"""
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 pdb2gmx command line options
cmdline_options = {
Required("o", default="conf.gro"): str,
Required("p", default="topol.top"): str,
Required("i", default="posre.itp"): str,
Optional("n"): str,
Optional("q"): str,
Optional("chainsep"): str,
Optional("merge"): str,
Required("ff", default="oplsaa"): str,
Required("water", default="spce"): str,
Optional("inter"): str,
Optional("ss"): str,
Optional("ter"): str,
Optional("lys"): str,
Optional("arg"): str,
Optional("asp"): str,
Optional("glu"): str,
Optional("gln"): str,
Optional("his"): str,
Optional("angle"): str,
Optional("dist"): str,
Optional("una"): str,
Optional("ignh"): str,
Optional("missing"): str,
Optional("v"): str,
Optional("posrefc"): str,
Optional("vsite"): str,
Optional("heavyh"): str,
Optional("deuterate"): str,
Optional("chargegrp"): str,
Optional("cmap"): str,
Optional("renum"): str,
Optional("rtpres"): str,
}
[docs]
class Pdb2gmxParameters(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: ``Pdb2gmxParameters(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(Pdb2gmxParameters).schema.schema
:param parameters_dict: dictionary with commandline parameters
:param type parameters_dict: dict
:returns: validated dictionary
"""
return Pdb2gmxParameters.schema(parameters_dict)
[docs]
def cmdline_params(self, pdbfile):
"""Synthesize command line parameters.
e.g. [ '--ignore-case', 'filename1', 'filename2']
:param pdbfile: Name of input pdb file
:param type pdbfile: str
"""
parameters = []
parameters.append("pdb2gmx")
parameters.extend(["-f", pdbfile])
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