#!/usr/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
XML I/O parser for the SMIRNOFF (SMIRKS Native Open Force Field) format.
.. codeauthor:: John D. Chodera <john.chodera@choderalab.org>
.. codeauthor:: David L. Mobley <dmobley@mobleylab.org>
.. codeauthor:: Peter K. Eastman <peastman@stanford.edu>
"""
__all__ = [
"ParameterIOHandler",
"XMLParameterIOHandler",
]
# =============================================================================================
# GLOBAL IMPORTS
# =============================================================================================
import logging
import xmltodict
from simtk import unit
# =============================================================================================
# CONFIGURE LOGGER
# =============================================================================================
logger = logging.getLogger(__name__)
# =============================================================================================
# QUANTITY PARSING UTILITIES
# =============================================================================================
def _ast_unit_eval(node):
"""
Performs a safe algebraic syntax tree evaluation of a unit.
This will likely be replaced by the native implementation in Pint
if/when we'll switch over to Pint units.
"""
import ast
import operator as op
operators = {
ast.Add: op.add,
ast.Sub: op.sub,
ast.Mult: op.mul,
ast.Div: op.truediv,
ast.Pow: op.pow,
ast.BitXor: op.xor,
ast.USub: op.neg,
}
if isinstance(node, ast.Num): # <number>
return node.n
elif isinstance(node, ast.BinOp): # <left> <operator> <right>
return operators[type(node.op)](
_ast_unit_eval(node.left), _ast_unit_eval(node.right)
)
elif isinstance(node, ast.UnaryOp): # <operator>( <operand> ) e.g., -1
return operators[type(node.op)](_ast_unit_eval(node.operand))
elif isinstance(node, ast.Name):
# Check if this is a simtk unit.
u = getattr(unit, node.id)
if not isinstance(u, unit.Unit):
raise ValueError("No unit named {} found in simtk.unit.".format(node.id))
return u
else:
raise TypeError(node)
# =============================================================================================
# Base ParameterIOHandler
# =============================================================================================
[docs]class ParameterIOHandler:
"""
Base class for handling serialization/deserialization of SMIRNOFF ForceField objects
"""
_FORMAT = None
[docs] def __init__(self):
"""
Create a new ParameterIOHandler.
"""
pass
[docs] def parse_file(self, file_path):
"""
Parameters
----------
file_path
Returns
-------
"""
pass
[docs] def parse_string(self, data):
"""
Parse a SMIRNOFF force field definition in a seriaized format
Parameters
----------
data
Returns
-------
"""
pass
[docs] def to_file(self, file_path, smirnoff_data):
"""
Write the current forcefield parameter set to a file.
Parameters
----------
file_path : str
The path to the file to write to.
smirnoff_data : dict
A dictionary structured in compliance with the SMIRNOFF spec
Returns
-------
"""
pass
[docs] def to_string(self, smirnoff_data):
"""
Render the forcefield parameter set to a string
Parameters
----------
smirnoff_data : dict
A dictionary structured in compliance with the SMIRNOFF spec
Returns
-------
str
"""
pass
# =============================================================================================
# XML I/O
# =============================================================================================
[docs]class XMLParameterIOHandler(ParameterIOHandler):
"""
Handles serialization/deserialization of SMIRNOFF ForceField objects from OFFXML format.
"""
# TODO: Come up with a better keyword for format
_FORMAT = "XML"
[docs] def parse_file(self, source):
"""Parse a SMIRNOFF force field definition in XML format, read from a file.
Parameters
----------
source : str or io.RawIOBase
File path of file-like object implementing a ``read()`` method
specifying a SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_.
Raises
------
ParseError
If the XML cannot be processed.
FileNotFoundError
If the file could not found.
"""
# If this is a file-like object, we should be able to read it.
try:
raw_data = source.read()
except AttributeError:
# This raises FileNotFoundError if the file doesn't exist.
raw_data = open(source).read()
# Parse the data in string format.
return self.parse_string(raw_data)
[docs] def parse_string(self, data):
"""Parse a SMIRNOFF force field definition in XML format.
A ``ParseError`` is raised if the XML cannot be processed.
Parameters
----------
data : str
A SMIRNOFF force field definition in `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_.
"""
from pyexpat import ExpatError
from openforcefield.typing.engines.smirnoff.forcefield import ParseError
# Parse XML file
try:
smirnoff_data = xmltodict.parse(data, attr_prefix="")
return smirnoff_data
except ExpatError as e:
raise ParseError(str(e))
[docs] def to_file(self, file_path, smirnoff_data):
"""Write the current forcefield parameter set to a file.
Parameters
----------
file_path : str
The path to the file to be written.
The `.offxml` or `.xml` file extension must be present.
smirnoff_data : dict
A dict structured in compliance with the SMIRNOFF data spec.
"""
xml_string = self.to_string(smirnoff_data)
with open(file_path, "w") as of:
of.write(xml_string)
[docs] def to_string(self, smirnoff_data):
"""
Write the current forcefield parameter set to an XML string.
Parameters
----------
smirnoff_data : dict
A dictionary structured in compliance with the SMIRNOFF spec
Returns
-------
serialized_forcefield : str
XML String representation of this forcefield.
"""
def prepend_all_keys(d, char="@", ignore_keys=frozenset()):
"""
Modify a dictionary in-place, prepending a specified string to each key
that doesn't refer to a value that is list or dict.
Parameters
----------
d : dict
Hierarchical dictionary to traverse and modify keys
char : string, optional. Default='@'
String to prepend onto each applicable dictionary key
ignore_keys : iterable of str
A set or list of strings, indicating keys not to prepend in the data structure
"""
if isinstance(d, dict):
for key in list(d.keys()):
if key in ignore_keys:
continue
if isinstance(d[key], list) or isinstance(d[key], dict):
prepend_all_keys(d[key], char=char, ignore_keys=ignore_keys)
else:
new_key = char + key
d[new_key] = d[key]
del d[key]
prepend_all_keys(d[new_key], char=char, ignore_keys=ignore_keys)
elif isinstance(d, list):
for item in d:
prepend_all_keys(item, char=char, ignore_keys=ignore_keys)
# the "xmltodict" library defaults to print out all element attributes on separate lines
# unless they're prepended by "@"
prepend_all_keys(smirnoff_data["SMIRNOFF"], ignore_keys=["Author", "Date"])
# Reorder parameter sections to put Author and Date at the top (this is the only
# way to change the order of items in a dict, as far as I can tell)
for key, value in list(smirnoff_data["SMIRNOFF"].items()):
if key in ["Author", "Date"]:
continue
del smirnoff_data["SMIRNOFF"][key]
smirnoff_data["SMIRNOFF"][key] = value
return xmltodict.unparse(smirnoff_data, pretty=True)
