from pymatgen.core.structure import Molecule
import json
import os.path as op
[docs]
class Collection:
"""Collection of molecular data.
Used for obtaining pymatgen objects from a small database file.
Example of use:
>>> from pyxtal.database.collection import Collection
>>> test=Collection('molecules')
>>> test['H2O']
Molecule Summary
Site: O (0.0000, 0.0000, 0.0000)
Site: H (0.2774, 0.8929, 0.2544)
Site: H (0.6068, -0.2383, -0.7169)
>>> list(test)
['C60', 'H2O', 'CH4', 'NH3', 'benzene', 'naphthalene', 'anthracene', 'tetracene', 'pentacene', 'coumarin', 'resorcinol', 'benzamide', 'aspirin', 'ddt', 'lindane', 'glycine', 'glucose', 'ROY']
Args:
name: the type of collection to get. Defaults to "molecules"
"""
def __init__(self, name="molecules"):
"""Create a collection lazily.
Will read data from json file when needed.
A collection can be iterated over to get the Atoms objects and indexed
with names to get individual members.
Attributes:
name: str
Name of collection.
data: object
Pymetgen molecule object
filename: str
Location of json file.
"""
self.name = name
self._data = {}
self.filename = op.join(op.dirname(__file__), name + ".json")
with open(self.filename, "r") as f:
self.content = json.load(f)
def __getitem__(self, name):
self._read(name)
if len(self._data) == 0:
names = ""
for dct in self.content:
names += dct["name"] + ", "
msg = name + " is not supported\n"
msg += "Available molecules are:\n"
msg += names
raise NameError(msg)
else:
return self._data
def __iter__(self):
for dct in self.content:
yield dct["name"]
def _read(self, name):
if self.name == "molecules":
"""
read the data by name and convert it to pymatgen format
"""
for dct in self.content:
if dct["name"].lower() == name.lower():
pos = dct["xyz"]
symbols = dct["elements"]
self._data = Molecule(symbols, pos)
elif self.name == "clusters":
for dct in self.content:
if dct["name"] == int(name):
self._data = dct
[docs]
def show_names(self):
names = []
for dct in self.content:
names.append(dct["name"])
print(names)