diff --git a/poetry.lock b/poetry.lock
index beb12597e8dee2dd14b720cd5350b784d486e5e0..dffbd83e785a00dfc3b603e2fa77c5127fdd3ad1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -64,6 +64,30 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[package.dependencies]
pytz = ">=2015.7"
+[[package]]
+name = "black"
+version = "22.1.0"
+description = "The uncompromising code formatter."
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
+[package.dependencies]
+click = ">=8.0.0"
+dataclasses = {version = ">=0.6", markers = "python_version < \"3.7\""}
+mypy-extensions = ">=0.4.3"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = ">=1.1.0"
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""}
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
[[package]]
name = "certifi"
version = "2021.10.8"
@@ -83,6 +107,18 @@ python-versions = ">=3.5.0"
[package.extras]
unicode_backport = ["unicodedata2"]
+[[package]]
+name = "click"
+version = "8.0.4"
+description = "Composable command line interface toolkit"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+
[[package]]
name = "colorama"
version = "0.4.4"
@@ -118,7 +154,7 @@ name = "cowsay"
version = "4.0"
description = "The famous cowsay for GNU/Linux is now available for python"
category = "main"
-optional = false
+optional = true
python-versions = "*"
[[package]]
@@ -365,6 +401,14 @@ numpy = ">=1.6"
pyparsing = "*"
scipy = "*"
+[[package]]
+name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "dev"
+optional = false
+python-versions = "*"
+
[[package]]
name = "myst-parser"
version = "0.13.7"
@@ -406,6 +450,14 @@ python-versions = ">=3.6"
[package.dependencies]
pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+[[package]]
+name = "pathspec"
+version = "0.9.0"
+description = "Utility library for gitignore style pattern matching of file paths."
+category = "dev"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
[[package]]
name = "pep8-naming"
version = "0.10.0"
@@ -924,6 +976,14 @@ category = "dev"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+[[package]]
+name = "tomli"
+version = "1.2.3"
+description = "A lil' TOML parser"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
[[package]]
name = "tox"
version = "3.24.5"
@@ -1023,14 +1083,6 @@ category = "main"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-[[package]]
-name = "yapf"
-version = "0.31.0"
-description = "A formatter for Python code."
-category = "dev"
-optional = false
-python-versions = "*"
-
[[package]]
name = "zipp"
version = "3.6.0"
@@ -1049,8 +1101,8 @@ docs = ["Sphinx", "sphinx-autoapi", "sphinx-rtd-theme", "myst-parser"]
[metadata]
lock-version = "1.1"
-python-versions = "^3.6"
-content-hash = "5f56853204a0856745eb9a253e385e0e78aad5aae07beeb448223306065f6b15"
+python-versions = "^3.6.2"
+content-hash = "bcf4d72f6cd263cc2d0668b472751140f6934655d2a34477d026089e6eff50bf"
[metadata.files]
alabaster = [
@@ -1077,6 +1129,31 @@ babel = [
{file = "Babel-2.9.1-py2.py3-none-any.whl", hash = "sha256:ab49e12b91d937cd11f0b67cb259a57ab4ad2b59ac7a3b41d6c06c0ac5b0def9"},
{file = "Babel-2.9.1.tar.gz", hash = "sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0"},
]
+black = [
+ {file = "black-22.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:1297c63b9e1b96a3d0da2d85d11cd9bf8664251fd69ddac068b98dc4f34f73b6"},
+ {file = "black-22.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2ff96450d3ad9ea499fc4c60e425a1439c2120cbbc1ab959ff20f7c76ec7e866"},
+ {file = "black-22.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0e21e1f1efa65a50e3960edd068b6ae6d64ad6235bd8bfea116a03b21836af71"},
+ {file = "black-22.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e2f69158a7d120fd641d1fa9a921d898e20d52e44a74a6fbbcc570a62a6bc8ab"},
+ {file = "black-22.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:228b5ae2c8e3d6227e4bde5920d2fc66cc3400fde7bcc74f480cb07ef0b570d5"},
+ {file = "black-22.1.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b1a5ed73ab4c482208d20434f700d514f66ffe2840f63a6252ecc43a9bc77e8a"},
+ {file = "black-22.1.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:35944b7100af4a985abfcaa860b06af15590deb1f392f06c8683b4381e8eeaf0"},
+ {file = "black-22.1.0-cp36-cp36m-win_amd64.whl", hash = "sha256:7835fee5238fc0a0baf6c9268fb816b5f5cd9b8793423a75e8cd663c48d073ba"},
+ {file = "black-22.1.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:dae63f2dbf82882fa3b2a3c49c32bffe144970a573cd68d247af6560fc493ae1"},
+ {file = "black-22.1.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5fa1db02410b1924b6749c245ab38d30621564e658297484952f3d8a39fce7e8"},
+ {file = "black-22.1.0-cp37-cp37m-win_amd64.whl", hash = "sha256:c8226f50b8c34a14608b848dc23a46e5d08397d009446353dad45e04af0c8e28"},
+ {file = "black-22.1.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:2d6f331c02f0f40aa51a22e479c8209d37fcd520c77721c034517d44eecf5912"},
+ {file = "black-22.1.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:742ce9af3086e5bd07e58c8feb09dbb2b047b7f566eb5f5bc63fd455814979f3"},
+ {file = "black-22.1.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:fdb8754b453fb15fad3f72cd9cad3e16776f0964d67cf30ebcbf10327a3777a3"},
+ {file = "black-22.1.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f5660feab44c2e3cb24b2419b998846cbb01c23c7fe645fee45087efa3da2d61"},
+ {file = "black-22.1.0-cp38-cp38-win_amd64.whl", hash = "sha256:6f2f01381f91c1efb1451998bd65a129b3ed6f64f79663a55fe0e9b74a5f81fd"},
+ {file = "black-22.1.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:efbadd9b52c060a8fc3b9658744091cb33c31f830b3f074422ed27bad2b18e8f"},
+ {file = "black-22.1.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:8871fcb4b447206904932b54b567923e5be802b9b19b744fdff092bd2f3118d0"},
+ {file = "black-22.1.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:ccad888050f5393f0d6029deea2a33e5ae371fd182a697313bdbd835d3edaf9c"},
+ {file = "black-22.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:07e5c049442d7ca1a2fc273c79d1aecbbf1bc858f62e8184abe1ad175c4f7cc2"},
+ {file = "black-22.1.0-cp39-cp39-win_amd64.whl", hash = "sha256:373922fc66676133ddc3e754e4509196a8c392fec3f5ca4486673e685a421321"},
+ {file = "black-22.1.0-py3-none-any.whl", hash = "sha256:3524739d76b6b3ed1132422bf9d82123cd1705086723bc3e235ca39fd21c667d"},
+ {file = "black-22.1.0.tar.gz", hash = "sha256:a7c0192d35635f6fc1174be575cb7915e92e5dd629ee79fdaf0dcfa41a80afb5"},
+]
certifi = [
{file = "certifi-2021.10.8-py2.py3-none-any.whl", hash = "sha256:d62a0163eb4c2344ac042ab2bdf75399a71a2d8c7d47eac2e2ee91b9d6339569"},
{file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
@@ -1085,6 +1162,10 @@ charset-normalizer = [
{file = "charset-normalizer-2.0.12.tar.gz", hash = "sha256:2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597"},
{file = "charset_normalizer-2.0.12-py3-none-any.whl", hash = "sha256:6881edbebdb17b39b4eaaa821b438bf6eddffb4468cf344f09f89def34a8b1df"},
]
+click = [
+ {file = "click-8.0.4-py3-none-any.whl", hash = "sha256:6a7a62563bbfabfda3a38f3023a1db4a35978c0abd76f6c9605ecd6554d6d9b1"},
+ {file = "click-8.0.4.tar.gz", hash = "sha256:8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb"},
+]
colorama = [
{file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
{file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
@@ -1319,6 +1400,10 @@ mdplus = [
mdtraj = [
{file = "mdtraj-1.9.7.tar.gz", hash = "sha256:8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757"},
]
+mypy-extensions = [
+ {file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
+ {file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
+]
myst-parser = [
{file = "myst-parser-0.13.7.tar.gz", hash = "sha256:e4bc99e43e19f70d22e528de8e7cce59f7e8e7c4c34dcba203de92de7a7c7c85"},
{file = "myst_parser-0.13.7-py3-none-any.whl", hash = "sha256:260355b4da8e8865fe080b0638d7f1ab1791dc4bed02a7a48630b6bad4249219"},
@@ -1357,6 +1442,10 @@ packaging = [
{file = "packaging-21.3-py3-none-any.whl", hash = "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"},
{file = "packaging-21.3.tar.gz", hash = "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"},
]
+pathspec = [
+ {file = "pathspec-0.9.0-py2.py3-none-any.whl", hash = "sha256:7d15c4ddb0b5c802d161efc417ec1a2558ea2653c2e8ad9c19098201dc1c993a"},
+ {file = "pathspec-0.9.0.tar.gz", hash = "sha256:e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1"},
+]
pep8-naming = [
{file = "pep8-naming-0.10.0.tar.gz", hash = "sha256:f3b4a5f9dd72b991bf7d8e2a341d2e1aa3a884a769b5aaac4f56825c1763bf3a"},
{file = "pep8_naming-0.10.0-py2.py3-none-any.whl", hash = "sha256:5d9f1056cb9427ce344e98d1a7f5665710e2f20f748438e308995852cfa24164"},
@@ -1594,6 +1683,10 @@ toml = [
{file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
{file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
]
+tomli = [
+ {file = "tomli-1.2.3-py3-none-any.whl", hash = "sha256:e3069e4be3ead9668e21cb9b074cd948f7b3113fd9c8bba083f48247aab8b11c"},
+ {file = "tomli-1.2.3.tar.gz", hash = "sha256:05b6166bff487dc068d322585c7ea4ef78deed501cc124060e0f238e89a9231f"},
+]
tox = [
{file = "tox-3.24.5-py2.py3-none-any.whl", hash = "sha256:be3362472a33094bce26727f5f771ca0facf6dafa217f65875314e9a6600c95c"},
{file = "tox-3.24.5.tar.gz", hash = "sha256:67e0e32c90e278251fea45b696d0fef3879089ccbe979b0c556d35d5a70e2993"},
@@ -1698,10 +1791,6 @@ wrapt = [
{file = "wrapt-1.13.3-cp39-cp39-win_amd64.whl", hash = "sha256:81bd7c90d28a4b2e1df135bfbd7c23aee3050078ca6441bead44c42483f9ebfb"},
{file = "wrapt-1.13.3.tar.gz", hash = "sha256:1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185"},
]
-yapf = [
- {file = "yapf-0.31.0-py2.py3-none-any.whl", hash = "sha256:e3a234ba8455fe201eaa649cdac872d590089a18b661e39bbac7020978dd9c2e"},
- {file = "yapf-0.31.0.tar.gz", hash = "sha256:408fb9a2b254c302f49db83c59f9aa0b4b0fd0ec25be3a5c51181327922ff63d"},
-]
zipp = [
{file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
{file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
diff --git a/pycgtool/__main__.py b/pycgtool/__main__.py
index ae46fed1a6b14793baa5af90de659ca2d987e25d..fde95790a7a808910b0dad14f58a698bbf54b458 100755
--- a/pycgtool/__main__.py
+++ b/pycgtool/__main__.py
@@ -34,7 +34,8 @@ class PyCGTOOL:
topology_file=self.config.topology,
trajectory_file=self.config.trajectory, # May be None
frame_start=self.config.begin,
- frame_end=self.config.end)
+ frame_end=self.config.end,
+ )
self.mapping = None
self.out_frame = self.in_frame
@@ -43,7 +44,9 @@ class PyCGTOOL:
if self.out_frame.natoms == 0:
# The following steps won't work with frames containing no atoms
- logger.warning('Mapped trajectory contains no atoms - check your mapping file is correct!')
+ logger.warning(
+ "Mapped trajectory contains no atoms - check your mapping file is correct!"
+ )
return
self.bondset = None
@@ -52,7 +55,7 @@ class PyCGTOOL:
self.measure_bonds()
if self.config.output_xtc:
- self.out_frame.save(self.get_output_filepath('xtc'))
+ self.out_frame.save(self.get_output_filepath("xtc"))
def get_output_filepath(self, ext: PathLike) -> pathlib.Path:
"""Get file path for an output file by extension.
@@ -61,22 +64,22 @@ class PyCGTOOL:
"""
out_dir = pathlib.Path(self.config.out_dir)
out_dir.mkdir(parents=True, exist_ok=True)
- return out_dir.joinpath(self.config.output_name + '.' + ext)
+ return out_dir.joinpath(self.config.output_name + "." + ext)
def apply_mapping(self, in_frame: Frame) -> typing.Tuple[Mapping, Frame]:
"""Map input frame to output using requested mapping file."""
- mapping = Mapping(self.config.mapping,
- self.config,
- itp_filename=self.config.itp)
+ mapping = Mapping(
+ self.config.mapping, self.config, itp_filename=self.config.itp
+ )
out_frame = mapping.apply(in_frame)
- out_frame.save(self.get_output_filepath('gro'), frame_number=0)
+ out_frame.save(self.get_output_filepath("gro"), frame_number=0)
if self.config.backmapper_resname and self.out_frame.n_frames > 1:
try:
self.train_backmapper(self.config.resname)
except ImportError:
- logger.error('MDPlus must be installed to perform backmapping')
+ logger.error("MDPlus must be installed to perform backmapping")
return mapping, out_frame
@@ -87,46 +90,47 @@ class PyCGTOOL:
if self.mapping is not None and self.out_frame.n_frames > 1:
# Only perform Boltzmann Inversion if we have a mapping and a trajectory.
# Otherwise we get infinite force constants.
- logger.info('Starting Boltzmann Inversion')
+ logger.info("Starting Boltzmann Inversion")
self.bondset.boltzmann_invert()
- logger.info('Finished Boltzmann Inversion')
+ logger.info("Finished Boltzmann Inversion")
if self.config.output_forcefield:
logger.info("Writing GROMACS forcefield directory")
out_dir = pathlib.Path(self.config.out_dir)
- forcefield = ForceField(self.config.output_name,
- dir_path=out_dir)
- forcefield.write(self.config.output_name, self.mapping,
- self.bondset)
+ forcefield = ForceField(self.config.output_name, dir_path=out_dir)
+ forcefield.write(self.config.output_name, self.mapping, self.bondset)
logger.info("Finished writing GROMACS forcefield directory")
else:
- self.bondset.write_itp(self.get_output_filepath('itp'),
- mapping=self.mapping)
+ self.bondset.write_itp(
+ self.get_output_filepath("itp"), mapping=self.mapping
+ )
if self.config.dump_measurements:
- logger.info('Writing bond measurements to file')
- self.bondset.dump_values(self.config.dump_n_values,
- self.config.out_dir)
- logger.info('Finished writing bond measurements to file')
+ logger.info("Writing bond measurements to file")
+ self.bondset.dump_values(self.config.dump_n_values, self.config.out_dir)
+ logger.info("Finished writing bond measurements to file")
def train_backmapper(self, resname: str):
from mdplus.multiscale import GLIMPS
- sel = f'resname {resname}'
+
+ sel = f"resname {resname}"
aa_subset_traj = self.in_frame._trajectory.atom_slice(
- self.in_frame._trajectory.topology.select(sel))
+ self.in_frame._trajectory.topology.select(sel)
+ )
cg_subset_traj = self.out_frame._trajectory.atom_slice(
- self.out_frame._trajectory.topology.select(sel))
+ self.out_frame._trajectory.topology.select(sel)
+ )
- logger.info('Training backmapper')
+ logger.info("Training backmapper")
# Param x_valence is approximate number of bonds per CG bead
# Values greater than 2 fail for small molecules e.g. sugar test case
backmapper = GLIMPS(x_valence=2)
backmapper.fit(cg_subset_traj.xyz, aa_subset_traj.xyz)
- logger.info('Finished training backmapper')
+ logger.info("Finished training backmapper")
- backmapper.save(self.get_output_filepath('backmapper.pkl'))
+ backmapper.save(self.get_output_filepath("backmapper.pkl"))
class BooleanAction(argparse.Action):
@@ -134,15 +138,16 @@ class BooleanAction(argparse.Action):
Based on https://thisdataguy.com/2017/07/03/no-options-with-argparse-and-python/
"""
+
def __init__(self, option_strings, dest, nargs=None, **kwargs):
super().__init__(option_strings, dest, nargs=0, **kwargs)
def __call__(self, parser, namespace, values, option_string=None):
- setattr(namespace, self.dest, not option_string.startswith('--no-'))
+ setattr(namespace, self.dest, not option_string.startswith("--no-"))
def parse_arguments(arg_list):
- # yapf: disable
+ # fmt: off
parser = argparse.ArgumentParser(
prog='pycgtool',
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -236,7 +241,7 @@ def parse_arguments(arg_list):
help=argparse.SUPPRESS)
secret_options.add_argument('--cow', default=False, action='store_true',
help=argparse.SUPPRESS)
- # yapf: enable
+ # fmt: on
args = parser.parse_args(arg_list)
@@ -257,15 +262,15 @@ def validate_arguments(args):
if not args.dump_measurements:
args.dump_measurements = bool(args.bondset) and not bool(args.mapping)
logger.info(
- 'Argument --dump-measurements has been set because you have provided a bondset but no mapping'
+ "Argument --dump-measurements has been set because you have provided a bondset but no mapping"
)
if not args.mapping and not args.bondset:
- raise ArgumentValidationError('One or both of -m and -b is required')
+ raise ArgumentValidationError("One or both of -m and -b is required")
if args.backmapper_resname:
logger.warning(
- 'Backmapping is an experimental feature and has not yet been fully validated'
+ "Backmapping is an experimental feature and has not yet been fully validated"
)
return args
@@ -279,10 +284,12 @@ def main():
logging.basicConfig(level=args.log_level)
else:
- logging.basicConfig(level=args.log_level,
- format='%(message)s',
- datefmt='[%X]',
- handlers=[RichHandler(rich_tracebacks=True)])
+ logging.basicConfig(
+ level=args.log_level,
+ format="%(message)s",
+ datefmt="[%X]",
+ handlers=[RichHandler(rich_tracebacks=True)],
+ )
banner = r"""
_____ _____ _____ _______ ____ ____ _
@@ -299,37 +306,39 @@ def main():
if args.cow:
try:
import cowsay
- banner = cowsay.cow('PyCGTOOL')
+
+ banner = cowsay.cow("PyCGTOOL")
except ImportError:
pass
else:
- logger.info('[bold blue]%s[/]',
- textwrap.dedent(banner),
- extra={'markup': True})
+ logger.info(
+ "[bold blue]%s[/]", textwrap.dedent(banner), extra={"markup": True}
+ )
- logger.info(30 * '-')
- logger.info('Topology:\t%s', args.topology)
- logger.info('Trajectory:\t%s', args.trajectory)
- logger.info('Mapping:\t%s', args.mapping)
- logger.info('Bondset:\t%s', args.bondset)
- logger.info(30 * '-')
+ logger.info(30 * "-")
+ logger.info("Topology:\t%s", args.topology)
+ logger.info("Trajectory:\t%s", args.trajectory)
+ logger.info("Mapping:\t%s", args.mapping)
+ logger.info("Bondset:\t%s", args.bondset)
+ logger.info(30 * "-")
try:
if args.profile:
with cProfile.Profile() as profiler:
pycgtool = PyCGTOOL(args)
- profiler.dump_stats('gprof.out')
+ profiler.dump_stats("gprof.out")
else:
pycgtool = PyCGTOOL(args)
elapsed_time = time.time() - start_time
- logger.info('Processed %d frames in %.2f s',
- pycgtool.out_frame.n_frames, elapsed_time)
- logger.info('Finished processing - goodbye!')
