Source code for aiida_gromacs.data.grompp
"""
Data types provided by plugin
Register data types via the "aiida.data" entry point in setup.json.
"""
# You can directly use or subclass aiida.orm.data.Data
# or any other data type listed under 'verdi data'
from voluptuous import Optional, Required, Schema
from aiida.orm import Dict
# A subset of grompp command line options
cmdline_options = {
Required("o", default="ions.tpr"): str,
Optional("po"): str,
Optional("pp"): str,
Optional("imd"): str,
Optional("r"): str,
Optional("v"): str,
Optional("time"): str,
Optional("rmvsbds"): str,
Optional("maxwarn"): str,
Optional("zero"): str,
Optional("renum"): str,
}
[docs]
class GromppParameters(Dict): # pylint: disable=too-many-ancestors
"""
Command line options for diff.
This class represents a python dictionary used to
pass command line options to the executable.
"""
# "voluptuous" schema to add automatic validation
schema = Schema(cmdline_options)
# pylint: disable=redefined-builtin
[docs]
def __init__(self, dict=None, **kwargs):
"""
Constructor for the data class
Usage: ``GromppParameters(dict{'ignore-case': True})``
:param parameters_dict: dictionary with commandline parameters
:param type parameters_dict: dict
"""
dict = self.validate(dict)
super().__init__(dict=dict, **kwargs)
[docs]
def validate(self, parameters_dict):
"""Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using::
print(GromppParameters).schema.schema
:param parameters_dict: dictionary with commandline parameters
:param type parameters_dict: dict
:returns: validated dictionary
"""
return GromppParameters.schema(parameters_dict)
[docs]
def cmdline_params(self, input_files):
"""Synthesize command line parameters.
e.g. [ '--ignore-case', 'filename1', 'filename2']
:param pdbfile: Name of input pdb file
:param type pdbfile: str
"""
parameters = []
parameters.append("grompp")
parameters.extend(["-f", input_files["mdpfile"]])
parameters.extend(["-c", input_files["grofile"]])
parameters.extend(["-p", input_files["topfile"]])
if "r_file" in input_files: parameters.extend(["-r", input_files["r_file"]])
if "rb_file" in input_files: parameters.extend(["-rb", input_files["rb_file"]])
if "n_file" in input_files: parameters.extend(["-n", input_files["n_file"]])
if "t_file" in input_files: parameters.extend(["-t", input_files["t_file"]])
if "e_file" in input_files: parameters.extend(["-e", input_files["e_file"]])
if "qmi_file" in input_files: parameters.extend(["-qmi", input_files["qmi_file"]])
if "ref_file" in input_files: parameters.extend(["-ref", input_files["ref_file"]])
parm_dict = self.get_dict()
for key, value in parm_dict.items():
parameters.extend(["-" + key, value])
return [str(p) for p in parameters]
[docs]
def __str__(self):
"""String representation of node.
Append values of dictionary to usual representation. E.g.::
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}
"""
string = super().__str__()
string += "\n" + str(self.get_dict())
return string