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mbuild/__init__.py

@@ -1,4 +1,5 @@
 """mBuild: a hierarchical, component based molecule builder."""
+
 from mbuild.box import Box
 from mbuild.coarse_graining import coarse_grain
 from mbuild.compound import *

mbuild/box.py

@@ -1,4 +1,5 @@
 """mBuild box module."""
+
 from warnings import warn
 
 import numpy as np

mbuild/coarse_graining.py

@@ -1,4 +1,5 @@
 """Tools for coarse-grained systems."""
+
 from collections import OrderedDict
 from copy import deepcopy
 

mbuild/compound.py

@@ -1,4 +1,5 @@
 """Module for working with mBuild Compounds."""
+
 __all__ = ["clone", "Compound", "Particle"]
 
 import itertools

mbuild/conversion.py

@@ -1,4 +1,5 @@
 """Module for handling conversions in mBuild."""
+
 import os
 import sys
 from collections import defaultdict

mbuild/coordinate_transform.py

@@ -1,4 +1,5 @@
 """Coordinate transformation functions."""
+
 from warnings import simplefilter, warn
 
 simplefilter("always", DeprecationWarning)

mbuild/formats/cassandramcf.py

@@ -2,6 +2,7 @@
 
 https://cassandra-mc.readthedocs.io/en/latest/guides/input_files.html#molecular-connectivity-file
 """
+
 from __future__ import division
 
 import warnings

mbuild/formats/gsdwriter.py

@@ -2,6 +2,7 @@
 
 https://gsd.readthedocs.io/en/stable/
 """
+
 import numpy as np
 
 from mbuild.utils.geometry import coord_shift

mbuild/formats/hoomd_forcefield.py

@@ -1,4 +1,5 @@
 """HOOMD v3 forcefield format."""
+
 import itertools
 import operator
 import warnings

mbuild/formats/hoomd_simulation.py

@@ -1,4 +1,5 @@
 """HOOMD simulation format."""
+
 import itertools
 import operator
 import warnings

mbuild/formats/hoomd_snapshot.py

@@ -1,4 +1,5 @@
 """HOOMD snapshot format."""
+
 import operator
 from collections import namedtuple
 

mbuild/formats/hoomdxml.py

@@ -1,4 +1,5 @@
 """HOOMD xml format."""
+
 import operator
 from collections import namedtuple
 from math import radians

mbuild/formats/json_formats.py

@@ -1,4 +1,5 @@
 """JSON format."""
+
 import json
 from collections import OrderedDict
 

mbuild/formats/lammpsdata.py

@@ -1,4 +1,5 @@
 """LAMMPS data format."""
+
 import itertools as it
 from collections import OrderedDict
 from warnings import warn
@@ -708,9 +709,7 @@ def _get_bond_types(
             (
                 round(
                     bond.type.k
-                    * (
-                        sigma_conversion_factor**2 / epsilon_conversion_factor
-                    ),
+                    * (sigma_conversion_factor**2 / epsilon_conversion_factor),
                     bond_precision,
                 ),
                 round(bond.type.req / sigma_conversion_factor, bond_precision),

mbuild/formats/par_writer.py

@@ -1,4 +1,5 @@
 """CHARMM Par format."""
+
 import warnings
 
 __all__ = ["write_par"]

mbuild/formats/protobuf.py

@@ -3,6 +3,7 @@
 A language-agnostic data serialization format developed by Google
 https://developers.google.com/protocol-buffers
 """
+
 import ele
 import numpy as np
 from google.protobuf.text_format import Merge, PrintMessage

mbuild/formats/vasp.py

@@ -1,4 +1,5 @@
 """VASP POSCAR format."""
+
 import warnings
 from itertools import chain
 

mbuild/formats/xyz.py

@@ -1,4 +1,5 @@
 """XYZ format."""
+
 from warnings import warn
 
 import numpy as np

mbuild/lattice.py

@@ -1,4 +1,5 @@
 """mBuild lattice module for working with crystalline systems."""
+
 import itertools as it
 import pathlib
 import warnings
@@ -679,8 +680,8 @@ def populate(self, compound_dict=None, x=1, y=1, z=1):
 
         # if coordinates are below a certain threshold, set to 0
         tolerance = 1e-12
-        ret_lattice.xyz_with_ports[
-            ret_lattice.xyz_with_ports <= tolerance
-        ] = 0.0
+        ret_lattice.xyz_with_ports[ret_lattice.xyz_with_ports <= tolerance] = (
+            0.0
+        )
 
         return ret_lattice

mbuild/lib/atoms/__init__.py

@@ -1,4 +1,5 @@
 """mBuild library of atoms."""
+
 from mbuild.lib.atoms.c3 import C3
 from mbuild.lib.atoms.h import H
 from mbuild.lib.atoms.n4 import N4

mbuild/lib/atoms/c3.py

@@ -1,4 +1,5 @@
 """A tri-valent, planar carbon atom."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/atoms/h.py

@@ -1,4 +1,5 @@
 """An H atom."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/atoms/n4.py

@@ -1,4 +1,5 @@
 """mBuild atom library for tetravalent nitrogen."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/bulk_materials/__init__.py

@@ -1,2 +1,3 @@
 """mBuild bulk materials library."""
+
 from mbuild.lib.bulk_materials.amorphous_silica_bulk import AmorphousSilicaBulk

mbuild/lib/bulk_materials/amorphous_silica_bulk.py

@@ -1,4 +1,5 @@
 """A bulk structure of amorphous silica."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/__init__.py