+ logger.info(
+ "Processed %d frames in %.2f s", pycgtool.out_frame.n_frames, elapsed_time
+ )
+ logger.info("Finished processing - goodbye!")
except Exception as exc:
logger.exception(exc)
diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py
index 4910b7d90291d431799c4a18b2134e7a5ad89b21..3a4dca5a41f8236b10ba3ae387567c5c85bb1efa 100644
--- a/pycgtool/bondset.py
+++ b/pycgtool/bondset.py
@@ -34,10 +34,13 @@ class Bond:
Bond lengths, angles and dihedrals are all equivalent, distinguished by the number of atoms present.
"""
- def __init__(self,
- atoms: typing.Iterable[str],
- atom_numbers: typing.Optional[typing.Iterable[int]] = None,
- func_form=None):
+
+ def __init__(
+ self,
+ atoms: typing.Iterable[str],
+ atom_numbers: typing.Optional[typing.Iterable[int]] = None,
+ func_form=None,
+ ):
"""Create a single bond definition.
:param List[str] atoms: List of atom names defining the bond
@@ -62,8 +65,9 @@ class Bond:
:param temp: Temperature at which the simulation was performed
"""
if len(self.values) == 0:
- raise ValueError("No bonds were measured between beads {0}".format(
- self.atoms))
+ raise ValueError(
+ "No bonds were measured between beads {0}".format(self.atoms)
+ )
values = self.values
if not isinstance(self.values, np.ndarray):
@@ -77,7 +81,7 @@ class Bond:
if len(self.atoms) == 4:
two_pi = 2 * np.pi
self.eqm -= np.pi
- self.eqm = (((self.eqm + np.pi) % two_pi) - np.pi)
+ self.eqm = ((self.eqm + np.pi) % two_pi) - np.pi
try:
self.fconst = self._func_form.fconst(values, temp)
@@ -89,7 +93,8 @@ class Bond:
def __repr__(self) -> str:
try:
return "<Bond containing atoms {0} with r_0 {1:.3f} and force constant {2:.3e}>".format(
- ", ".join(self.atoms), self.eqm, self.fconst)
+ ", ".join(self.atoms), self.eqm, self.fconst
+ )
except (AttributeError, TypeError):
return "<Bond containing atoms {0}>".format(", ".join(self.atoms))
@@ -99,6 +104,7 @@ class BondSet:
BondSet contains a dictionary of lists of Bonds. Each list corresponds to a single molecule.
"""
+
def _get_default_func_forms(self, options):
try:
@@ -109,33 +115,32 @@ class BondSet:
if default_fc:
default_forms = [
- 'MartiniDefaultLength', 'MartiniDefaultAngle',
- 'MartiniDefaultDihedral'
+ "MartiniDefaultLength",
+ "MartiniDefaultAngle",
+ "MartiniDefaultDihedral",
]
else:
- default_forms = ['Harmonic', 'CosHarmonic', 'Harmonic']
+ default_forms = ["Harmonic", "CosHarmonic", "Harmonic"]
functional_forms_map = get_functional_forms()
functional_forms = [None, None]
functional_forms.extend(
- [functional_forms_map[ff].value for ff in default_forms])
+ [functional_forms_map[ff].value for ff in default_forms]
+ )
try:
- functional_forms[2] = functional_forms_map[
- options.length_form].value
+ functional_forms[2] = functional_forms_map[options.length_form].value
except AttributeError:
pass
try:
- functional_forms[3] = functional_forms_map[
- options.angle_form].value
+ functional_forms[3] = functional_forms_map[options.angle_form].value
except AttributeError:
pass
try:
- functional_forms[4] = functional_forms_map[
- options.dihedral_form].value
+ functional_forms[4] = functional_forms_map[options.dihedral_form].value
except AttributeError:
pass
@@ -154,7 +159,7 @@ class BondSet:
try:
self._temperature = options.temperature
except AttributeError:
- self._temperature = 310.
+ self._temperature = 310.0
self._functional_forms = self._get_default_func_forms(options)
@@ -166,19 +171,26 @@ class BondSet:
angles_defined = False
for atomlist in mol_section:
is_angle_or_dihedral = len(atomlist) > 2
- mean_function = circular_mean if is_angle_or_dihedral else np.nanmean
- variance_function = circular_variance if is_angle_or_dihedral else np.nanvar
+ mean_function = (
+ circular_mean if is_angle_or_dihedral else np.nanmean
+ )
+ variance_function = (
+ circular_variance if is_angle_or_dihedral else np.nanvar
+ )
# Construct instance of Boltzmann Inversion function and
# inject dependencies for mean and variance functions
# TODO: Should we allow overriding functional forms per bond?
func_form = self._functional_forms[len(atomlist)](
- mean_function, variance_function)
+ mean_function, variance_function
+ )
if {x for x in atomlist if atomlist.count(x) > 1}:
raise ValueError(
- "Defined bond '{0}' contains duplicate atoms".
- format(atomlist))
+ "Defined bond '{0}' contains duplicate atoms".format(
+ atomlist
+ )
+ )
mol_bonds.append(Bond(atoms=atomlist, func_form=func_form))
if len(atomlist) > 2:
@@ -190,16 +202,24 @@ class BondSet:
if options.generate_angles:
for atomlist in angles:
mol_bonds.append(
- Bond(atoms=atomlist,
- func_form=self._functional_forms[3](
- circular_mean, circular_variance)))
+ Bond(
+ atoms=atomlist,
+ func_form=self._functional_forms[3](
+ circular_mean, circular_variance
+ ),
+ )
+ )
if options.generate_dihedrals:
for atomlist in dihedrals:
mol_bonds.append(
- Bond(atoms=atomlist,
- func_form=self._functional_forms[4](
- circular_mean, circular_variance)))
+ Bond(
+ atoms=atomlist,
+ func_form=self._functional_forms[4](
+ circular_mean, circular_variance
+ ),
+ )
+ )
@staticmethod
def _create_angles(mol_bonds):
@@ -217,7 +237,7 @@ class BondSet:
self,
mol: str,
natoms: int,
- select: typing.Callable[[Bond], bool] = lambda x: True
+ select: typing.Callable[[Bond], bool] = lambda x: True,
) -> typing.List[Bond]:
"""Return list of bonds from molecule containing natoms atoms.
@@ -230,7 +250,8 @@ class BondSet:
return [bond for bond in self._molecules[mol] if select(bond)]
return [
- bond for bond in self._molecules[mol]
+ bond
+ for bond in self._molecules[mol]
if len(bond.atoms) == natoms and select(bond)
]
@@ -242,13 +263,12 @@ class BondSet:
:return: List of bonds
"""
if with_constr:
- return [
- bond for bond in self._molecules[mol] if len(bond.atoms) == 2
- ]
+ return [bond for bond in self._molecules[mol] if len(bond.atoms) == 2]
return [
- bond for bond in self._molecules[mol] if len(bond.atoms) == 2
- and bond.fconst < self._fconst_constr_threshold
+ bond
+ for bond in self._molecules[mol]
+ if len(bond.atoms) == 2 and bond.fconst < self._fconst_constr_threshold
]
def get_bond_length_constraints(self, mol):
@@ -258,8 +278,9 @@ class BondSet:
:return: List of bonds
"""
return [
- bond for bond in self._molecules[mol] if len(bond.atoms) == 2
- and bond.fconst >= self._fconst_constr_threshold
+ bond
+ for bond in self._molecules[mol]
+ if len(bond.atoms) == 2 and bond.fconst >= self._fconst_constr_threshold
]
def get_bond_angles(self, mol, exclude_triangle=True):
@@ -269,9 +290,7 @@ class BondSet:
:param exclude_triangle: Exclude angles that are part of a triangle?
:return: List of bonds
"""
- angles = [
- bond for bond in self._molecules[mol] if len(bond.atoms) == 3
- ]
+ angles = [bond for bond in self._molecules[mol] if len(bond.atoms) == 3]
if exclude_triangle:
edges = [
@@ -282,15 +301,14 @@ class BondSet:
def is_triangle(atoms):
triangle_edges = 0
for j in range(3):
- if (atoms[j - 1],
- atoms[j]) in edges or (atoms[j],
- atoms[j - 1]) in edges:
+ if (atoms[j - 1], atoms[j]) in edges or (
+ atoms[j],
+ atoms[j - 1],
+ ) in edges:
triangle_edges += 1
return triangle_edges >= 3
- angles = [
- angle for angle in angles if not is_triangle(angle.atoms)
- ]
+ angles = [angle for angle in angles if not is_triangle(angle.atoms)]
return angles
@@ -332,12 +350,13 @@ class BondSet:
]
except ValueError as e:
missing = [
- atom for atom in bond.atoms
- if atom.lstrip("+-") not in index
+ atom for atom in bond.atoms if atom.lstrip("+-") not in index
]
e.args = (
"Bead(s) {0} do(es) not exist in residue {1}".format(
- missing, mol), )
+ missing, mol
+ ),
+ )
raise
def write_itp(self, filename, mapping):
@@ -352,22 +371,19 @@ class BondSet:
def itp_text(self, mapping):
atom_template = {
"nomass": "{0:4d} {1:4s} {2:4d} {3:4s} {4:4s} {5:4d} {6:8.3f}",
- "mass":
- "{0:4d} {1:4s} {2:4d} {3:4s} {4:4s} {5:4d} {6:8.3f} {7:8.3f}"
+ "mass": "{0:4d} {1:4s} {2:4d} {3:4s} {4:4s} {5:4d} {6:8.3f} {7:8.3f}",
}
- def write_bond_angle_dih(bonds,
- section_header,
- print_fconst=True,
- multiplicity=None,
- rad2deg=False):
+ def write_bond_angle_dih(
+ bonds, section_header, print_fconst=True, multiplicity=None, rad2deg=False
+ ):
ret_lines = []
if bonds:
ret_lines.append("\n[ {0:s} ]".format(section_header))
for bond in bonds:
- line = " ".join([
- "{0:4d}".format(atnum + 1) for atnum in bond.atom_numbers
- ])
+ line = " ".join(
+ ["{0:4d}".format(atnum + 1) for atnum in bond.atom_numbers]
+ )
eqm = math.degrees(bond.eqm) if rad2deg else bond.eqm
line += " {0:4d} {1:12.5f}".format(bond.gromacs_type_id, eqm)
if print_fconst:
@@ -384,20 +400,29 @@ class BondSet:
"; James Graham <J.A.Graham@soton.ac.uk> 2016",
"; University of Southampton",
"; https://github.com/jag1g13/pycgtool",
- ";"
- ] # yapf: disable
+ ";",
+ ] # fmt: skip
# Print molecule
for mol in self._molecules:
if mol not in mapping:
- logger.warning((
- "Molecule '%s' present in bonding file, but not in mapping. "
- "Parameters have not been calculated."), mol)
+ logger.warning(
+ (
+ "Molecule '%s' present in bonding file, but not in mapping. "
+ "Parameters have not been calculated."
+ ),
+ mol,
+ )
continue
if not all(bond.fconst is not None for bond in self._molecules[mol]):
- logger.warning(("Molecule '%s' has no measured bond values. "
- "Parameters have not been calculated."), mol)
+ logger.warning(
+ (
+ "Molecule '%s' has no measured bond values. "
+ "Parameters have not been calculated."
+ ),
+ mol,
+ )
continue
ret_lines.append("\n[ moleculetype ]")
@@ -408,48 +433,63 @@ class BondSet:
for i, bead in enumerate(mapping[mol], start=1):
# atnum type resnum resname atname c-group charge (mass)
if isinstance(bead, VirtualMap):
- ret_lines.append(atom_template["mass"].format(
- i, bead.type, 1, mol, bead.name, i, bead.charge,
- bead.mass))
+ ret_lines.append(
+ atom_template["mass"].format(
+ i, bead.type, 1, mol, bead.name, i, bead.charge, bead.mass
+ )
+ )
else:
- ret_lines.append(atom_template["nomass"].format(
- i, bead.type, 1, mol, bead.name, i, bead.charge))
+ ret_lines.append(
+ atom_template["nomass"].format(
+ i, bead.type, 1, mol, bead.name, i, bead.charge
+ )
+ )
virtual_beads = self.get_virtual_beads(mapping[mol])
if len(virtual_beads) != 0:
ret_lines.append("\n[ virtual_sitesn ]")
- excl_lines = ["\n[ exclusions ]"
- ] # Exclusions section for virtual sites
+ excl_lines = [
+ "\n[ exclusions ]"
+ ] # Exclusions section for virtual sites
for vbead in virtual_beads:
- cg_ids = sorted([
- bead.num + 1 for bead in mapping[mol]
- if bead.name in vbead.atoms
- ])
+ cg_ids = sorted(
+ [
+ bead.num + 1
+ for bead in mapping[mol]
+ if bead.name in vbead.atoms
+ ]
+ )
cg_ids_string = " ".join(map(str, cg_ids))
- ret_lines.append("{0:^6d} {1:^6d} {2}".format(
- vbead.num + 1, vbead.gromacs_type_id, cg_ids_string))
- vsite_exclusions = "{} ".format(vbead.num +
- 1) + cg_ids_string
+ ret_lines.append(
+ "{0:^6d} {1:^6d} {2}".format(
+ vbead.num + 1, vbead.gromacs_type_id, cg_ids_string
+ )
+ )
+ vsite_exclusions = "{} ".format(vbead.num + 1) + cg_ids_string
excl_lines.append(vsite_exclusions)
ret_lines.extend(excl_lines)
+ ret_lines.extend(write_bond_angle_dih(self.get_bond_lengths(mol), "bonds"))
ret_lines.extend(
- write_bond_angle_dih(self.get_bond_lengths(mol), "bonds"))
+ write_bond_angle_dih(self.get_bond_angles(mol), "angles", rad2deg=True)
+ )
ret_lines.extend(
- write_bond_angle_dih(self.get_bond_angles(mol),
- "angles",
- rad2deg=True))
+ write_bond_angle_dih(
+ self.get_bond_dihedrals(mol),
+ "dihedrals",
+ multiplicity=1,
+ rad2deg=True,
+ )
+ )
ret_lines.extend(
- write_bond_angle_dih(self.get_bond_dihedrals(mol),
- "dihedrals",
- multiplicity=1,
- rad2deg=True))
- ret_lines.extend(
- write_bond_angle_dih(self.get_bond_length_constraints(mol),
- "constraints",
- print_fconst=False))
+ write_bond_angle_dih(
+ self.get_bond_length_constraints(mol),
+ "constraints",
+ print_fconst=False,
+ )
+ )
return ret_lines
@@ -461,25 +501,27 @@ class BondSet:
calc = {
2: mdtraj.compute_distances,
3: mdtraj.compute_angles,
- 4: mdtraj.compute_dihedrals
+ 4: mdtraj.compute_dihedrals,
}
for mol_name, mol_bonds in self._molecules.items():
for bond in mol_bonds:
bond_indices = []
- for prev_residue, residue, next_residue in sliding(
- frame.residues):
+ for prev_residue, residue, next_residue in sliding(frame.residues):
adj_res = {"-": prev_residue, "+": next_residue}
# Need access to adjacent residues, so can't just iterate over these directly
if residue.name == mol_name:
try:
- bond_indices.append([
- adj_res.get(atom_name[0], residue).atom(
- atom_name.lstrip('-+')).index
- for atom_name in bond.atoms
- ])
+ bond_indices.append(
+ [
+ adj_res.get(atom_name[0], residue)
+ .atom(atom_name.lstrip("-+"))
+ .index
+ for atom_name in bond.atoms
+ ]
+ )
except AttributeError:
# AttributeError is raised when residues on end of chain calc bond to next
@@ -497,9 +539,9 @@ class BondSet:
pass
@staticmethod
- def _get_lines_for_bond_dump(bonds,
- target_number: typing.Optional[int] = None,
- rad2deg: bool = False) -> typing.List[str]:
+ def _get_lines_for_bond_dump(
+ bonds, target_number: typing.Optional[int] = None, rad2deg: bool = False
+ ) -> typing.List[str]:
"""Return a dump of bond measurements as a list of lines of text.
