Commit ⋅ slochower/openforcefield

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...enforcefield/typing/engines/smirnoff/forcefield.py changed.

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docs/releasehistory.rst has changed.

openforcefield/tests/test_forcefield.py has changed.

@@ -267,6 +267,7 @@

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    def __init__(
        self,
        *sources,
        aromaticity_model=DEFAULT_AROMATICITY_MODEL,
        parameter_handler_classes=None,
        parameter_io_handler_classes=None,
        disable_version_check=False,

@@ -285,6 +286,8 @@

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            If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible,
            with files appearing later in the sequence resulting in parameters that have higher precedence.
            Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence.
        aromaticity_model : string, default='OEAroModel_MDL'
            The aromaticity model used by the force field. Currently, only 'OEAroModel_MDL' is supported
        parameter_handler_classes : iterable of ParameterHandler classes, optional, default=None
            If not None, the specified set of ParameterHandler classes will be instantiated to create the parameter object model.
            By default, all imported subclasses of ParameterHandler are automatically registered.

@@ -320,6 +323,7 @@

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        # Clear all object fields
        self._initialize()

        self.aromaticity_model = aromaticity_model
        # Store initialization options
        self.disable_version_check = disable_version_check
        # if True, we won't check which SMIRNOFF version number we're parsing

@@ -361,7 +365,7 @@

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        self._disable_version_check = (
            False  # if True, will disable checking compatibility version
        )
        self._aromaticity_model = DEFAULT_AROMATICITY_MODEL  # aromaticity model
        self._aromaticity_model = None
        self._parameter_handler_classes = (
            OrderedDict()
        )  # Parameter handler classes that _can_ be initialized if needed

@@ -374,7 +378,6 @@

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        self._parameter_io_handlers = (
            OrderedDict()
        )  # ParameterIO classes to be used for each file type
        self._aromaticity_model = None
        self._author = None
        self._date = None


@@ -414,7 +417,19 @@

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                )
            )

    def _set_aromaticity_model(self, aromaticity_model):
    @property
    def aromaticity_model(self):
        """Returns the aromaticity model for this ForceField object.

        Returns
        -------
        aromaticity_model
            The aromaticity model for this force field.
        """
        return self._aromaticity_model

    @aromaticity_model.setter
    def aromaticity_model(self, aromaticity_model):
        """
        Register that this forcefield is using an aromaticity model. Will check for
        compatibility with other aromaticity model(s) already in use.

@@ -441,17 +456,6 @@

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        self._aromaticity_model = aromaticity_model

    @property
    def aromaticity_model(self):
        """Returns the aromaticity model for this ForceField object.

        Returns
        -------
        aromaticity_model
            The aromaticity model for this force field.
        """
        return self._aromaticity_model

    def _add_author(self, author):
        """
        Add an author to this forcefield. If this functional is called multiple times, all provided authors

@@ -964,7 +968,7 @@

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        # others loaded by this ForceField
        if "aromaticity_model" in smirnoff_data["SMIRNOFF"]:
            aromaticity_model = smirnoff_data["SMIRNOFF"]["aromaticity_model"]
            self._set_aromaticity_model(aromaticity_model)
            self.aromaticity_model = aromaticity_model

        elif self._aromaticity_model is None:
            raise ParseError(

Files		•	•	•	Coverage
openforcefield	5,907	4,182	0	1,725	70.80%
Project Totals (18 files)	5,907	4,182	0	1,725	70.80%

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267	267		def __init__(
268	268		self,
269	269		*sources,
	270	+	aromaticity_model=DEFAULT_AROMATICITY_MODEL,
270	271		parameter_handler_classes=None,
271	272		parameter_io_handler_classes=None,
272	273		disable_version_check=False,

320	323		# Clear all object fields
321	324		self._initialize()
322	325
	326	+	self.aromaticity_model = aromaticity_model
323	327		# Store initialization options
324	328		self.disable_version_check = disable_version_check
325	329		# if True, we won't check which SMIRNOFF version number we're parsing

361	365		self._disable_version_check = (
362	366		False # if True, will disable checking compatibility version
363	367		)
364		-	self._aromaticity_model = DEFAULT_AROMATICITY_MODEL # aromaticity model
	368	+	self._aromaticity_model = None
365	369		self._parameter_handler_classes = (
366	370		OrderedDict()
367	371		) # Parameter handler classes that _can_ be initialized if needed

374	378		self._parameter_io_handlers = (
375	379		OrderedDict()
376	380		) # ParameterIO classes to be used for each file type
377		-	self._aromaticity_model = None
378	381		self._author = None
379	382		self._date = None
380	383

414	417		)
415	418		)
416	419
417		-	def _set_aromaticity_model(self, aromaticity_model):
	420	+	@property
	421	+	def aromaticity_model(self):
	422	+	"""Returns the aromaticity model for this ForceField object.
	423	+
	424	+	Returns
	425	+	-------
	426	+	aromaticity_model
	427	+	The aromaticity model for this force field.
	428	+	"""
	429	+	return self._aromaticity_model
	430	+
	431	+	@aromaticity_model.setter
	432	+	def aromaticity_model(self, aromaticity_model):
418	433		"""
419	434		Register that this forcefield is using an aromaticity model. Will check for
420	435		compatibility with other aromaticity model(s) already in use.

285	286		If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible,
286	287		with files appearing later in the sequence resulting in parameters that have higher precedence.
287	288		Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence.
	289	+	aromaticity_model : string, default='OEAroModel_MDL'
	290	+	The aromaticity model used by the force field. Currently, only 'OEAroModel_MDL' is supported
288	291		parameter_handler_classes : iterable of ParameterHandler classes, optional, default=None
289	292		If not None, the specified set of ParameterHandler classes will be instantiated to create the parameter object model.
290	293		By default, all imported subclasses of ParameterHandler are automatically registered.

441	456
442	457		self._aromaticity_model = aromaticity_model
443	458
444		-	@property
445		-	def aromaticity_model(self):
446		-	"""Returns the aromaticity model for this ForceField object.
447		-
448		-	Returns
449		-	-------
450		-	aromaticity_model
451		-	The aromaticity model for this force field.
452		-	"""
453		-	return self._aromaticity_model
454		-
455	459		def _add_author(self, author):
456	460		"""
457	461		Add an author to this forcefield. If this functional is called multiple times, all provided authors

964	968		# others loaded by this ForceField
965	969		if "aromaticity_model" in smirnoff_data["SMIRNOFF"]:
966	970		aromaticity_model = smirnoff_data["SMIRNOFF"]["aromaticity_model"]
967		-	self._set_aromaticity_model(aromaticity_model)
	971	+	self.aromaticity_model = aromaticity_model
968	972
969	973		elif self._aromaticity_model is None:
970	974		raise ParseError(

1	# Codecov configuration to make it a bit less noisy
2	coverage:
3	status:
4	patch: false
5	project:
6	default:
7	threshold: 50%
8	comment:
9	layout: "header"
10	require_changes: false
11	branches: null
12	behavior: default
13	flags: null
14	paths: null

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