This package contains standard serializers that can work generally for all pymatgen objects.
New in version 1.9.0.
This module implements the abstract base class for msonable pymatgen objects, i.e., objects that can be converted to a json representation. MSON stands for materials json.
It also implements general JSON encoders and decoders for pymatgen. Only supports pymatgen object version >= 1.9.0.
Current support for all core objects that obey the to_dict/from_dict API, including Site, PeriodicSite, Structure, Specie, Dos, Lattice, etc. and all Entry and all Transformations. Note that nested lists and dicts of these objects are supported as well.
The decoder depends on finding a “module” and “class” key in the dict in order to decode the necessary python object. All to_dict properties must therefore have the module name and class embedded. In general, the PMGJSONEncoder will add these keys if they are not present, but for better long term stability, the easiest way is to add the following to any to_dict property:
d["module"] = self.__class__.__module__ d["class"] = self.__class__.__name__
This is an abstract base class specifying an API for msonable objects. MSON is Materials JSON. Essentially, MSONable objects must implement a to_dict property and a from_dict static method.
This simply raises a NotImplementedError to force subclasses to implement this static method. Abstract static methods are not implemented until Python 3+.
A JSON serializable dict representation of an object.
Returns a json string representation of the MSONable object.
Writes the mson representation to a file.
A Pymatgen Json Decoder which supports the from_dict API. By default, the decoder attempts to find a module and name associated with a dict. If found, the decoder will generate a Pymatgen as a priority. If that fails, the original decoded dictionary from the string is returned. Note that nested lists and dicts containing pymatgen object will be decoded correctly as well.
encoding determines the encoding used to interpret any str objects decoded by this instance (utf-8 by default). It has no effect when decoding unicode objects.
Note that currently only encodings that are a superset of ASCII work, strings of other encodings should be passed in as unicode.
object_hook, if specified, will be called with the result of every JSON object decoded and its return value will be used in place of the given dict. This can be used to provide custom deserializations (e.g. to support JSON-RPC class hinting).
object_pairs_hook, if specified will be called with the result of every JSON object decoded with an ordered list of pairs. The return value of object_pairs_hook will be used instead of the dict. This feature can be used to implement custom decoders that rely on the order that the key and value pairs are decoded (for example, collections.OrderedDict will remember the order of insertion). If object_hook is also defined, the object_pairs_hook takes priority.
parse_float, if specified, will be called with the string of every JSON float to be decoded. By default this is equivalent to float(num_str). This can be used to use another datatype or parser for JSON floats (e.g. decimal.Decimal).
parse_int, if specified, will be called with the string of every JSON int to be decoded. By default this is equivalent to int(num_str). This can be used to use another datatype or parser for JSON integers (e.g. float).
parse_constant, if specified, will be called with one of the following strings: -Infinity, Infinity, NaN. This can be used to raise an exception if invalid JSON numbers are encountered.
If strict is false (true is the default), then control characters will be allowed inside strings. Control characters in this context are those with character codes in the 0-31 range, including '\t' (tab), '\n', '\r' and '\0'.
Recursive method to support decoding dicts and lists containing pymatgen objects.
A Pymatgen Json Encoder which supports the to_dict API.
Constructor for JSONEncoder, with sensible defaults.
If skipkeys is false, then it is a TypeError to attempt encoding of keys that are not str, int, long, float or None. If skipkeys is True, such items are simply skipped.
If ensure_ascii is true (the default), all non-ASCII characters in the output are escaped with uXXXX sequences, and the results are str instances consisting of ASCII characters only. If ensure_ascii is False, a result may be a unicode instance. This usually happens if the input contains unicode strings or the encoding parameter is used.
If check_circular is true, then lists, dicts, and custom encoded objects will be checked for circular references during encoding to prevent an infinite recursion (which would cause an OverflowError). Otherwise, no such check takes place.
If sort_keys is true, then the output of dictionaries will be sorted by key; this is useful for regression tests to ensure that JSON serializations can be compared on a day-to-day basis.
If indent is a non-negative integer, then JSON array elements and object members will be pretty-printed with that indent level. An indent level of 0 will only insert newlines. None is the most compact representation. Since the default item separator is ‘, ‘, the output might include trailing whitespace when indent is specified. You can use separators=(‘,’, ‘: ‘) to avoid this.
If specified, separators should be a (item_separator, key_separator) tuple. The default is (‘, ‘, ‘: ‘). To get the most compact JSON representation you should specify (‘,’, ‘:’) to eliminate whitespace.
If specified, default is a function that gets called for objects that can’t otherwise be serialized. It should return a JSON encodable version of the object or raise a TypeError.
If encoding is not None, then all input strings will be transformed into unicode using that encoding prior to JSON-encoding. The default is UTF-8.
Overriding default method for JSON encoding. This method does two things: (a) If an object has a to_dict property, return the to_dict output. (b) If the @module and @class keys are not in the to_dict, add them to the output automatically. If the object has no to_dict property, the default Python json encoder default method is called.
Deserialize a file containing a JSON document to a Python object.
Serialize obj as a JSON formatted stream to the given filename ( pretty printing version)