:param bonds: Iterable of bonds
@@ -508,49 +550,53 @@ class BondSet:
:return List[str]: Lines of bond measurements dump
"""
ret_lines = []
- for row in transpose_and_sample((bond.values for bond in bonds),
- n=target_number):
+ for row in transpose_and_sample(
+ (bond.values for bond in bonds), n=target_number
+ ):
if rad2deg:
row = [math.degrees(val) for val in row]
- ret_lines.append((len(row) * '{:12.5f}').format(*row))
+ ret_lines.append((len(row) * "{:12.5f}").format(*row))
return ret_lines
- def dump_values(self, target_number: int = 10000,
- output_dir: typing.Optional[typing.Union[pathlib.Path, str]] = None) -> None:
+ def dump_values(
+ self,
+ target_number: int = 10000,
+ output_dir: typing.Optional[typing.Union[pathlib.Path, str]] = None,
+ ) -> None:
"""Output measured bond values to files for length, angles and dihedrals.
:param int target_number: Approx number of sample measurements to output. If None, all samples will be output.
:param output_dir: Directory to write output files to.
"""
if output_dir is None:
- output_dir = '.'
+ output_dir = "."
# Cast to Path type
output_dir = pathlib.Path(output_dir)
for mol in self._molecules:
- if mol == 'SOL':
+ if mol == "SOL":
continue
bonds = self.get_bond_lengths(mol, with_constr=True)
if bonds:
lines = BondSet._get_lines_for_bond_dump(bonds, target_number)
- file_write_lines(output_dir.joinpath(f'{mol}_length.dat'), lines)
+ file_write_lines(output_dir.joinpath(f"{mol}_length.dat"), lines)
bonds = self.get_bond_angles(mol)
if bonds:
- lines = BondSet._get_lines_for_bond_dump(bonds,
- target_number,
- rad2deg=True)
- file_write_lines(output_dir.joinpath(f'{mol}_angle.dat'), lines)
+ lines = BondSet._get_lines_for_bond_dump(
+ bonds, target_number, rad2deg=True
+ )
+ file_write_lines(output_dir.joinpath(f"{mol}_angle.dat"), lines)
bonds = self.get_bond_dihedrals(mol)
if bonds:
- lines = BondSet._get_lines_for_bond_dump(bonds,
- target_number,
- rad2deg=True)
- file_write_lines(output_dir.joinpath(f'{mol}_dihedral.dat'), lines)
+ lines = BondSet._get_lines_for_bond_dump(
+ bonds, target_number, rad2deg=True
+ )
+ file_write_lines(output_dir.joinpath(f"{mol}_dihedral.dat"), lines)
def __len__(self):
return len(self._molecules)
diff --git a/pycgtool/forcefield.py b/pycgtool/forcefield.py
index be34b5727fe000f62e2a0b13ec82c766bfe0c5d6..8fb63398c1b2e6c7ae00791d675b27684a3fef0e 100644
--- a/pycgtool/forcefield.py
+++ b/pycgtool/forcefield.py
@@ -13,7 +13,9 @@ from .util import any_starts_with, backup_file, file_write_lines
PathLike = typing.Union[pathlib.Path, str]
-def copy_files(src_dir: pathlib.Path, dest_dir: pathlib.Path, files: typing.Iterable[str]) -> None:
+def copy_files(
+ src_dir: pathlib.Path, dest_dir: pathlib.Path, files: typing.Iterable[str]
+) -> None:
"""Copy files from one directory to another."""
for f in files:
src_path = src_dir.joinpath(f)
@@ -25,37 +27,44 @@ class ForceField:
"""
Class used to output a GROMACS .ff forcefield
"""
- def __init__(self, name: str, dir_path: PathLike = pathlib.Path('.')):
+
+ def __init__(self, name: str, dir_path: PathLike = pathlib.Path(".")):
"""
Open a named forcefield directory. If it does not exist it is created.
:param str name: Forcefield name to open/create
"""
- self.directory = pathlib.Path(dir_path).joinpath(f'ff{name}.ff')
+ self.directory = pathlib.Path(dir_path).joinpath(f"ff{name}.ff")
backup_file(self.directory)
self.directory.mkdir(parents=True, exist_ok=True)
- with open(self.directory.joinpath('forcefield.itp'), 'w') as itp:
- print(f'#define _FF_PYCGTOOL_{name}', file=itp)
+ with open(self.directory.joinpath("forcefield.itp"), "w") as itp:
+ print(f"#define _FF_PYCGTOOL_{name}", file=itp)
print('#include "martini_v2.2.itp"', file=itp)
- data_dir = pathlib.Path(__file__).parent.joinpath('data')
+ data_dir = pathlib.Path(__file__).parent.joinpath("data")
# Copy MARTINI files
- copy_files(data_dir, self.directory, [
- 'martini_v2.2.itp',
- 'watermodels.dat',
- 'w.itp',
- ])
+ copy_files(
+ data_dir,
+ self.directory,
+ [
+ "martini_v2.2.itp",
+ "watermodels.dat",
+ "w.itp",
+ ],
+ )
# Create atomtypes.atp required for correct masses with pdb2gmx
- atomtypes_atp = os.path.join(self.directory, 'atomtypes.atp')
- with CFG(data_dir.joinpath('martini_v2.2.itp')) as itp, open(atomtypes_atp, 'w') as atomtypes:
- for toks in itp['atomtypes']:
- print(' '.join(toks), file=atomtypes)
+ atomtypes_atp = os.path.join(self.directory, "atomtypes.atp")
+ with CFG(data_dir.joinpath("martini_v2.2.itp")) as itp, open(
+ atomtypes_atp, "w"
+ ) as atomtypes:
+ for toks in itp["atomtypes"]:
+ print(" ".join(toks), file=atomtypes)
- with open(self.directory.joinpath('forcefield.doc'), 'w') as doc:
- print(f'PyCGTOOL produced MARTINI force field - {name}', file=doc)
+ with open(self.directory.joinpath("forcefield.doc"), "w") as doc:
+ print(f"PyCGTOOL produced MARTINI force field - {name}", file=doc)
def write(self, filename: str, mapping, bonds):
"""
@@ -66,10 +75,10 @@ class ForceField:
:param Iterable[Bond] bonds: CG Bonds object
"""
lines, nterms, cterms = ForceField.write_rtp(mapping, bonds)
- file_write_lines(self.directory.joinpath(f'{filename}.rtp'), lines)
+ file_write_lines(self.directory.joinpath(f"{filename}.rtp"), lines)
lines = ForceField.write_r2b(nterms, cterms)
- file_write_lines(self.directory.joinpath(f'{filename}.r2b'), lines)
+ file_write_lines(self.directory.joinpath(f"{filename}.r2b"), lines)
@staticmethod
def bond_section(bonds, section_header, multiplicity=None):
@@ -113,36 +122,38 @@ class ForceField:
"""
def write_residue(mol_name, mol_mapping, strip=None, prepend=""):
- ret_lines = [
- "[ {0} ]".format(prepend + mol_name),
- " [ atoms ]"
- ]
+ ret_lines = ["[ {0} ]".format(prepend + mol_name), " [ atoms ]"]
for bead in mol_mapping:
# name type charge chg-group
- ret_lines.append(" {:>4s} {:>4s} {:3.6f} {:4d}".format(
- bead.name, bead.type, bead.charge, 0
- ))
-
- for natoms, (section, multiplicity) in enumerate((("bonds", None),
- ("angles", None),
- ("dihedrals", 1)), start=2):
+ ret_lines.append(
+ " {:>4s} {:>4s} {:3.6f} {:4d}".format(
+ bead.name, bead.type, bead.charge, 0
+ )
+ )
+
+ for natoms, (section, multiplicity) in enumerate(
+ (("bonds", None), ("angles", None), ("dihedrals", 1)), start=2
+ ):
if strip is None:
bond_list = bonds.get_bonds(mol_name, natoms)
else:
- bond_list = bonds.get_bonds(mol_name, natoms, select=lambda bond: not any_starts_with(bond, strip))
+ bond_list = bonds.get_bonds(
+ mol_name,
+ natoms,
+ select=lambda bond: not any_starts_with(bond, strip),
+ )
- ret_lines.extend(ForceField.bond_section(bond_list, section, multiplicity))
+ ret_lines.extend(
+ ForceField.bond_section(bond_list, section, multiplicity)
+ )
return ret_lines
n_terms = set()
c_terms = set()
- rtp_lines = [
- "[ bondedtypes ]",
- ("{:4d}" * 8).format(1, 1, 1, 1, 1, 1, 0, 0)
- ]
+ rtp_lines = ["[ bondedtypes ]", ("{:4d}" * 8).format(1, 1, 1, 1, 1, 1, 0, 0)]
for mol_name, mol_mapping in mapping.items():
try:
@@ -153,14 +164,22 @@ class ForceField:
needs_terminal_entry = ForceField.needs_terminal_entries(mol_name, bonds)
if needs_terminal_entry[0]:
- rtp_lines.extend(write_residue(mol_name, mol_mapping, strip="-", prepend="N"))
+ rtp_lines.extend(
+ write_residue(mol_name, mol_mapping, strip="-", prepend="N")
+ )
n_terms.add(mol_name)
if needs_terminal_entry[1]:
- rtp_lines.extend(write_residue(mol_name, mol_mapping, strip="+", prepend="C"))
+ rtp_lines.extend(
+ write_residue(mol_name, mol_mapping, strip="+", prepend="C")
+ )
c_terms.add(mol_name)
if needs_terminal_entry[0]:
- rtp_lines.extend(write_residue(mol_name, mol_mapping, strip=("-", "+"), prepend="2"))
+ rtp_lines.extend(
+ write_residue(
+ mol_name, mol_mapping, strip=("-", "+"), prepend="2"
+ )
+ )
return rtp_lines, n_terms, c_terms
@@ -177,13 +196,17 @@ class ForceField:
"""
ret_lines = [
"; rtp residue to rtp building block table",
- "; main N-ter C-ter 2-ter"
+ "; main N-ter C-ter 2-ter",
]
for resname in sorted(n_terms | c_terms):
nter_str = ("N" + resname) if resname in n_terms else "-"
cter_str = ("C" + resname) if resname in c_terms else "-"
both_ter_str = ("2" + resname) if resname in (n_terms & c_terms) else "-"
- ret_lines.append("{0:5s} {0:5s} {1:5s} {2:5s} {3:5s}".format(resname, nter_str, cter_str, both_ter_str))
+ ret_lines.append(
+ "{0:5s} {0:5s} {1:5s} {2:5s} {3:5s}".format(
+ resname, nter_str, cter_str, both_ter_str
+ )
+ )
return ret_lines
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index f1f303a706663cd50d06dfc3e71ce89f86674976..b4f7ae2320d5496d9059a897bab935b8b5cc393f 100644
--- a/pycgtool/frame.py
+++ b/pycgtool/frame.py
@@ -22,6 +22,7 @@ PathLike = typing.Union[pathlib.Path, str]
class UnsupportedFormatException(Exception):
"""Exception raised when a topology/trajectory format cannot be parsed."""
+
def __init__(self, msg=None):
if msg is None:
msg = "Topology/Trajectory format not supported by this reader"
@@ -30,6 +31,7 @@ class UnsupportedFormatException(Exception):
class NonMatchingSystemError(ValueError):
"""Exception raised when topology and trajectory do not match."""
+
def __init__(self, msg=None):
if msg is None:
msg = "Number of atoms does not match between topology and trajectory files"
@@ -40,9 +42,9 @@ def load_traj(filepath: PathLike, **kwargs) -> mdtraj.Trajectory:
"""Load a trajectory, if a PDB fails with zero box volume disable volume check and try again."""
filepath = pathlib.Path(filepath)
- if filepath.suffix.lower() == '.pdb':
+ if filepath.suffix.lower() == ".pdb":
# PDBs have a couple of things that can go wrong - we handle these here...
- kwargs.pop('top', None) # Can't specify a topology for `load_pdb`
+ kwargs.pop("top", None) # Can't specify a topology for `load_pdb`
try:
return mdtraj.load_pdb(str(filepath), **kwargs)
@@ -52,8 +54,8 @@ def load_traj(filepath: PathLike, **kwargs) -> mdtraj.Trajectory:
# This can fail if the box volume is zero
trajectory = mdtraj.load_pdb(str(filepath), no_boxchk=True, **kwargs)
logger.warning(
- 'Unitcell has zero volume - periodic boundaries will not be accounted for. '
- 'If the molecule is split by a periodic boundary, results will be incorrect.'
+ "Unitcell has zero volume - periodic boundaries will not be accounted for. "
+ "If the molecule is split by a periodic boundary, results will be incorrect."
)
return trajectory
@@ -63,11 +65,14 @@ def load_traj(filepath: PathLike, **kwargs) -> mdtraj.Trajectory:
class Frame:
"""Load and store data from a simulation trajectory."""
- def __init__(self,
- topology_file: typing.Optional[PathLike] = None,
- trajectory_file: typing.Optional[PathLike] = None,
- frame_start: int = 0,
- frame_end: typing.Optional[int] = None):
+
+ def __init__(
+ self,
+ topology_file: typing.Optional[PathLike] = None,
+ trajectory_file: typing.Optional[PathLike] = None,
+ frame_start: int = 0,
+ frame_end: typing.Optional[int] = None,
+ ):
"""Load a simulation trajectory.
:param topology_file: File containing system topology
@@ -77,19 +82,24 @@ class Frame:
"""
if topology_file is not None:
try:
- logging.info('Loading topology file')
+ logging.info("Loading topology file")
self._trajectory = load_traj(topology_file)
self._topology = self._trajectory.topology
- logging.info('Finished loading topology file')
+ logging.info("Finished loading topology file")
if trajectory_file is not None:
try:
- logging.info('Loading trajectory file - this may take a while')
- self._trajectory = load_traj(trajectory_file, top=self._topology)
- self._trajectory = self._slice_trajectory(frame_start, frame_end)
+ logging.info("Loading trajectory file - this may take a while")
+ self._trajectory = load_traj(
+ trajectory_file, top=self._topology
+ )
+ self._trajectory = self._slice_trajectory(
+ frame_start, frame_end
+ )
logging.info(
- 'Finished loading trajectory file - loaded %d frames',
- self._trajectory.n_frames)
+ "Finished loading trajectory file - loaded %d frames",
+ self._trajectory.n_frames,
+ )
except ValueError as exc:
raise NonMatchingSystemError from exc
@@ -97,7 +107,7 @@ class Frame:
self._load_trajectory()
except OSError as exc:
- if 'no loader' in str(exc) or 'format is not supported' in str(exc):
+ if "no loader" in str(exc) or "format is not supported" in str(exc):
raise UnsupportedFormatException from exc
raise
@@ -107,9 +117,8 @@ class Frame:
self._topology = mdtraj.Topology()
def _slice_trajectory(
- self,
- frame_start: int = 0,
- frame_end: typing.Optional[int] = None) -> mdtraj.Trajectory:
+ self, frame_start: int = 0, frame_end: typing.Optional[int] = None
+ ) -> mdtraj.Trajectory:
"""Slice input simulation trajectory to a subset of frames.
