens.__doc__ = BabelAddHydrogens.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/babelm/babel_convert.py b/biobb_chemistry/babelm/babel_convert.py index 61ba89eb..66513e57 100755 --- a/biobb_chemistry/babelm/babel_convert.py +++ b/biobb_chemistry/babelm/babel_convert.py @@ -195,7 +195,7 @@ def launch(self) -> int: self.copy_to_host() # remove temporary folder(s) - self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) + # self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) @@ -213,6 +213,8 @@ def babel_convert( input_path=input_path, output_path=output_path, properties=properties, **kwargs ).launch() + babel_convert.__doc__ = BabelConvert.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/babelm/babel_minimize.py b/biobb_chemistry/babelm/babel_minimize.py index 420191c0..a317461d 100755 --- a/biobb_chemistry/babelm/babel_minimize.py +++ b/biobb_chemistry/babelm/babel_minimize.py @@ -170,9 +170,9 @@ def launch(self) -> int: self.copy_to_host() # remove temporary folder(s) - self.tmp_files.extend([ + '''self.tmp_files.extend([ self.stage_io_dict.get("unique_dir", "") - ]) + ])''' self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) @@ -188,6 +188,8 @@ def babel_minimize(input_path: str, output_path: str, properties: Optional[dict] output_path=output_path, properties=properties, **kwargs).launch() + babel_minimize.__doc__ = BabelMinimize.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation.""" diff --git a/biobb_chemistry/babelm/babel_remove_hydrogens.py b/biobb_chemistry/babelm/babel_remove_hydrogens.py index e5d5280c..f18f7e96 100755 --- a/biobb_chemistry/babelm/babel_remove_hydrogens.py +++ b/biobb_chemistry/babelm/babel_remove_hydrogens.py @@ -191,7 +191,7 @@ def launch(self) -> int: self.copy_to_host() # remove temporary folder(s) - self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) + # self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) @@ -209,6 +209,8 @@ def babel_remove_hydrogens( input_path=input_path, output_path=output_path, properties=properties, **kwargs ).launch() + babel_remove_hydrogens.__doc__ = BabelRemoveHydrogens.__doc__ + def main(): """Command line execution of this building block. Please check the command line documentation."""