@@ -1,4 +1,5 @@
 """mBuild library of common chemical moieties."""
+
 from mbuild.lib.moieties.ch2 import CH2
 from mbuild.lib.moieties.ch3 import CH3
 from mbuild.lib.moieties.ester import Ester

mbuild/lib/moieties/ch2.py

@@ -1,4 +1,5 @@
 """CH2 moiety."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/ch3.py

@@ -1,4 +1,5 @@
 """mBuild CH3 moiety."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/ester.py

@@ -1,4 +1,5 @@
 """Ester moiety."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/moieties/h2o.py

@@ -1,4 +1,5 @@
 """A water molecule."""
+
 import mbuild as mb
 
 

mbuild/lib/moieties/peg.py

@@ -1,4 +1,5 @@
 """mBuild polyethylene glycol (PEG) monomer moiety."""
+
 __author__ = "jonestj1"
 
 import mbuild as mb

mbuild/lib/moieties/silane.py

@@ -1,4 +1,5 @@
 """A Silane (Si(OH)2) moiety."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/molecules/__init__.py

@@ -1,4 +1,5 @@
 """Library of molecules for mBuild."""
+
 from mbuild.lib.molecules.ethane import Ethane
 from mbuild.lib.molecules.methane import Methane
 from mbuild.lib.molecules.water import (

mbuild/lib/molecules/ethane.py

@@ -1,4 +1,5 @@
 """An ethane molecule."""
+
 import mbuild as mb
 from mbuild.lib.moieties import CH3
 

mbuild/lib/molecules/methane.py

@@ -1,4 +1,5 @@
 """A methane molecule."""
+
 import mbuild as mb
 
 

mbuild/lib/molecules/water.py

@@ -1,4 +1,5 @@
 """Water molecules with geometries from different models."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/lib/recipes/__init__.py

@@ -1,4 +1,5 @@
 """Library of recipes for mBuild."""
+
 from mbuild.lib.recipes.alkane import Alkane
 from mbuild.lib.recipes.monolayer import Monolayer
 from mbuild.lib.recipes.polymer import Polymer

mbuild/lib/recipes/alkane.py

@@ -1,4 +1,5 @@
 """mBuild recipe for a generic alkane chain."""
+
 import mbuild as mb
 from mbuild.lib.moieties import CH2, CH3
 from mbuild.lib.molecules import Ethane, Methane

mbuild/lib/recipes/monolayer.py

@@ -1,4 +1,5 @@
 """mBuild monolayer recipe."""
+
 from copy import deepcopy
 from warnings import warn
 

mbuild/lib/recipes/polymer.py

@@ -1,4 +1,5 @@
 """Recipe for an mBuild polymer."""
+
 import itertools as it
 
 import numpy as np

mbuild/lib/recipes/silica_interface.py

@@ -1,4 +1,5 @@
 """mBuild recipe for a silica interface."""
+
 import math
 import random
 

mbuild/lib/recipes/tiled_compound.py

@@ -1,4 +1,5 @@
 """Module for creating TiledCompounds."""
+
 __all__ = ["TiledCompound"]
 
 import itertools as it

mbuild/lib/recipes/water_box.py

@@ -1,4 +1,5 @@
 """mBuild recipe for building a water box."""
+
 import itertools
 import math as math
 from collections.abc import Iterable

mbuild/lib/surfaces/__init__.py

@@ -1,3 +1,4 @@
 """mBuild surface library."""
+
 from mbuild.lib.surfaces.amorphous_silica_surface import AmorphousSilicaSurface
 from mbuild.lib.surfaces.betacristobalite import Betacristobalite

mbuild/lib/surfaces/amorphous_silica_surface.py

@@ -1,4 +1,5 @@
 """Amorphous silica surface."""
+
 import mbuild as mb
 
 

mbuild/lib/surfaces/betacristobalite.py

@@ -1,4 +1,5 @@
 """Beta-cristobalite surface."""
+
 import mbuild as mb
 
 

mbuild/packing.py

@@ -2,6 +2,7 @@
 
 http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml
 """
+
 import os
 import sys
 import tempfile

mbuild/pattern.py

@@ -1,4 +1,5 @@
 """mBuild pattern module."""
+
 from itertools import product
 
 import numpy as np

mbuild/port.py

@@ -1,4 +1,5 @@
 """Ports used to facilitate bond formation."""
+
 import itertools
 from warnings import warn
 

mbuild/utils/conversion.py

@@ -1,4 +1,5 @@
 """mBuild conversion utilities."""
+
 from warnings import warn
 
 import numpy as np

mbuild/utils/decorators.py

@@ -1,4 +1,5 @@
 """Some helpful decorators."""
+
 from functools import wraps
 from warnings import warn
 

mbuild/utils/geometry.py

@@ -1,4 +1,5 @@
 """mBuild utilites for geometrical operations."""
+
 import numpy as np
 
 import mbuild as mb

mbuild/utils/io.py

@@ -18,6 +18,7 @@
 # License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
 ##############################################################################
 """
+
 import importlib
 import inspect
 import os

mbuild/utils/jsutils.py

@@ -4,6 +4,7 @@
 underlying 'js' libraries by the various notebook visualization libraries used
 by mBuild.
 """
+
 from .io import import_
 
 

mbuild/utils/orderedset.py

@@ -1,4 +1,5 @@
 """Ordered set module."""
+
 from collections.abc import MutableSet
 
 

mbuild/utils/sorting.py

@@ -1,4 +1,5 @@
 """mBuild sorting utilities."""
+
 import re