:param frame_start: First frame of trajectory to use
@@ -177,20 +186,20 @@ class Frame:
"""Number of frames in the trajectory."""
return self._trajectory.n_frames
- def add_residue(self,
- name,
- chain: typing.Optional[
- mdtraj.core.topology.Residue] = None,
- **kwargs) -> mdtraj.core.topology.Residue:
+ def add_residue(
+ self,
+ name,
+ chain: typing.Optional[mdtraj.core.topology.Residue] = None,
+ **kwargs
+ ) -> mdtraj.core.topology.Residue:
"""Add a residue to the frame topology.
:param name: Name of residue
:param chain: MDTraj chain of residue
:return: New residue
"""
- if hasattr(self, '_trajectory'):
- raise TypeError(
- 'Cannot edit residues if a trajectory has been loaded')
+ if hasattr(self, "_trajectory"):
+ raise TypeError("Cannot edit residues if a trajectory has been loaded")
if chain is None:
try:
@@ -202,8 +211,10 @@ class Frame:
return self._topology.add_residue(name, chain, **kwargs)
def add_atom(
- self, name: str, element: typing.Optional[mdtraj.element.Element],
- residue: mdtraj.core.topology.Residue
+ self,
+ name: str,
+ element: typing.Optional[mdtraj.element.Element],
+ residue: mdtraj.core.topology.Residue,
) -> mdtraj.core.topology.Atom:
"""Add an atom or CG bead to the frame topology.
@@ -212,16 +223,14 @@ class Frame:
:param residue: MDTraj residue of atom
:return: New atom
"""
- if hasattr(self, '_trajectory'):
- raise TypeError(
- 'Cannot edit atoms if a trajectory has been loaded')
+ if hasattr(self, "_trajectory"):
+ raise TypeError("Cannot edit atoms if a trajectory has been loaded")
return self._topology.add_atom(name, element, residue)
- def save(self,
- filename: PathLike,
- frame_number: typing.Optional[int] = None,
- **kwargs) -> None:
+ def save(
+ self, filename: PathLike, frame_number: typing.Optional[int] = None, **kwargs
+ ) -> None:
"""Write trajctory to file.
:param filename: Name of output file
@@ -249,14 +258,14 @@ class Frame:
optional_values = {
attr: getattr(self, attr, None)
- for attr in {'time', 'unitcell_lengths', 'unitcell_angles'}
- } # yapf: disable
+ for attr in {"time", "unitcell_lengths", "unitcell_angles"}
+ }
- new_trajectory = mdtraj.Trajectory(xyz,
- topology=self._topology,
- **optional_values)
+ new_trajectory = mdtraj.Trajectory(
+ xyz, topology=self._topology, **optional_values
+ )
- if hasattr(self, '_trajectory'):
+ if hasattr(self, "_trajectory"):
self._trajectory += new_trajectory
else:
diff --git a/pycgtool/functionalforms.py b/pycgtool/functionalforms.py
index e55df800f8e026310ee4b8ea164f55037e288791..f237fe94a9c500620ddeec40faee3986a6e7a9d9 100644
--- a/pycgtool/functionalforms.py
+++ b/pycgtool/functionalforms.py
@@ -21,14 +21,17 @@ def get_functional_forms() -> enum.Enum:
name = subclass.__name__
enum_dict[name] = subclass
- return enum.Enum('FunctionalForms', enum_dict)
+ return enum.Enum("FunctionalForms", enum_dict)
class FunctionalForm(metaclass=abc.ABCMeta):
"""Parent class of any functional form used in Boltzmann Inversion to convert variance to a force constant."""
- def __init__(self,
- mean_func: typing.Callable = np.nanmean,
- variance_func: typing.Callable = np.nanvar):
+
+ def __init__(
+ self,
+ mean_func: typing.Callable = np.nanmean,
+ variance_func: typing.Callable = np.nanvar,
+ ):
"""Inject functions for calculating the mean and variance into the Boltzmann Inversion equations.
:param mean_func: Function to calculate the mean - default is np.nanmean
@@ -37,7 +40,9 @@ class FunctionalForm(metaclass=abc.ABCMeta):
self._mean_func = mean_func
self._variance_func = variance_func
- def eqm(self, values: typing.Iterable[float], temp: float) -> float: # pylint: disable=unused-argument
+ def eqm(
+ self, values: typing.Iterable[float], temp: float
+ ) -> float: # pylint: disable=unused-argument
"""Calculate equilibrium value.
May be overridden by functional forms.
@@ -78,7 +83,8 @@ class FunctionalForm(metaclass=abc.ABCMeta):
if tipe is None:
raise TypeError(
f"The functional form {cls.__name__} does not have a defined GROMACS "
- f"potential type when used with {natoms} atoms.")
+ f"potential type when used with {natoms} atoms."
+ )
return tipe
@@ -88,11 +94,12 @@ class Harmonic(FunctionalForm):
See http://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html#harmonic-potential # noqa
"""
+
# TODO: Consider whether to use improper (type 2) instead, it is actually harmonic
gromacs_type_ids = (1, 1, 1)
def fconst(self, values: typing.Iterable[float], temp: float) -> float:
- rt = 8.314 * temp / 1000. # pylint: disable=invalid-name
+ rt = 8.314 * temp / 1000.0 # pylint: disable=invalid-name
var = self._variance_func(values)
return rt / var
@@ -104,34 +111,38 @@ class CosHarmonic(FunctionalForm):
Uses the transformation in eqn 20 of the above source.
"""
+
gromacs_type_ids = (None, 2, None)
def fconst(self, values: typing.Iterable[float], temp: float) -> float:
- rt = 8.314 * temp / 1000. # pylint: disable=invalid-name
+ rt = 8.314 * temp / 1000.0 # pylint: disable=invalid-name
mean = self.eqm(values, temp)
var = self._variance_func(values)
- return rt / (math.sin(mean)**2 * var)
+ return rt / (math.sin(mean) ** 2 * var)
class MartiniDefaultLength(FunctionalForm):
"""Dummy functional form which returns a fixed force constant."""
+
gromacs_type_ids = (1, None, None)
def fconst(self, values: typing.Iterable[float], temp: float) -> float:
- return 1250.
+ return 1250.0
class MartiniDefaultAngle(FunctionalForm):
"""Dummy functional form which returns a fixed force constant."""
+
gromacs_type_ids = (None, 2, None)
def fconst(self, values: typing.Iterable[float], temp: float) -> float:
- return 25.
+ return 25.0
class MartiniDefaultDihedral(FunctionalForm):
"""Dummy functional form which returns a fixed force constant."""
+
gromacs_type_ids = (None, None, 1)
def fconst(self, values: typing.Iterable[float], temp: float) -> float:
- return 50.
+ return 50.0
diff --git a/pycgtool/mapping.py b/pycgtool/mapping.py
index 03fd2ab3e68750c48fd6eb2f497210af5a3c780f..a02d3e3ef6b5248c20ff3ba5dfe7d0ae0fb27430 100644
--- a/pycgtool/mapping.py
+++ b/pycgtool/mapping.py
@@ -25,13 +25,16 @@ PathLike = typing.Union[str, pathlib.Path]
class BeadMap:
"""Class holding values relating to the AA->CG transformation for a single bead."""
- def __init__(self,
- name: str,
- num: int,
- type: str = None,
- atoms=None,
- charge: float = 0,
- mass: float = 0):
+
+ def __init__(
+ self,
+ name: str,
+ num: int,
+ type: str = None,
+ atoms=None,
+ charge: float = 0,
+ mass: float = 0,
+ ):
"""Create a single bead mapping.
:param str name: The name of the bead
@@ -50,10 +53,8 @@ class BeadMap:
self.atoms = atoms
# NB: Mass weights are added in Mapping.__init__ if an itp file is provided
self.weights_dict = {
- "geom": np.array([1. / len(atoms) for _ in atoms],
- dtype=np.float32),
- "first": np.array([1.] + [0. for _ in atoms[1:]],
- dtype=np.float32)
+ "geom": np.array([1.0 / len(atoms) for _ in atoms], dtype=np.float32),
+ "first": np.array([1.0] + [0.0 for _ in atoms[1:]], dtype=np.float32),
}
self.weights = self.weights_dict["geom"]
@@ -88,7 +89,8 @@ class BeadMap:
except KeyError:
raise RuntimeError(
f"Mass of atom {atom} could not be automatically assigned, "
- "map_center=mass is not available.")
+ "map_center=mass is not available."
+ )
mass_array[i] = mass
@@ -97,7 +99,8 @@ class BeadMap:
if not np.all(mass_array):
raise RuntimeError(
"Some atom masses could not be automatically assigned, "
- "map_center=mass is not available")
+ "map_center=mass is not available"
+ )
mass_array /= self.mass
self.weights_dict["mass"] = mass_array
@@ -113,12 +116,7 @@ class VirtualMap(BeadMap):
:param List[str] atoms: The CG bead names from which the bead position is determined
:param float charge: The net charge on the bead
"""
- super().__init__(name,
- num,
- type=type,
- atoms=atoms,
- charge=charge,
- mass=0.)
+ super().__init__(name, num, type=type, atoms=atoms, charge=charge, mass=0.0)
self.gromacs_type_id_dict = {"geom": 1, "mass": 2}
self.gromacs_type_id = self.gromacs_type_id_dict["geom"]
@@ -133,7 +131,13 @@ class Mapping:
Contains a dictionary of lists of BeadMaps. Each list corresponds to a single molecule.
"""
- def __init__(self, filename: PathLike, options, itp_filename: typing.Optional[PathLike] = None):
+
+ def __init__(
+ self,
+ filename: PathLike,
+ options,
+ itp_filename: typing.Optional[PathLike] = None,
+ ):
"""Read in the AA->CG mapping from a file.
:param filename: File from which to read mapping
@@ -148,8 +152,7 @@ class Mapping:
with CFG(filename) as cfg:
for mol_name, mol_section in cfg.items():
- mol_map, manual_charges = self._mol_map_from_section(
- mol_section)
+ mol_map, manual_charges = self._mol_map_from_section(mol_section)
self._mappings[mol_name] = mol_map
self._manual_charges[mol_name] = manual_charges
@@ -157,8 +160,9 @@ class Mapping:
if itp_filename is not None:
self._load_itp(itp_filename)
- if ((self._map_center == "mass" or self._virtual_map_center == "mass")
- and not self._masses_are_set):
+ if (
+ self._map_center == "mass" or self._virtual_map_center == "mass"
+ ) and not self._masses_are_set:
self._guess_atom_masses()
self._set_bead_weights()
@@ -176,16 +180,20 @@ class Mapping:
manual_charges = self._manual_charges[mol_name]
if manual_charges:
logger.warning(
- 'Charges assigned in mapping for molecule %s, ignoring itp charges',
- mol_name)
+ "Charges assigned in mapping for molecule %s, ignoring itp charges",
+ mol_name,
+ )
- self._itp_section_into_mol_map(mol_map, itp_mol_entry,
- manual_charges)
+ self._itp_section_into_mol_map(
+ mol_map, itp_mol_entry, manual_charges
+ )
except KeyError:
logger.warning(
"No itp information for molecule %s found in %s",
- mol_name, itp.filename)
+ mol_name,
+ itp.filename,
+ )
self._masses_are_set = True
@@ -196,14 +204,16 @@ class Mapping:
if isinstance(bmap, VirtualMap):
bmap.weights = bmap.weights_dict[self._virtual_map_center]
bmap.gromacs_type_id = bmap.gromacs_type_id_dict[
- self._virtual_map_center]
+ self._virtual_map_center
+ ]
else:
bmap.weights = bmap.weights_dict[self._map_center]
@staticmethod
- def _itp_section_into_mol_map(mol_map: typing.List[BeadMap], itp_mol_entry,
- manual_charges: bool) -> None:
+ def _itp_section_into_mol_map(
+ mol_map: typing.List[BeadMap], itp_mol_entry, manual_charges: bool
+ ) -> None:
atoms = {}
for toks in itp_mol_entry["atoms"]:
# Store charge and mass
@@ -222,38 +232,41 @@ class Mapping:
for bead in mol_map:
if isinstance(bead, VirtualMap):
- mass_array = np.array([
- real_bead.mass
- for real_bead in mol_map if real_bead.name in bead
- ])
+ mass_array = np.array(
+ [real_bead.mass for real_bead in mol_map if real_bead.name in bead]
+ )
weights_array = mass_array / sum(mass_array)
bead.weights_dict["mass"] = weights_array
if not manual_charges:
- bead.charge = sum([
- real_bead.charge for real_bead in mol_map
- if real_bead.name in bead
- ])
+ bead.charge = sum(
+ [
+ real_bead.charge
+ for real_bead in mol_map
+ if real_bead.name in bead
+ ]
+ )
@staticmethod
- def _mol_map_from_section(
- mol_section) -> typing.Tuple[typing.List[BeadMap], bool]:
+ def _mol_map_from_section(mol_section) -> typing.Tuple[typing.List[BeadMap], bool]:
mol_map = []
manual_charges = False
- prefix_to_class = {'@v': VirtualMap}
+ prefix_to_class = {"@v": VirtualMap}
for i, (name, typ, first, *atoms) in enumerate(mol_section):
bead_class = BeadMap
charge = 0
- if name.startswith('@'):
+ if name.startswith("@"):
try:
bead_class = prefix_to_class[name]
name, typ, first, *atoms = mol_section[i][1:]
except KeyError as exc:
- raise ValueError(f'Invalid line prefix "{name}" in mapping file') from exc
+ raise ValueError(
+ f'Invalid line prefix "{name}" in mapping file'
+ ) from exc
try:
# Allow optional charge in mapping file
@@ -266,10 +279,9 @@ class Mapping:
atoms.insert(0, first)
if not atoms:
- raise ValueError(f'Bead {name} specification contains no atoms')
+ raise ValueError(f"Bead {name} specification contains no atoms")
- mol_map.append(
- bead_class(name, i, type=typ, atoms=atoms, charge=charge))
+ mol_map.append(bead_class(name, i, type=typ, atoms=atoms, charge=charge))
return mol_map, manual_charges
@@ -300,8 +312,7 @@ class Mapping:
for bead in mol_map:
bead.atoms = [
- atom_replacements[atom]
- if atom in atom_replacements else atom
+ atom_replacements[atom] if atom in atom_replacements else atom
for atom in bead.atoms
]
@@ -331,10 +342,14 @@ class Mapping:
# Do this afterwards as it depends on real atom masses
for bead in mol_mapping:
if isinstance(bead, VirtualMap):
- mass_array = np.array([
- real_bead.mass
- for real_bead in mol_mapping if real_bead.name in bead
- ], dtype=np.float32) # yapf: disable
+ mass_array = np.array(
+ [
+ real_bead.mass
+ for real_bead in mol_mapping
+ if real_bead.name in bead
+ ],
+ dtype=np.float32,
+ )
weights_array = mass_array / sum(mass_array)
bead.weights_dict["mass"] = weights_array
@@ -342,12 +357,13 @@ class Mapping:
self._masses_are_set = True
def _cg_frame_setup(
- self, aa_residues: typing.Iterable[mdtraj.core.topology.Residue]):
+ self, aa_residues: typing.Iterable[mdtraj.core.topology.Residue]
+ ):
"""Create a new CG Frame and populate beads
:param aa_residues: Iterable of atomistic residues to map from
:return: New CG Frame instance
"""
- logger.info('Initialising output frame')
+ logger.info("Initialising output frame")
cg_frame = Frame()
missing_mappings = set()
@@ -360,7 +376,8 @@ class Mapping:
missing_mappings.add(aa_res.name)
logger.warning(
"A mapping has not been provided for '%s' residues, they will not be mapped",
- aa_res.name)
+ aa_res.name,
+ )
continue
@@ -368,7 +385,7 @@ class Mapping:
for bmap in mol_map:
cg_frame.add_atom(bmap.name, None, cg_res)
- logger.info('Finished initialising output frame')
+ logger.info("Finished initialising output frame")
return cg_frame
def apply(self, frame: Frame, cg_frame: typing.Optional[Frame] = None):
@@ -390,9 +407,8 @@ class Mapping:
if not np.all(unitcell_lengths):
unitcell_lengths = None
- logger.info('Applying AA->CG mapping')
- residues_to_map = (res for res in frame.residues
- if res.name in self._mappings)
+ logger.info("Applying AA->CG mapping")
+ residues_to_map = (res for res in frame.residues if res.name in self._mappings)
for aa_res, cg_res in zip(residues_to_map, cg_frame.residues):
mol_map = self._mappings[aa_res.name]
@@ -406,24 +422,24 @@ class Mapping:
else:
coords = np.array(
- [aa_res.atom(atom).coords for atom in bmap],
- dtype=np.float32)
- bead.coords = calc_coords_weight(ref_coords, coords,
- bmap.weights,
- unitcell_lengths)
+ [aa_res.atom(atom).coords for atom in bmap], dtype=np.float32
+ )
+ bead.coords = calc_coords_weight(
+ ref_coords, coords, bmap.weights, unitcell_lengths
+ )
for bead, bmap in zip(cg_res.atoms, mol_map):
if isinstance(bmap, VirtualMap):
coords = np.array(
- [cg_res.atom(atom).coords for atom in bmap],
- dtype=np.float32)
- bead.coords = calc_coords_weight(coords[0], coords,
- bmap.weights,
- unitcell_lengths)
+ [cg_res.atom(atom).coords for atom in bmap], dtype=np.float32
+ )
+ bead.coords = calc_coords_weight(
+ coords[0], coords, bmap.weights, unitcell_lengths
+ )
cg_frame.build_trajectory()
- logger.info('Finished applying AA->CG mapping')
+ logger.info("Finished applying AA->CG mapping")
return cg_frame
diff --git a/pycgtool/parsers/__init__.py b/pycgtool/parsers/__init__.py
index 99af7b3744a487be1861b5b4d8548c4be562fbcd..a454904887990bad117fe9d4db83377e665844d2 100644
--- a/pycgtool/parsers/__init__.py
+++ b/pycgtool/parsers/__init__.py
@@ -1,7 +1,4 @@
from .cfg import CFG
from .itp import ITP
-__all__ = [
- 'CFG',
- 'ITP'
-]
+__all__ = ["CFG", "ITP"]
diff --git a/pycgtool/parsers/cfg.py b/pycgtool/parsers/cfg.py
index 081fa697b415408003c40ee5063e35189553de06..060e1a63529acc161f6ba4043934d23b7d943e1b 100644
--- a/pycgtool/parsers/cfg.py
+++ b/pycgtool/parsers/cfg.py
@@ -13,6 +13,7 @@ PathLike = typing.Union[str, pathlib.Path]
class DuplicateSectionError(KeyError):
"""Exception used to indicate that a section has appeared twice in a file."""
