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Add PDB as output in acpype_cns
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Adam Hospital Gasch authored and Adam Hospital Gasch committed Dec 14, 2023
1 parent 0e3abc9 commit 497fbf1
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Showing 2 changed files with 41 additions and 6 deletions.
19 changes: 13 additions & 6 deletions biobb_chemistry/acpype/acpype_params_cns.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
from biobb_chemistry.acpype.common import get_binary_path, check_input_path, check_output_path, get_basename, get_charge, create_unique_name, get_default_value, process_output
from biobb_chemistry.acpype.common import get_binary_path, check_input_path, check_output_path, get_basename, get_charge, create_unique_name, get_default_value, process_output_cns


class AcpypeParamsCNS(BiobbObject):
Expand All @@ -19,6 +19,7 @@ class AcpypeParamsCNS(BiobbObject):
output_path_par (str): Path to the PAR output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.cns.par>`_. Accepted formats: par (edam:format_3881).
output_path_inp (str): Path to the INP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.cns.inp>`_. Accepted formats: inp (edam:format_3878).
output_path_top (str): Path to the TOP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.cns.top>`_. Accepted formats: top (edam:format_3881).
output_path_pdb (str): Path to the PDB output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.cns.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **basename** (*str*) - ("BBB") A basename for the project (folder and output files).
* **charge** (*int*) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype.
Expand All @@ -44,6 +45,7 @@ class AcpypeParamsCNS(BiobbObject):
output_path_par='/path/to/newPAR.par',
output_path_inp='/path/to/newINP.inp',
output_path_top='/path/to/newTOP.top',
output_path_top='/path/to/newPDB.pdb',
properties=prop)
Info:
Expand All @@ -57,7 +59,7 @@ class AcpypeParamsCNS(BiobbObject):
"""

def __init__(self, input_path, output_path_par, output_path_inp, output_path_top,
def __init__(self, input_path, output_path_par, output_path_inp, output_path_top, output_path_pdb,
properties=None, **kwargs) -> None:
properties = properties or {}

Expand All @@ -68,7 +70,7 @@ def __init__(self, input_path, output_path_par, output_path_inp, output_path_top
# Input/Output files
self.io_dict = {
"in": {"input_path": input_path},
"out": {"output_path_par": output_path_par, "output_path_inp": output_path_inp, "output_path_top": output_path_top}
"out": {"output_path_par": output_path_par, "output_path_inp": output_path_inp, "output_path_top": output_path_top, "output_path_pdb": output_path_pdb}
}

# Properties specific for BB
Expand All @@ -87,10 +89,12 @@ def check_data_params(self, out_log, err_log):
self.io_dict["out"]["output_path_par"] = check_output_path(self.io_dict["out"]["output_path_par"], 'par', out_log, self.__class__.__name__)
self.io_dict["out"]["output_path_inp"] = check_output_path(self.io_dict["out"]["output_path_inp"], 'inp', out_log, self.__class__.__name__)
self.io_dict["out"]["output_path_top"] = check_output_path(self.io_dict["out"]["output_path_top"], 'top', out_log, self.__class__.__name__)
self.io_dict["out"]["output_path_pdb"] = check_output_path(self.io_dict["out"]["output_path_pdb"], 'pdb', out_log, self.__class__.__name__)
self.output_files = {
'par': self.io_dict["out"]["output_path_par"],
'inp': self.io_dict["out"]["output_path_inp"],
'top': self.io_dict["out"]["output_path_top"],
'pdb': self.io_dict["out"]["output_path_pdb"],
}

def create_cmd(self, container_io_dict, out_log, err_log):
Expand Down Expand Up @@ -148,14 +152,14 @@ def launch(self) -> int:

# move files to output_path and removes temporary folder
if self.container_path:
process_output(self.unique_name,
process_output_cns(self.unique_name,
self.stage_io_dict['unique_dir'],
self.remove_tmp,
self.basename,
get_default_value(self.__class__.__name__),
self.output_files, self.out_log)
else:
process_output(self.unique_name,
process_output_cns(self.unique_name,
self.basename + "." + self.unique_name + ".acpype",
self.remove_tmp,
self.basename,
Expand All @@ -167,14 +171,15 @@ def launch(self) -> int:
return self.return_code


def acpype_params_cns(input_path: str, output_path_par: str, output_path_inp: str, output_path_top: str, properties: dict = None, **kwargs) -> int:
def acpype_params_cns(input_path: str, output_path_par: str, output_path_inp: str, output_path_top: str, output_path_pdb: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`AcpypeParamsCNS <acpype.acpype_params_cns.AcpypeParamsCNS>` class and
execute the :meth:`launch() <acpype.acpype_params_cns.AcpypeParamsCNS.launch>` method."""

return AcpypeParamsCNS(input_path=input_path,
output_path_par=output_path_par,
output_path_inp=output_path_inp,
output_path_top=output_path_top,
output_path_pdb=output_path_pdb,
properties=properties, **kwargs).launch()


Expand All @@ -189,6 +194,7 @@ def main():
required_args.add_argument('--output_path_par', required=True, help='Path to the PAR output file. Accepted formats: par.')
required_args.add_argument('--output_path_inp', required=True, help='Path to the INP output file. Accepted formats: inp.')
required_args.add_argument('--output_path_top', required=True, help='Path to the TOP output file. Accepted formats: top.')
required_args.add_argument('--output_path_pdb', required=True, help='Path to the PDB output file. Accepted formats: pdb.')

args = parser.parse_args()
args.config = args.config or "{}"
Expand All @@ -199,6 +205,7 @@ def main():
output_path_par=args.output_path_par,
output_path_inp=args.output_path_inp,
output_path_top=args.output_path_top,
output_path_pdb=args.output_path_pdb,
properties=properties)


Expand Down
28 changes: 28 additions & 0 deletions biobb_chemistry/acpype/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -151,6 +151,34 @@ def process_output_gmx(unique_name, files_folder, remove_tmp, basename, class_pa
shutil.copy(file_name, output_files[file_extension[1:]])
fu.log('File %s succesfully created' % output_files[file_extension[1:]], out_log)

def process_output_cns(unique_name, files_folder, remove_tmp, basename, class_params, output_files, out_log):
""" Moves and removes temporal files generated by the wrapper """
path = files_folder
suffix = class_params['suffix']
src_files = glob.glob(path + '/' + basename + '.' + unique_name + suffix + '*')

# copy files for the requested topology to the output_path
for file_name in src_files:
# replace random name by original name in all files
with fileinput.FileInput(file_name, inplace=True) as file:
for line in file:
print(line.replace(basename + '.' + unique_name, basename), end='')

if (Path(file_name).is_file()):
file_extension = PurePath(file_name).suffix
fu.log('Files: %s' % str(file_name), out_log)
shutil.copy(file_name, output_files[file_extension[1:]])
fu.log('File %s succesfully created' % output_files[file_extension[1:]], out_log)

file_extension = ".pdb"
file_name = path + '/' + basename + '.' + unique_name + "_NEW.pdb"
with open(file_name) as f:
newText = f.read().replace(basename + '_NEW.pdb', PurePath(output_files['pdb']).name)
with open(file_name, "w") as f:
f.write(newText)
shutil.copy(file_name, output_files[file_extension[1:]])
fu.log('File %s succesfully created' % output_files[file_extension[1:]], out_log)

if remove_tmp:
# remove temporary folder
fu.rm(files_folder)
Expand Down

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