+
def __init__(self, section, filename):
msg = f"Section '{section}' appears twice in file '{filename}'."
super().__init__(msg)
@@ -20,6 +21,7 @@ class DuplicateSectionError(KeyError):
class NoSectionError(KeyError):
"""Exception used to indicate that a file contains no sections."""
+
def __init__(self, filename):
msg = f"File '{filename}' contains no '[]' section headers."
super().__init__(msg)
@@ -30,6 +32,7 @@ class CFG(collections.OrderedDict, contextlib.AbstractContextManager):
Contains a dictionary of Sections.
"""
+
def __init__(self, filepath: typing.Optional[PathLike] = None):
"""Parse a config file and extract Sections."""
super().__init__()
@@ -41,15 +44,15 @@ class CFG(collections.OrderedDict, contextlib.AbstractContextManager):
def _read_line(self, line: str, filepath: pathlib.Path) -> str:
# Strip comments
- line = line.split(';')[0].strip()
+ line = line.split(";")[0].strip()
# Handle include directive
- if line.startswith('#include'):
+ if line.startswith("#include"):
include_file = line.split()[1].strip('"')
other = type(self)(filepath.parent.joinpath(include_file))
self.update(other)
- return '' # Handle include then treat as empty line
+ return "" # Handle include then treat as empty line
return line
diff --git a/pycgtool/parsers/itp.py b/pycgtool/parsers/itp.py
index 6e19e7ddfea710783d6c4a3c165c1d1f1f053a2f..15b2a12bb6cc389b2c3fabf25317ad4e8d9440c3 100644
--- a/pycgtool/parsers/itp.py
+++ b/pycgtool/parsers/itp.py
@@ -14,6 +14,7 @@ class ITP(CFG):
Contains a dictionary of sections for every molecule definition.
"""
+
def _read_file(self, filepath: pathlib.Path) -> None:
mol_sections = ["atoms", "bonds", "angles", "dihedrals"]
@@ -54,5 +55,8 @@ class ITP(CFG):
raise NoSectionError(filepath)
else:
- logger.info("File '%s' contains unexpected section '%s'",
- filepath, curr_section)
+ logger.info(
+ "File '%s' contains unexpected section '%s'",
+ filepath,
+ curr_section,
+ )
diff --git a/pycgtool/util.py b/pycgtool/util.py
index c308ca95b0a984761964e9c35deeffc65e37db0c..7ec74bc3ddaf823c128920a42f867eac91a2d0d9 100644
--- a/pycgtool/util.py
+++ b/pycgtool/util.py
@@ -84,10 +84,16 @@ def extend_graph_chain(extend, pairs):
if node2.startswith("+"):
for pair2 in pairs:
if node2.strip("+") == pair2[0] and "+" + pair2[1] not in chain:
- append_if_not_in(ret, spare + (node1, node2, "+" + pair2[1]))
+ append_if_not_in(
+ ret, spare + (node1, node2, "+" + pair2[1])
+ )
- elif node2.strip("+") == pair2[1] and "+" + pair2[0] not in chain:
- append_if_not_in(ret, spare + (node1, node2, "+" + pair2[0]))
+ elif (
+ node2.strip("+") == pair2[1] and "+" + pair2[0] not in chain
+ ):
+ append_if_not_in(
+ ret, spare + (node1, node2, "+" + pair2[0])
+ )
except AttributeError:
pass
@@ -98,7 +104,9 @@ def extend_graph_chain(extend, pairs):
return ret
-def transpose_and_sample(sequence: typing.Iterable, n: typing.Optional[int] = None) -> typing.List:
+def transpose_and_sample(
+ sequence: typing.Iterable, n: typing.Optional[int] = None
+) -> typing.List:
"""Transpose a sequence of lists and sample to provide target number of rows.
Skip rows containing non-finite numbers (e.g. NaN).
@@ -106,6 +114,7 @@ def transpose_and_sample(sequence: typing.Iterable, n: typing.Optional[int] = No
:param sequence: 2d sequence object to transpose
:param n: Number of samples to take
"""
+
def no_nans(row):
return np.isfinite(row).all()
@@ -143,12 +152,12 @@ def backup_file(path: PathLike) -> pathlib.Path:
counter = 1
while new_path.exists():
- new_path = path.parent.joinpath(f'#{path.name}.{counter}#')
+ new_path = path.parent.joinpath(f"#{path.name}.{counter}#")
counter += 1
if new_path != path:
path.rename(new_path)
- logger.warning('Existing file %s backed up as %s', path.name, new_path.name)
+ logger.warning("Existing file %s backed up as %s", path.name, new_path.name)
return new_path
@@ -166,7 +175,7 @@ def sliding(vals: typing.Iterable):
current = next(it)
except StopIteration:
- raise EmptyIterableError('Cannot make sliding window over empty iterable')
+ raise EmptyIterableError("Cannot make sliding window over empty iterable")
for nxt in it:
yield (prev, current, nxt)
@@ -221,7 +230,9 @@ def cmp_whitespace_float(ref_lines, test_lines, rtol=0.01, verbose=False):
:return: True if all lines are the same, else False
"""
diff_lines = []
- for i, (ref_line, test_line) in enumerate(itertools.zip_longest(ref_lines, test_lines)):
+ for i, (ref_line, test_line) in enumerate(
+ itertools.zip_longest(ref_lines, test_lines)
+ ):
# Shortcut trivial comparisons
if ref_line is None or test_line is None:
diff_lines.append((i, ref_line, test_line))
@@ -234,8 +245,9 @@ def cmp_whitespace_float(ref_lines, test_lines, rtol=0.01, verbose=False):
test_toks = test_line.split()
# Check for float comparison of tokens on line
- for ref_tok, test_tok in itertools.zip_longest(map(number_or_string, ref_toks),
- map(number_or_string, test_toks)):
+ for ref_tok, test_tok in itertools.zip_longest(
+ map(number_or_string, ref_toks), map(number_or_string, test_toks)
+ ):
if ref_tok != test_tok:
try:
if abs(ref_tok - test_tok) > abs(ref_tok) * rtol:
@@ -287,8 +299,9 @@ def any_starts_with(iterable: typing.Iterable, char: str) -> bool:
def load_optional_topology(
- trajfile: typing.Union[str, pathlib.Path],
- topfile: typing.Optional[typing.Union[str, pathlib.Path]] = None) -> mdtraj.Trajectory:
+ trajfile: typing.Union[str, pathlib.Path],
+ topfile: typing.Optional[typing.Union[str, pathlib.Path]] = None,
+) -> mdtraj.Trajectory:
"""Load an MDTraj trajectory with or without a separate topology file.
:param trajfile: Trajectory file
@@ -301,9 +314,11 @@ def load_optional_topology(
return mdtraj.load(str(trajfile), top=str(topfile))
-def compare_trajectories(*trajectory_files: typing.Union[str, pathlib.Path],
- topology_file: typing.Optional[typing.Union[str, pathlib.Path]] = None,
- rtol: float = 0.001) -> bool:
+def compare_trajectories(
+ *trajectory_files: typing.Union[str, pathlib.Path],
+ topology_file: typing.Optional[typing.Union[str, pathlib.Path]] = None,
+ rtol: float = 0.001,
+) -> bool:
"""Compare multiple trajectory files for equality.
:param trajectory_files: Paths of trajectory file to compare
@@ -317,22 +332,22 @@ def compare_trajectories(*trajectory_files: typing.Union[str, pathlib.Path],
traj = load_optional_topology(traj_file, topology_file)
except ValueError as exc:
- raise ValueError('Topology does not match') from exc
+ raise ValueError("Topology does not match") from exc
# Conditions from Trajectory.__hash__
if traj.topology != ref_traj.topology:
- raise ValueError('Topology does not match')
+ raise ValueError("Topology does not match")
if len(traj) != len(ref_traj):
- raise ValueError('Length does not match')
+ raise ValueError("Length does not match")
if not np.allclose(traj.xyz, ref_traj.xyz, rtol=rtol):
- raise ValueError('Coordinates do not match')
+ raise ValueError("Coordinates do not match")
if not np.allclose(traj.time, ref_traj.time, rtol=rtol):
- raise ValueError('Time does not match')
+ raise ValueError("Time does not match")
if not np.allclose(traj.unitcell_vectors, ref_traj.unitcell_vectors, rtol=rtol):
- raise ValueError('Unitcell does not match')
+ raise ValueError("Unitcell does not match")
return True
diff --git a/pyproject.toml b/pyproject.toml
index ac464376ababd877acd90efb0ca2d279cc8a72b7..bd967815f08ac9f3d6f15f1714db6bf61d2622da 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,7 @@ classifiers = [
pycgtool = "pycgtool.__main__:main"
[tool.poetry.dependencies]
-python = "^3.6"
+python = "^3.6.2"
wheel = "^0.35.1"
numpy = [
{ version = "^1.19.1", python = "<3.7" }, # Support for Python 3.6 was dropped in 1.20
@@ -48,7 +48,6 @@ myst-parser = { version = "^0.13.5", optional = true }
prospector = "^1.3.0"
pytest = "^6.0.1"
pytest-cov = "^2.10.1"
-yapf = "^0.31.0"
vulture = "^2.1"
rstcheck = "^3.3.1"
flake8 = "^3.8.4"
@@ -57,14 +56,12 @@ sphinx-autoapi = "^1.5.1"
sphinx-rtd-theme = "^0.5.1"
myst-parser = "^0.13.5"
tox = "^3.23.0"
+black = "^22.1.0"
[tool.poetry.extras]
backmapping = ["mdplus"]
docs = ["Sphinx", "sphinx-autoapi", "sphinx-rtd-theme", "myst-parser"]
-[tool.yapf]
-column_limit = 110
-
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
diff --git a/tests/test_bondset.py b/tests/test_bondset.py
index e98f742265903aff89563eeb8c5ac78012540c30..b4bf52cbbb5b8a610459ef5da7881bfb286a2a34 100644
--- a/tests/test_bondset.py
+++ b/tests/test_bondset.py
@@ -1,4 +1,3 @@
-
import math
import os
import pathlib
@@ -13,8 +12,8 @@ from pycgtool.util import cmp_file_whitespace_float
class DummyOptions:
constr_threshold = 100000
- map_center = 'geom'
- virtual_map_center = 'geom'
+ map_center = "geom"
+ virtual_map_center = "geom"
angle_default_fc = False
generate_angles = True
generate_dihedrals = False
@@ -34,9 +33,7 @@ class DummyBond:
# TODO add setup and teardown to put all files in a tmp directory
class BondSetTest(unittest.TestCase):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
-
- # Columns are: eqm value, standard fc, MARTINI defaults fc
+ data_dir = base_dir.joinpath("data")
invert_test_ref_data = [
( 0.220474419132, 72658.18163, 1250),
( 0.221844516963, 64300.01188, 1250),
@@ -55,40 +52,43 @@ class BondSetTest(unittest.TestCase):
( 2.768063749729, 135.50927, 50),
(-2.213755550432, 51.13975, 50),
( 1.456495664734, 59.38162, 50),
- (-1.826134298998, 279.80889, 50)
- ]
+ (-1.826134298998, 279.80889, 50),
+ ] # fmt: skip
def test_bondset_create(self):
- measure = BondSet(self.data_dir.joinpath('sugar.bnd'), DummyOptions)
+ measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
self.assertEqual(1, len(measure))
- self.assertTrue('ALLA' in measure)
- self.assertEqual(18, len(measure['ALLA']))
+ self.assertTrue("ALLA" in measure)
+ self.assertEqual(18, len(measure["ALLA"]))
def test_bondset_apply(self):
- measure = BondSet(self.data_dir.joinpath('sugar.bnd'), DummyOptions)
- frame = Frame(self.data_dir.joinpath('sugar-cg.gro'))
+ measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
+ frame = Frame(self.data_dir.joinpath("sugar-cg.gro"))
measure.apply(frame)
# First six are bond lengths
- self.assertEqual(1, len(measure['ALLA'][0].values))
- self.assertAlmostEqual(0.2225376, measure['ALLA'][0].values[0],
- delta=0.2225376 / 500)
+ self.assertEqual(1, len(measure["ALLA"][0].values))
+ self.assertAlmostEqual(
+ 0.2225376, measure["ALLA"][0].values[0], delta=0.2225376 / 500
+ )
# Second six are angles
- self.assertEqual(1, len(measure['ALLA'][6].values))
+ self.assertEqual(1, len(measure["ALLA"][6].values))
expected = math.radians(77.22779289)
- self.assertAlmostEqual(expected, measure['ALLA'][6].values[0],
- delta=expected / 500)
+ self.assertAlmostEqual(
+ expected, measure["ALLA"][6].values[0], delta=expected / 500
+ )
# Final six are dihedrals
- self.assertEqual(1, len(measure['ALLA'][12].values))
+ self.assertEqual(1, len(measure["ALLA"][12].values))
expected = math.radians(-89.5552903)
- self.assertAlmostEqual(expected, measure['ALLA'][12].values[0],
- delta=abs(expected) / 500)
+ self.assertAlmostEqual(
+ expected, measure["ALLA"][12].values[0], delta=abs(expected) / 500
+ )
def test_bondset_remove_triangles(self):
- bondset = BondSet(self.data_dir.joinpath('triangle.bnd'), DummyOptions)
- angles = bondset.get_bond_angles('TRI', exclude_triangle=False)
+ bondset = BondSet(self.data_dir.joinpath("triangle.bnd"), DummyOptions)
+ angles = bondset.get_bond_angles("TRI", exclude_triangle=False)
self.assertEqual(3, len(angles))
- angles = bondset.get_bond_angles('TRI', exclude_triangle=True)
+ angles = bondset.get_bond_angles("TRI", exclude_triangle=True)
self.assertEqual(0, len(angles))
def support_check_mean_fc(self, mol_bonds, fc_column_number):
@@ -98,87 +98,95 @@ class BondSetTest(unittest.TestCase):
for i, bond in enumerate(mol_bonds):
ref = self.invert_test_ref_data
- self.assertAlmostEqual(ref[i][0], bond.eqm,
- delta=abs(ref[i][0] * accuracy))
- self.assertAlmostEqual(ref[i][fc_column_number], bond.fconst,
- delta=abs(ref[i][fc_column_number] * accuracy))
+ self.assertAlmostEqual(ref[i][0], bond.eqm, delta=abs(ref[i][0] * accuracy))
+ self.assertAlmostEqual(
+ ref[i][fc_column_number],
+ bond.fconst,
+ delta=abs(ref[i][fc_column_number] * accuracy),
+ )
def test_bondset_boltzmann_invert(self):
- measure = BondSet(self.data_dir.joinpath('sugar.bnd'), DummyOptions)
- frame = Frame(self.data_dir.joinpath('sugar.gro'), self.data_dir.joinpath('sugar.xtc'))
- mapping = Mapping(self.data_dir.joinpath('sugar.map'), DummyOptions)
+ measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
+ frame = Frame(
+ self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc")
+ )
+ mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
- self.support_check_mean_fc(measure['ALLA'], 1)
+ self.support_check_mean_fc(measure["ALLA"], 1)
def test_bondset_boltzmann_invert_default_fc(self):
class DefaultOptions(DummyOptions):
default_fc = True
- measure = BondSet(self.data_dir.joinpath('sugar.bnd'), DefaultOptions)
- frame = Frame(self.data_dir.joinpath('sugar.gro'), self.data_dir.joinpath('sugar.xtc'))
- mapping = Mapping(self.data_dir.joinpath('sugar.map'), DefaultOptions)
+ measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DefaultOptions)
+ frame = Frame(
+ self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc")
+ )
+ mapping = Mapping(self.data_dir.joinpath("sugar.map"), DefaultOptions)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
- self.support_check_mean_fc(measure['ALLA'], 2)
+ self.support_check_mean_fc(measure["ALLA"], 2)
def test_bondset_boltzmann_invert_manual_default_fc(self):
class FuncFormOptions(DummyOptions):
- length_form = 'MartiniDefaultLength'
- angle_form = 'MartiniDefaultAngle'
- dihedral_form = 'MartiniDefaultDihedral'
+ length_form = "MartiniDefaultLength"
+ angle_form = "MartiniDefaultAngle"
+ dihedral_form = "MartiniDefaultDihedral"
- measure = BondSet(self.data_dir.joinpath('sugar.bnd'), FuncFormOptions)
- frame = Frame(self.data_dir.joinpath('sugar.gro'), self.data_dir.joinpath('sugar.xtc'))
- mapping = Mapping(self.data_dir.joinpath('sugar.map'), DummyOptions)
+ measure = BondSet(self.data_dir.joinpath("sugar.bnd"), FuncFormOptions)
+ frame = Frame(
+ self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc")
+ )
+ mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
- self.support_check_mean_fc(measure['ALLA'], 2)
+ self.support_check_mean_fc(measure["ALLA"], 2)
def test_bondset_polymer(self):
- bondset = BondSet(self.data_dir.joinpath('polyethene.bnd'), DummyOptions)
- frame = Frame(self.data_dir.joinpath('polyethene.gro'))
+ bondset = BondSet(self.data_dir.joinpath("polyethene.bnd"), DummyOptions)
+ frame = Frame(self.data_dir.joinpath("polyethene.gro"))
bondset.apply(frame)
- self.assertEqual(5, len(bondset['ETH'][0].values))
- self.assertEqual(4, len(bondset['ETH'][1].values))
- self.assertEqual(4, len(bondset['ETH'][2].values))
- self.assertEqual(4, len(bondset['ETH'][3].values))
+ self.assertEqual(5, len(bondset["ETH"][0].values))
+ self.assertEqual(4, len(bondset["ETH"][1].values))
+ self.assertEqual(4, len(bondset["ETH"][2].values))
+ self.assertEqual(4, len(bondset["ETH"][3].values))
bondset.boltzmann_invert()
- self.assertAlmostEqual(0.107, bondset['ETH'][0].eqm,
- delta=0.107 / 500)
- self.assertAlmostEqual(0.107, bondset['ETH'][1].eqm,
- delta=0.107 / 500)
+ self.assertAlmostEqual(0.107, bondset["ETH"][0].eqm, delta=0.107 / 500)
+ self.assertAlmostEqual(0.107, bondset["ETH"][1].eqm, delta=0.107 / 500)
def test_bondset_pbc(self):
- bondset = BondSet(self.data_dir.joinpath('polyethene.bnd'), DummyOptions)
- frame = Frame(self.data_dir.joinpath('pbcpolyethene.gro'))
+ bondset = BondSet(self.data_dir.joinpath("polyethene.bnd"), DummyOptions)
+ frame = Frame(self.data_dir.joinpath("pbcpolyethene.gro"))
bondset.apply(frame)
bondset.boltzmann_invert()
- for bond in bondset.get_bond_lengths('ETH', True):
- self.assertAlmostEqual(1., bond.eqm)
+ for bond in bondset.get_bond_lengths("ETH", True):
+ self.assertAlmostEqual(1.0, bond.eqm)
self.assertEqual(math.inf, bond.fconst)
def test_full_itp_sugar(self):
- measure = BondSet(self.data_dir.joinpath('sugar.bnd'), DummyOptions)
- frame = Frame(self.data_dir.joinpath('sugar.gro'), self.data_dir.joinpath('sugar.xtc'))
- mapping = Mapping(self.data_dir.joinpath('sugar.map'), DummyOptions)
+ measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
+ frame = Frame(
+ self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc")
+ )
+ mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions)
cg_frame = mapping.apply(frame)
@@ -188,23 +196,25 @@ class BondSetTest(unittest.TestCase):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- measure.write_itp(tmp_path.joinpath('sugar_out.itp'), mapping)
+ measure.write_itp(tmp_path.joinpath("sugar_out.itp"), mapping)
self.assertTrue(
cmp_file_whitespace_float(
- tmp_path.joinpath('sugar_out.itp'),
- self.data_dir.joinpath('sugar_out.itp'),
+ tmp_path.joinpath("sugar_out.itp"),
+ self.data_dir.joinpath("sugar_out.itp"),
rtol=0.005,
- verbose=True))
+ verbose=True,
+ )
+ )
def test_full_itp_vsites(self):
"""Test full operation to output of .itp file for molecule with vsites."""
options = DummyOptions()
options.generate_angles = False
- measure = BondSet(self.data_dir.joinpath('martini3/naphthalene.bnd'), options)
- frame = Frame(self.data_dir.joinpath('martini3/naphthalene.gro'))
- mapping = Mapping(self.data_dir.joinpath('martini3/naphthalene.map'), options)
+ measure = BondSet(self.data_dir.joinpath("martini3/naphthalene.bnd"), options)
+ frame = Frame(self.data_dir.joinpath("martini3/naphthalene.gro"))
+ mapping = Mapping(self.data_dir.joinpath("martini3/naphthalene.map"), options)
cg_frame = mapping.apply(frame)
@@ -213,24 +223,27 @@ class BondSetTest(unittest.TestCase):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- measure.write_itp(tmp_path.joinpath('naphthalene_out.itp'),
- mapping)
+ measure.write_itp(tmp_path.joinpath("naphthalene_out.itp"), mapping)
self.assertTrue(
cmp_file_whitespace_float(
- tmp_path.joinpath('naphthalene_out.itp'),
- self.data_dir.joinpath('martini3/naphthalene_out.itp'),
+ tmp_path.joinpath("naphthalene_out.itp"),
+ self.data_dir.joinpath("martini3/naphthalene_out.itp"),
rtol=0.005,
- verbose=True))
+ verbose=True,
+ )
+ )
def test_duplicate_atoms_in_bond(self):
with self.assertRaises(ValueError):
- _ = BondSet(self.data_dir.joinpath('duplicate_atoms.bnd'), DummyOptions)
+ _ = BondSet(self.data_dir.joinpath("duplicate_atoms.bnd"), DummyOptions)
def test_dump_bonds(self):
- measure = BondSet(self.data_dir.joinpath('sugar.bnd'), DummyOptions)
- frame = Frame(self.data_dir.joinpath('sugar.gro'), self.data_dir.joinpath('sugar.xtc'))
- mapping = Mapping(self.data_dir.joinpath('sugar.map'), DummyOptions)
+ measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
+ frame = Frame(
+ self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc")
+ )
+ mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions)
cg_frame = mapping.apply(frame)
@@ -238,27 +251,27 @@ class BondSetTest(unittest.TestCase):
measure.boltzmann_invert()
measure.dump_values()
- filenames = ('ALLA_length.dat', 'ALLA_angle.dat', 'ALLA_dihedral.dat')
+ filenames = ("ALLA_length.dat", "ALLA_angle.dat", "ALLA_dihedral.dat")
for filename in filenames:
self.assertTrue(
- cmp_file_whitespace_float(self.data_dir.joinpath(filename),
- filename,
- rtol=0.008,
- verbose=True))
+ cmp_file_whitespace_float(
+ self.data_dir.joinpath(filename), filename, rtol=0.008, verbose=True
+ )
+ )
os.remove(filename)
def test_get_lines_for_bond_dump(self):
expected = [
- ' 0.00000 1.00000 2.00000',
- ' 1.00000 2.00000 3.00000',
- ' 2.00000 3.00000 4.00000',
- ' 3.00000 4.00000 5.00000'
+ " 0.00000 1.00000 2.00000",
+ " 1.00000 2.00000 3.00000",
+ " 2.00000 3.00000 4.00000",
+ " 3.00000 4.00000 5.00000",
]
bonds = [
DummyBond(None, None, None, values=[0, 1, 2, 3]),
DummyBond(None, None, None, values=[1, 2, 3, 4]),
- DummyBond(None, None, None, values=[2, 3, 4, 5])
+ DummyBond(None, None, None, values=[2, 3, 4, 5]),
]
output = BondSet._get_lines_for_bond_dump(bonds)
@@ -267,16 +280,16 @@ class BondSetTest(unittest.TestCase):
def test_get_lines_for_bond_dump_sample(self):
expected = [
- ' 0.00000 1.00000 2.00000',
- ' 1.00000 2.00000 3.00000',
- ' 2.00000 3.00000 4.00000',
- ' 3.00000 4.00000 5.00000'
+ " 0.00000 1.00000 2.00000",
+ " 1.00000 2.00000 3.00000",
+ " 2.00000 3.00000 4.00000",
+ " 3.00000 4.00000 5.00000",
]
bonds = [
DummyBond(None, None, None, values=[0, 1, 2, 3]),
DummyBond(None, None, None, values=[1, 2, 3, 4]),
- DummyBond(None, None, None, values=[2, 3, 4, 5])
+ DummyBond(None, None, None, values=[2, 3, 4, 5]),
]
nlines = 2
diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py
index 57d5ed869f3d70e42f600c6627320f91158cbb56..30e0c11304976c9228972869bec0c8a6a72f6236 100644
--- a/tests/test_forcefield.py
+++ b/tests/test_forcefield.py
@@ -29,7 +29,9 @@ class DummyBondSet:
def get_bonds(self, mol, natoms, select=lambda x: True):
if natoms == -1:
return [bond for bond in self.bonds if select(bond)]
- return [bond for bond in self.bonds if len(bond.atoms) == natoms and select(bond)]
+ return [
+ bond for bond in self.bonds if len(bond.atoms) == natoms and select(bond)
+ ]
def get_bond_lengths(self, *args, **kwargs):
return self.get_bonds(None, 2)
@@ -44,16 +46,18 @@ class DummyBondSet:
class ForceFieldTest(unittest.TestCase):
def setUp(self):
self.bonds = [
- DummyBond(["a", "b"], 1, 100),
- DummyBond(["b", "c"], 2, 50),
- DummyBond(["c", "+a"], 3, 20),
+ DummyBond(["a", "b"], 1, 100),
+ DummyBond(["b", "c"], 2, 50),
+ DummyBond(["c", "+a"], 3, 20),
]
- self.mapping = {"Dummy": [
- DummyBMap("a", "a1", 1),
+ self.mapping = {
+ "Dummy": [
+ DummyBMap("a", "a1", 1),
DummyBMap("b", "b2", -1),
- DummyBMap("c", "c3", 0),
- ]}
+ DummyBMap("c", "c3", 0),
+ ]
+ }
self.bondset = DummyBondSet(self.bonds, "Dummy")
@@ -62,7 +66,7 @@ class ForceFieldTest(unittest.TestCase):
tmp_dir = pathlib.Path(t)
name = "test"
- ff_dir = tmp_dir.joinpath('fftest.ff')
+ ff_dir = tmp_dir.joinpath("fftest.ff")
ForceField(name, dir_path=tmp_dir)
self.assertTrue(ff_dir.exists())
@@ -76,7 +80,7 @@ class ForceFieldTest(unittest.TestCase):
" [ section ]",
" a b 1.00000 100.00000",
" b c 2.00000 50.00000",
- " c +a 3.00000 20.00000"
+ " c +a 3.00000 20.00000",
]
self.assertListEqual(expected, ForceField.bond_section(self.bonds, "section"))
@@ -91,7 +95,7 @@ class ForceFieldTest(unittest.TestCase):
"a a Na Ca 2a ",
"b b Nb - - ",
"c c - Cc - ",
- "d d Nd Cd 2d "
+ "d d Nd Cd 2d ",
]
output = ForceField.write_r2b(nter, cter)
@@ -117,7 +121,7 @@ class ForceFieldTest(unittest.TestCase):
" c c3 0.000000 0",
" [ bonds ]",
" a b 1.00000 100.00000",
- " b c 2.00000 50.00000"
+ " b c 2.00000 50.00000",
]
output, nter, cter = ForceField.write_rtp(self.mapping, self.bondset)
@@ -135,5 +139,5 @@ class ForceFieldTest(unittest.TestCase):
self.assertTrue(cter)
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/tests/test_frame.py b/tests/test_frame.py
index 8a98b0a6105f62e29ded79bfe7c2a2b1a0e9f048..fafb8db5adc9adb1bfe7ce505fd58224bf3360e9 100644
--- a/tests/test_frame.py
+++ b/tests/test_frame.py
@@ -22,7 +22,7 @@ def try_remove(filename) -> None:
# TODO add ITP parsing tests
class FrameTest(unittest.TestCase):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
+ data_dir = base_dir.joinpath("data")
def check_reference_topology(self, frame, skip_names=True):
self.assertEqual(663, frame.natoms)
@@ -33,8 +33,8 @@ class FrameTest(unittest.TestCase):
self.assertEqual(3, residue.n_atoms)
if not skip_names: # MDTraj renames water
- self.assertEqual('SOL', residue.name)
- self.assertEqual('OW', residue.atom(0).name)
+ self.assertEqual("SOL", residue.name)
+ self.assertEqual("OW", residue.atom(0).name)
def check_reference_frame(self, frame, check_box: bool = True):
self.check_reference_topology(frame)
@@ -44,122 +44,140 @@ class FrameTest(unittest.TestCase):
np.testing.assert_allclose(atom0_coords, frame.atom(0).coords)
if check_box:
- np.testing.assert_allclose(box_vectors, frame.unitcell_lengths,
- rtol=1e-4) # PDB files are f9.3
+ np.testing.assert_allclose(
+ box_vectors, frame.unitcell_lengths, rtol=1e-4
+ ) # PDB files are f9.3
def check_reference_trajectory(self, frame):
self.check_reference_topology(frame)
-
- atom0_coords = np.array([
- [1.176 , 1.1520001 , 1.5860001 ],
- [1.1220001 , 1.13 , 1.534 ],
- [1.0580001 , 1.1620001 , 1.462 ],
- [0.91600007, 1.276 , 1.5580001 ],
- [0.73200005, 1.1240001 , 1.286 ],
- [0.64000005, 1.2160001 , 1.258 ],
- [0.632 , 1.312 , 1.2520001 ],
- [0.606 , 1.284 , 1.246 ],
- [0.582 , 1.312 , 1.1600001 ],
- [0.68200004, 1.22 , 1.25 ],
- [0.69600004, 1.33 , 1.21 ],
- ], dtype=np.float32) # yapf: disable
-
- unitcell_lengths = np.array([
- [1.9052 , 1.9052 , 1.9052 ],
- [1.9032527, 1.9032527, 1.9032527],
- [1.9040661, 1.9040661, 1.9040661],
- [1.896811 , 1.896811 , 1.896811 ],
- [1.8985983, 1.8985983, 1.8985983],
- [1.9033976, 1.9033976, 1.9033976],
- [1.8904614, 1.8904614, 1.8904614],
- [1.9013108, 1.9013108, 1.9013108],
- [1.8946321, 1.8946321, 1.8946321],
- [1.898091 , 1.898091 , 1.898091 ],
- [1.898684 , 1.898684 , 1.898684 ],
- ], dtype=np.float32) # yapf: disable
+ atom0_coords = np.array(
+ [
+ [1.176 , 1.1520001 , 1.5860001 ],
+ [1.1220001 , 1.13 , 1.534 ],
+ [1.0580001 , 1.1620001 , 1.462 ],
+ [0.91600007, 1.276 , 1.5580001 ],
+ [0.73200005, 1.1240001 , 1.286 ],
+ [0.64000005, 1.2160001 , 1.258 ],
+ [0.632 , 1.312 , 1.2520001 ],
+ [0.606 , 1.284 , 1.246 ],
+ [0.582 , 1.312 , 1.1600001 ],
+ [0.68200004, 1.22 , 1.25 ],
+ [0.69600004, 1.33 , 1.21 ],
+ ],
+ dtype=np.float32,
+ ) # fmt: skip
+ unitcell_lengths = np.array(
+ [
+ [1.9052 , 1.9052 , 1.9052 ],
+ [1.9032527, 1.9032527, 1.9032527],
+ [1.9040661, 1.9040661, 1.9040661],
+ [1.896811 , 1.896811 , 1.896811 ],
+ [1.8985983, 1.8985983, 1.8985983],
+ [1.9033976, 1.9033976, 1.9033976],
+ [1.8904614, 1.8904614, 1.8904614],
+ [1.9013108, 1.9013108, 1.9013108],
+ [1.8946321, 1.8946321, 1.8946321],
+ [1.898091 , 1.898091 , 1.898091 ],
+ [1.898684 , 1.898684 , 1.898684 ],
+ ],
+ dtype=np.float32,
+ ) # fmt: skip
np.testing.assert_allclose(atom0_coords, frame.atom(0).coords)
- np.testing.assert_allclose(unitcell_lengths,
- frame.unitcell_lengths,
- rtol=1e-4) # PDB files are f9.3
+ np.testing.assert_allclose(
+ unitcell_lengths, frame.unitcell_lengths, rtol=1e-4
+ ) # PDB files are f9.3
def test_frame_create(self):
Frame()
def test_frame_add_residue(self):
frame = Frame()
- residue = frame.add_residue('TEST_RESIDUE')
+ residue = frame.add_residue("TEST_RESIDUE")
self.assertTrue(residue is frame.residue(0))
def test_frame_read_gro(self):
- frame = Frame(self.data_dir.joinpath('water.gro'))
+ frame = Frame(self.data_dir.joinpath("water.gro"))
self.check_reference_frame(frame)
def test_frame_read_pdb(self):
- frame = Frame(self.data_dir.joinpath('water.pdb'))
+ frame = Frame(self.data_dir.joinpath("water.pdb"))
self.check_reference_frame(frame)
def test_frame_read_pdb_nobox(self):
"""Test reading a PDB with zero box volume."""
- frame = Frame(self.data_dir.joinpath('water-nobox.pdb'))
+ frame = Frame(self.data_dir.joinpath("water-nobox.pdb"))
self.check_reference_frame(frame, check_box=False)
def test_frame_read_zero_box(self):
- frame = Frame(self.data_dir.joinpath('polyethene.gro'))
+ frame = Frame(self.data_dir.joinpath("polyethene.gro"))
self.assertIsNone(frame.unitcell_lengths)
def test_frame_any_read_unsupported(self):
with self.assertRaises(UnsupportedFormatException):
- _ = Frame(self.data_dir.joinpath('dppc.map'))
+ _ = Frame(self.data_dir.joinpath("dppc.map"))
def test_frame_output_gro(self):
- frame = Frame(self.data_dir.joinpath('water.gro'))
+ frame = Frame(self.data_dir.joinpath("water.gro"))
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- frame.save(tmp_path.joinpath('water-out.gro'))
+ frame.save(tmp_path.joinpath("water-out.gro"))
self.assertTrue(
- filecmp.cmp(self.data_dir.joinpath('water.gro'),
- tmp_path.joinpath('water-out.gro')))
+ filecmp.cmp(
+ self.data_dir.joinpath("water.gro"),
+ tmp_path.joinpath("water-out.gro"),
+ )
+ )
def test_frame_read_xtc_numframes(self):
- frame = Frame(self.data_dir.joinpath('water.gro'), self.data_dir.joinpath('water.xtc'))
+ frame = Frame(
+ self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc")
+ )
self.assertEqual(11, frame.n_frames)
def test_frame_read_xtc(self):
- frame = Frame(self.data_dir.joinpath('water.gro'), self.data_dir.joinpath('water.xtc'))
+ frame = Frame(
+ self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc")
+ )
self.check_reference_trajectory(frame)
def test_frame_accept_path(self):
"""Test that Frame accepts :class:`pathlib.Path` arguments."""
- _ = Frame(self.data_dir.joinpath('water.gro'),
- self.data_dir.joinpath('water.xtc'))
+ _ = Frame(
+ self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc")
+ )
def test_frame_write_xtc(self):
"""Test that :class:`Frame` can save a trajectory file."""
- frame = Frame(self.data_dir.joinpath('water.gro'),
- self.data_dir.joinpath('water.xtc'))
+ frame = Frame(
+ self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc")
+ )
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- frame.save(tmp_path.joinpath('water.xtc'))
+ frame.save(tmp_path.joinpath("water.xtc"))
self.assertTrue(
util.compare_trajectories(
- self.data_dir.joinpath('water.xtc'),
- tmp_path.joinpath('water.xtc'),
- topology_file=self.data_dir.joinpath('water.gro')))
+ self.data_dir.joinpath("water.xtc"),
+ tmp_path.joinpath("water.xtc"),
+ topology_file=self.data_dir.joinpath("water.gro"),
+ )
+ )
def test_raise_nonmatching_system_mdtraj(self):
with self.assertRaises(NonMatchingSystemError):
- _ = Frame(self.data_dir.joinpath('water.gro'), self.data_dir.joinpath('sugar.xtc'))
+ _ = Frame(
+ self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("sugar.xtc")
+ )
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/tests/test_functionalforms.py b/tests/test_functionalforms.py
index 0266386571b2ed82a8063ccb07991d95cd393b9d..f8b13d61722875f864dcf8f0e3912e08199e6434 100644
--- a/tests/test_functionalforms.py
+++ b/tests/test_functionalforms.py
@@ -29,7 +29,7 @@ class FunctionalFormTest(unittest.TestCase):
return "TestResultFconst"
funcs = get_functional_forms()
- test_func = funcs['TestFunc'].value
+ test_func = funcs["TestFunc"].value
self.assertEqual("TestResultEqm", test_func.eqm(None, None))
self.assertEqual("TestResultFconst", test_func.fconst(None, None))
@@ -43,18 +43,11 @@ class FunctionalFormTest(unittest.TestCase):
func = funcs["Harmonic"].value()
- np.testing.assert_allclose(
- func.eqm(vals, None), np.pi
- )
+ np.testing.assert_allclose(func.eqm(vals, None), np.pi)
- func = funcs["Harmonic"].value(
- mean_func=circular_mean
- )
+ func = funcs["Harmonic"].value(mean_func=circular_mean)
- np.testing.assert_allclose(
- func.eqm(vals, None), 0,
- atol=1e-6
- )
+ np.testing.assert_allclose(func.eqm(vals, None), 0, atol=1e-6)
def test_inject_variance_function(self):
"""
@@ -62,19 +55,14 @@ class FunctionalFormTest(unittest.TestCase):
"""
funcs = get_functional_forms()
- func = funcs["Harmonic"].value(
- variance_func=circular_variance
- )
+ func = funcs["Harmonic"].value(variance_func=circular_variance)
vals = [0, 0.5 * np.pi]
ref = func.fconst(vals, 300)
vals = [0.25 * np.pi, 1.75 * np.pi]
- np.testing.assert_allclose(
- func.fconst(vals, 300), ref,
- atol=0
- )
+ np.testing.assert_allclose(func.fconst(vals, 300), ref, atol=0)
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index b8d2d93c9c77489e8e264d197794cef1973eab5e..273f6478ce1e25db0e0c2b31c08494d0536a8256 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -17,18 +17,18 @@ class DummyOptions:
class BeadMapTest(unittest.TestCase):
def test_beadmap_create(self):
"""Test that a BeadMap can be created."""
- bead = BeadMap('BEAD', 1, atoms=['ATOM1', 'ATOM2'])
+ bead = BeadMap("BEAD", 1, atoms=["ATOM1", "ATOM2"])
- self.assertEqual('BEAD', bead.name)
+ self.assertEqual("BEAD", bead.name)
self.assertEqual(1, bead.num)
self.assertEqual(2, len(bead))
- self.assertEqual('ATOM1', bead[0])
- self.assertEqual('ATOM2', bead[1])
+ self.assertEqual("ATOM1", bead[0])
+ self.assertEqual("ATOM2", bead[1])
def test_beadmap_guess_masses(self):
"""Test that masses can be assigned from atom names."""
- bead = BeadMap('BEAD', 1, atoms=['C1', 'H1', 'H2'])
+ bead = BeadMap("BEAD", 1, atoms=["C1", "H1", "H2"])
bead.guess_atom_masses()
# Total mass of bead
@@ -36,173 +36,209 @@ class BeadMapTest(unittest.TestCase):
# Contribution of each atom to bead mass
np.testing.assert_allclose(
- np.array([12, 1, 1]) / 14,
- bead.weights_dict['mass'],
- rtol=0.01) # Account for 1% error in approximate masses
+ np.array([12, 1, 1]) / 14, bead.weights_dict["mass"], rtol=0.01
+ ) # Account for 1% error in approximate masses
class MappingTest(unittest.TestCase):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
+ data_dir = base_dir.joinpath("data")
def test_mapping_create(self):
"""Test that a mapping can be correctly read from a file."""
- mapping = Mapping(self.data_dir.joinpath('water.map'), DummyOptions)
+ mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
self.assertEqual(2, len(mapping)) # SOL and HOH
- self.assertTrue('SOL' in mapping)
+ self.assertTrue("SOL" in mapping)
- sol_map = mapping['SOL']
+ sol_map = mapping["SOL"]
self.assertEqual(1, len(sol_map))
self.assertEqual(3, len(sol_map[0].atoms))
- self.assertEqual('OW', sol_map[0].atoms[0])
- self.assertEqual('HW1', sol_map[0].atoms[1])
- self.assertEqual('HW2', sol_map[0].atoms[2])
+ self.assertEqual("OW", sol_map[0].atoms[0])
+ self.assertEqual("HW1", sol_map[0].atoms[1])
+ self.assertEqual("HW2", sol_map[0].atoms[2])
def test_mapping_rename(self):
"""Test that an alternate mapping is created using MDTraj conventions."""
- mapping = Mapping(self.data_dir.joinpath('water.map'), DummyOptions)
+ mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
self.assertEqual(2, len(mapping)) # SOL and HOH
- self.assertTrue('HOH' in mapping)
+ self.assertTrue("HOH" in mapping)
- sol_map = mapping['HOH']
+ sol_map = mapping["HOH"]
self.assertEqual(1, len(sol_map))
self.assertEqual(3, len(sol_map[0].atoms))
- self.assertEqual('O', sol_map[0].atoms[0])
- self.assertEqual('H1', sol_map[0].atoms[1])
- self.assertEqual('H2', sol_map[0].atoms[2])
+ self.assertEqual("O", sol_map[0].atoms[0])
+ self.assertEqual("H1", sol_map[0].atoms[1])
+ self.assertEqual("H2", sol_map[0].atoms[2])
def test_virtual_mapping_create(self):
- mapping = Mapping(self.data_dir.joinpath('martini3/naphthalene.map'), DummyOptions)
+ mapping = Mapping(
+ self.data_dir.joinpath("martini3/naphthalene.map"), DummyOptions
+ )
self.assertEqual(1, len(mapping))
self.assertTrue("NAPH" in mapping)
self.assertEqual(5, len(mapping["NAPH"]))
self.assertTrue(isinstance(mapping["NAPH"][2], VirtualMap))
self.assertEqual(4, len(mapping["NAPH"][2].atoms))
self.assertEqual("R1", mapping["NAPH"][2].atoms[0])
- self.assertEqual(1, [isinstance(bead, VirtualMap) for bead in mapping["NAPH"]].count(True))
+ self.assertEqual(
+ 1, [isinstance(bead, VirtualMap) for bead in mapping["NAPH"]].count(True)
+ )
def test_mapping_apply(self):
- mapping = Mapping(self.data_dir.joinpath('water.map'), DummyOptions)
- frame = Frame(self.data_dir.joinpath('water.gro'))
+ mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
+ frame = Frame(self.data_dir.joinpath("water.gro"))
cg_frame = mapping.apply(frame)
self.assertEqual(frame.natoms / 3, cg_frame.natoms)
cg_frame.save("water-cg.gro")
- self.assertTrue(filecmp.cmp(self.data_dir.joinpath('water-cg.gro'), "water-cg.gro"))
+ self.assertTrue(
+ filecmp.cmp(self.data_dir.joinpath("water-cg.gro"), "water-cg.gro")
+ )
os.remove("water-cg.gro")
def test_mapping_duplicate_atom_weight(self):
"""Test that an atom can be duplicated in a bead specification to act as a weighting."""
- frame = Frame(self.data_dir.joinpath('water.gro'))
+ frame = Frame(self.data_dir.joinpath("water.gro"))
- mapping = Mapping(self.data_dir.joinpath('water.map'), DummyOptions)
+ mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[0.716, 1.300, 1.198]]),
- cg_frame.residue(0).atom(0).coords, atol=0.0005)
-
- mapping = Mapping(self.data_dir.joinpath('water_double_weight.map'), DummyOptions)
+ np.testing.assert_allclose(
+ np.array([[0.716, 1.300, 1.198]]),
+ cg_frame.residue(0).atom(0).coords,
+ atol=0.0005,
+ )
+
+ mapping = Mapping(
+ self.data_dir.joinpath("water_double_weight.map"), DummyOptions
+ )
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[0.720, 1.294, 1.195]]),
- cg_frame.residue(0).atom(0).coords, atol=0.0005)
+ np.testing.assert_allclose(
+ np.array([[0.720, 1.294, 1.195]]),
+ cg_frame.residue(0).atom(0).coords,
+ atol=0.0005,
+ )
def test_mapping_charges(self):
- mapping = Mapping(self.data_dir.joinpath('dppc.map'), DummyOptions)
+ mapping = Mapping(self.data_dir.joinpath("dppc.map"), DummyOptions)
self.assertEqual(1, mapping["DPPC"][0].charge)
self.assertEqual(-1, mapping["DPPC"][1].charge)
def test_mapping_pbc(self):
- frame = Frame(self.data_dir.joinpath('pbcwater.gro'))
+ frame = Frame(self.data_dir.joinpath("pbcwater.gro"))
- mapping = Mapping(self.data_dir.joinpath('water.map'), DummyOptions)
+ mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
cg_frame = mapping.apply(frame)
np.testing.assert_allclose(frame.atom(0).coords, cg_frame.atom(0).coords)
def test_mapping_weights_geom(self):
- frame = Frame(self.data_dir.joinpath('two.gro'))
+ frame = Frame(self.data_dir.joinpath("two.gro"))
- mapping = Mapping(self.data_dir.joinpath('two.map'), DummyOptions)
+ mapping = Mapping(self.data_dir.joinpath("two.map"), DummyOptions)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[1.5, 1.5, 1.5]]),
- cg_frame.residue(0).atom(0).coords)
+ np.testing.assert_allclose(
+ np.array([[1.5, 1.5, 1.5]]), cg_frame.residue(0).atom(0).coords
+ )
def test_virtual_mapping_weights_geom(self):
- frame = Frame(self.data_dir.joinpath('martini3/four.gro'))
+ frame = Frame(self.data_dir.joinpath("martini3/four.gro"))
- mapping = Mapping(self.data_dir.joinpath('martini3/four.map'), DummyOptions)
+ mapping = Mapping(self.data_dir.joinpath("martini3/four.map"), DummyOptions)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[2.5, 2.5, 2.5]]),
- cg_frame.residue(0).atom(2).coords)
+ np.testing.assert_allclose(
+ np.array([[2.5, 2.5, 2.5]]), cg_frame.residue(0).atom(2).coords
+ )
def test_mapping_weights_mass(self):
- frame = Frame(self.data_dir.joinpath('two.gro'))
+ frame = Frame(self.data_dir.joinpath("two.gro"))
options = DummyOptions()
options.map_center = "mass"
- mapping = Mapping(self.data_dir.joinpath('two.map'), options, itp_filename=self.data_dir.joinpath('two.itp'))
+ mapping = Mapping(
+ self.data_dir.joinpath("two.map"),
+ options,
+ itp_filename=self.data_dir.joinpath("two.itp"),
+ )
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[2., 2., 2.]]),
- cg_frame.residue(0).atom(0).coords)
+ np.testing.assert_allclose(
+ np.array([[2.0, 2.0, 2.0]]), cg_frame.residue(0).atom(0).coords
+ )
def test_virtual_mapping_weights_mass(self):
- frame = Frame(self.data_dir.joinpath('martini3/four.gro'))
+ frame = Frame(self.data_dir.joinpath("martini3/four.gro"))
options = DummyOptions()
options.virtual_map_center = "mass"
- mapping = Mapping(self.data_dir.joinpath('martini3/four.map'),
- options,
- itp_filename=self.data_dir.joinpath('martini3/four.itp'))
+ mapping = Mapping(
+ self.data_dir.joinpath("martini3/four.map"),
+ options,
+ itp_filename=self.data_dir.joinpath("martini3/four.itp"),
+ )
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[3.0, 3.0, 3.0]]),
- cg_frame.residue(0).atom(2).coords)
+ np.testing.assert_allclose(
+ np.array([[3.0, 3.0, 3.0]]), cg_frame.residue(0).atom(2).coords
+ )
def test_mapping_weights_guess_mass(self):
- frame = Frame(self.data_dir.joinpath('two.gro'))
+ frame = Frame(self.data_dir.joinpath("two.gro"))
options = DummyOptions()
options.map_center = "mass"
- mapping = Mapping(self.data_dir.joinpath('two.map'), options)
+ mapping = Mapping(self.data_dir.joinpath("two.map"), options)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[1.922575, 1.922575, 1.922575]], dtype=np.float32),
- cg_frame.residue(0).atom(0).coords, rtol=0.01)
+ np.testing.assert_allclose(
+ np.array([[1.922575, 1.922575, 1.922575]], dtype=np.float32),
+ cg_frame.residue(0).atom(0).coords,
+ rtol=0.01,
+ )
def test_virtual_mapping_weights_guess_mass(self):
- frame = Frame(self.data_dir.joinpath('martini3/four.gro'))
+ frame = Frame(self.data_dir.joinpath("martini3/four.gro"))
options = DummyOptions()
options.virtual_map_center = "mass"
- mapping = Mapping(self.data_dir.joinpath('martini3/four.map'), options)
+ mapping = Mapping(self.data_dir.joinpath("martini3/four.map"), options)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[2.83337, 2.83337, 2.83337]], dtype=np.float32),
- cg_frame.residue(0).atom(2).coords, rtol=0.01)
+ np.testing.assert_allclose(
+ np.array([[2.83337, 2.83337, 2.83337]], dtype=np.float32),
+ cg_frame.residue(0).atom(2).coords,
+ rtol=0.01,
+ )
def test_mapping_weights_first(self):
- frame = Frame(self.data_dir.joinpath('two.gro'))
+ frame = Frame(self.data_dir.joinpath("two.gro"))
options = DummyOptions()
options.map_center = "first"
- mapping = Mapping(self.data_dir.joinpath('two.map'), options, itp_filename=self.data_dir.joinpath('two.itp'))
+ mapping = Mapping(
+ self.data_dir.joinpath("two.map"),
+ options,
+ itp_filename=self.data_dir.joinpath("two.itp"),
+ )
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([[1., 1., 1.]]),
- cg_frame.residue(0).atom(0).coords)
+ np.testing.assert_allclose(
+ np.array([[1.0, 1.0, 1.0]]), cg_frame.residue(0).atom(0).coords
+ )
def test_mapping_itp_multi(self):
- mapping = Mapping(self.data_dir.joinpath('membrane/membrane.map'),
- DummyOptions,
- itp_filename=self.data_dir.joinpath('membrane/membrane.top'))
+ mapping = Mapping(
+ self.data_dir.joinpath("membrane/membrane.map"),
+ DummyOptions,
+ itp_filename=self.data_dir.joinpath("membrane/membrane.top"),
+ )
self.assertAlmostEqual(-1.2, mapping["POPE"][0].charge, delta=0.0001)
self.assertAlmostEqual(0, mapping["POPG"][0].charge, delta=0.0001)
@@ -213,8 +249,8 @@ class MappingTest(unittest.TestCase):
This is instead checked and logged as a warning in the outer script.
"""
- frame = Frame(self.data_dir.joinpath('sugar.gro'))
- mapping = Mapping(self.data_dir.joinpath('water.map'), DummyOptions)
+ frame = Frame(self.data_dir.joinpath("sugar.gro"))
+ mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions)
cg_frame = mapping.apply(frame)
diff --git a/tests/test_parsers_cfg.py b/tests/test_parsers_cfg.py
index 68e7760b7df5daa118bec4cced856c36eabe42ec..ea20a4a9a2b7a0a044979bdaa4c88078a6d51743 100644
--- a/tests/test_parsers_cfg.py
+++ b/tests/test_parsers_cfg.py
@@ -7,46 +7,46 @@ from pycgtool.parsers import CFG
class TestParsersCFG(unittest.TestCase):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
+ data_dir = base_dir.joinpath("data")
- water_name = 'SOL'
+ water_name = "SOL"
watline = ("W", "P4", "OW", "HW1", "HW2")
def test_cfg_with(self):
- with CFG(self.data_dir.joinpath('water.map')):
+ with CFG(self.data_dir.joinpath("water.map")):
pass
def test_cfg_iterate_sections(self):
- with CFG(self.data_dir.joinpath('water.map')) as cfg:
+ with CFG(self.data_dir.joinpath("water.map")) as cfg:
for name in cfg:
self.assertEqual(self.water_name, name)
def test_cfg_iterate_lines(self):
- with CFG(self.data_dir.joinpath('water.map')) as cfg:
+ with CFG(self.data_dir.joinpath("water.map")) as cfg:
for name, section in cfg.items():
self.assertEqual(self.water_name, name)
for line in section:
self.assertEqual(self.watline, line)
def test_cfg_get_section(self):
- with CFG(self.data_dir.joinpath('water.map')) as cfg:
+ with CFG(self.data_dir.joinpath("water.map")) as cfg:
self.assertTrue(self.water_name in cfg)
for line in cfg[self.water_name]:
self.assertEqual(self.watline, line)
def test_cfg_duplicate_error(self):
with self.assertRaises(DuplicateSectionError):
- CFG(self.data_dir.joinpath('twice.cfg'))
+ CFG(self.data_dir.joinpath("twice.cfg"))
def test_include_file(self):
- with CFG(self.data_dir.joinpath('martini.map')) as cfg:
+ with CFG(self.data_dir.joinpath("martini.map")) as cfg:
self.assertTrue("DOPC" in cfg)
self.assertTrue("GLY" in cfg)
def test_error_no_sections(self):
with self.assertRaises(NoSectionError):
- CFG(self.data_dir.joinpath('nosections.cfg'))
+ CFG(self.data_dir.joinpath("nosections.cfg"))
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/tests/test_parsers_topology.py b/tests/test_parsers_topology.py
index 99133f293bc38d865f7a695bf37bf9a6e2e42324..289230d952baa73e311e915000ff22e9bf125f18 100644
--- a/tests/test_parsers_topology.py
+++ b/tests/test_parsers_topology.py
@@ -7,40 +7,40 @@ from pycgtool.parsers import ITP
class TestParsersITP(unittest.TestCase):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
+ data_dir = base_dir.joinpath("data")
def test_empty_itp(self):
itp = ITP()
self.assertEqual(0, len(itp))
def test_itp_with(self):
- with ITP(self.data_dir.joinpath('membrane/membrane.top')):
+ with ITP(self.data_dir.joinpath("membrane/membrane.top")):
pass
def test_itp_duplicate_error(self):
with self.assertRaises(DuplicateSectionError):
- ITP(self.data_dir.joinpath('membrane/twice.itp'))
+ ITP(self.data_dir.joinpath("membrane/twice.itp"))
def test_itp_include(self):
- with ITP(self.data_dir.joinpath('membrane/membrane.top')) as itp:
- self.assertIn('CDL2', itp)
- self.assertIn('POPE', itp)
+ with ITP(self.data_dir.joinpath("membrane/membrane.top")) as itp:
+ self.assertIn("CDL2", itp)
+ self.assertIn("POPE", itp)
def test_read_section(self):
pii_line = ["1", "CC3161", "1", "PII", "C13", "1", "0.1400", "12.0110"]
- with ITP(self.data_dir.joinpath('membrane/membrane.top')) as itp:
+ with ITP(self.data_dir.joinpath("membrane/membrane.top")) as itp:
self.assertEqual(len(itp["PII"]["atoms"]), 283)
self.assertListEqual(list(itp["PII"]["atoms"][0]), pii_line)
def test_double_sections(self):
- with ITP(self.data_dir.joinpath('two_double_section.itp')) as itp:
+ with ITP(self.data_dir.joinpath("two_double_section.itp")) as itp:
self.assertEqual(len(itp["TWO"]["atoms"]), 2)
def test_unknown_sections(self):
- with ITP(self.data_dir.joinpath('two_unknown_section.itp')) as itp:
+ with ITP(self.data_dir.joinpath("two_unknown_section.itp")) as itp:
self.assertEqual(len(itp["TWO"]["atoms"]), 2)
def test_error_no_sections(self):
with self.assertRaises(NoSectionError):
- ITP(self.data_dir.joinpath('nosections.cfg'))
+ ITP(self.data_dir.joinpath("nosections.cfg"))
diff --git a/tests/test_pycgtool.py b/tests/test_pycgtool.py
index bfecb005936f3cb0d1dec1dc36c32dc2c2788a6c..8eb365cbcf010422bbce60c5fb5dc87f62e7f635 100644
--- a/tests/test_pycgtool.py
+++ b/tests/test_pycgtool.py
@@ -13,22 +13,24 @@ import pycgtool.__main__ as main
def get_args(name, out_dir, extra: typing.Optional[typing.Mapping] = None):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
+ data_dir = base_dir.joinpath("data")
args = [
- data_dir.joinpath(f'{name}.gro'),
- data_dir.joinpath(f'{name}.xtc'),
+ data_dir.joinpath(f"{name}.gro"),
+ data_dir.joinpath(f"{name}.xtc"),
]
kwargs = {
- '-m': data_dir.joinpath(f'{name}.map'),
- '-b': data_dir.joinpath(f'{name}.bnd'),
- '--out-dir': out_dir,
+ "-m": data_dir.joinpath(f"{name}.map"),
+ "-b": data_dir.joinpath(f"{name}.bnd"),
+ "--out-dir": out_dir,
}
parsed_args = main.parse_arguments(
- itertools.chain(map(str, args),
- *[[key, str(value)] for key, value in kwargs.items()]))
+ itertools.chain(
+ map(str, args), *[[key, str(value)] for key, value in kwargs.items()]
+ )
+ )
if extra is not None:
for key, value in extra.items():
@@ -40,36 +42,42 @@ def get_args(name, out_dir, extra: typing.Optional[typing.Mapping] = None):
class PycgtoolTest(unittest.TestCase):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
+ data_dir = base_dir.joinpath("data")
def test_pycgtool_help(self):
subprocess.check_call(["python", "-m", "pycgtool", "-h"])
subprocess.check_call(["python", "-m", "pycgtool", "--help"])
def test_pycgtool_version(self):
- subprocess.check_call(['python', '-m', 'pycgtool', '-v'])
- subprocess.check_call(['python', '-m', 'pycgtool', '--version'])
+ subprocess.check_call(["python", "-m", "pycgtool", "-v"])
+ subprocess.check_call(["python", "-m", "pycgtool", "--version"])
def test_parse_arguments(self):
- args = main.parse_arguments([
- 'TOPOLOGY',
- '-m',
- 'MAP',
- '--begin',
- '1000',
- ])
-
- self.assertEqual('TOPOLOGY', args.topology)
- self.assertEqual('MAP', args.mapping)
+ args = main.parse_arguments(
+ [
+ "TOPOLOGY",
+ "-m",
+ "MAP",
+ "--begin",
+ "1000",
+ ]
+ )
+
+ self.assertEqual("TOPOLOGY", args.topology)
+ self.assertEqual("MAP", args.mapping)
self.assertEqual(1000, args.begin)
def test_map_only(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- args = get_args('sugar', tmp_path, extra={
- 'output_xtc': True,
- 'bnd': None,
- })
+ args = get_args(
+ "sugar",
+ tmp_path,
+ extra={
+ "output_xtc": True,
+ "bnd": None,
+ },
+ )
# Equivalent to
# pycgtool <top> <trj> -m <map> --output-xtc
@@ -77,14 +85,16 @@ class PycgtoolTest(unittest.TestCase):
self.assertTrue(
util.compare_trajectories(
- self.data_dir.joinpath('sugar_out.xtc'),
- tmp_path.joinpath('out.xtc'),
- topology_file=self.data_dir.joinpath('sugar_out.gro')))
+ self.data_dir.joinpath("sugar_out.xtc"),
+ tmp_path.joinpath("out.xtc"),
+ topology_file=self.data_dir.joinpath("sugar_out.gro"),
+ )
+ )
def test_full(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- args = get_args('sugar', tmp_path)
+ args = get_args("sugar", tmp_path)
# Equivalent to
# pycgtool <top> <trj> -m <map> -b <bnd>
@@ -95,87 +105,103 @@ class PycgtoolTest(unittest.TestCase):
tmp_path.joinpath("out.itp"),
self.data_dir.joinpath("sugar_out.itp"),
rtol=0.001,
- verbose=True))
+ verbose=True,
+ )
+ )
self.assertTrue(
util.compare_trajectories(
- self.data_dir.joinpath('sugar_out.gro'),
- tmp_path.joinpath('out.gro'),
- rtol=0.001))
+ self.data_dir.joinpath("sugar_out.gro"),
+ tmp_path.joinpath("out.gro"),
+ rtol=0.001,
+ )
+ )
def test_full_no_traj(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- args = get_args('sugar', tmp_path, extra={
- 'trajectory': None,
- })
+ args = get_args(
+ "sugar",
+ tmp_path,
+ extra={
+ "trajectory": None,
+ },
+ )
# Equivalent to
# pycgtool <top> -m <map> -b <bnd>
main.PyCGTOOL(args)
- self.assertFalse(tmp_path.joinpath('out.itp').exists())
+ self.assertFalse(tmp_path.joinpath("out.itp").exists())
self.assertTrue(
util.compare_trajectories(
- self.data_dir.joinpath('sugar_out.gro'),
- tmp_path.joinpath('out.gro'),
- rtol=0.001))
+ self.data_dir.joinpath("sugar_out.gro"),
+ tmp_path.joinpath("out.gro"),
+ rtol=0.001,
+ )
+ )
def test_measure_only(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- args = get_args('sugar', tmp_path, extra={
- 'mapping': None,
- 'trajectory': None,
- })
+ args = get_args(
+ "sugar",
+ tmp_path,
+ extra={
+ "mapping": None,
+ "trajectory": None,
+ },
+ )
# Equivalent to
# pycgtool <top> -b <bnd>
main.PyCGTOOL(args)
# Does not produce itp file
- self.assertFalse(tmp_path.joinpath('out.itp').exists())
+ self.assertFalse(tmp_path.joinpath("out.itp").exists())
# Check bond dump files against reference
- for bond_type in ['length', 'angle', 'dihedral']:
- out_file = tmp_path.joinpath(f'ALLA_{bond_type}.dat')
+ for bond_type in ["length", "angle", "dihedral"]:
+ out_file = tmp_path.joinpath(f"ALLA_{bond_type}.dat")
self.assertTrue(out_file.exists())
- self.assertTrue(util.cmp_file_whitespace_float(
- self.data_dir.joinpath(f'ALLA_{bond_type}_one.dat'),
- out_file
- ))
+ self.assertTrue(
+ util.cmp_file_whitespace_float(
+ self.data_dir.joinpath(f"ALLA_{bond_type}_one.dat"), out_file
+ )
+ )
def test_forcefield(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
- args = get_args('sugar',
- tmp_path,
- extra={
- 'output_forcefield': True,
- })
+ args = get_args(
+ "sugar",
+ tmp_path,
+ extra={
+ "output_forcefield": True,
+ },
+ )
# Equivalent to
# pycgtool <top> <trj> -m <map> -b <bnd> --output-forcefield
main.PyCGTOOL(args)
# Does not produce itp file
- self.assertFalse(tmp_path.joinpath('out.itp').exists())
+ self.assertFalse(tmp_path.joinpath("out.itp").exists())
- out_ff_dir = tmp_path.joinpath('ffout.ff')
+ out_ff_dir = tmp_path.joinpath("ffout.ff")
self.assertTrue(out_ff_dir.is_dir())
# Compare all files in ffout.ff to reference versions
for out_file in out_ff_dir.iterdir():
ref_file = self.data_dir.joinpath(out_file)
- self.assertTrue(
- util.cmp_file_whitespace_float(ref_file, out_file))
+ self.assertTrue(util.cmp_file_whitespace_float(ref_file, out_file))
# TODO more tests
# TODO test wrong args.end
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/tests/test_util.py b/tests/test_util.py
index 76fc44b1d70a114a63254b2ed38887a0995230a6..2015c3a77394dfb6b479be027d0de464f76b3b86 100644
--- a/tests/test_util.py
+++ b/tests/test_util.py
@@ -49,9 +49,9 @@ class UtilTest(unittest.TestCase):
tmp_dir = pathlib.Path(t)
paths = [
- tmp_dir.joinpath('testfile'),
- tmp_dir.joinpath('#testfile.1#'),
- tmp_dir.joinpath('#testfile.2#'),
+ tmp_dir.joinpath("testfile"),
+ tmp_dir.joinpath("#testfile.1#"),
+ tmp_dir.joinpath("#testfile.2#"),
]
path = paths[0]
@@ -85,9 +85,9 @@ class UtilTest(unittest.TestCase):
tmp_dir = pathlib.Path(t)
paths = [
- tmp_dir.joinpath('testfile'),
- tmp_dir.joinpath('#testfile.1#'),
- tmp_dir.joinpath('#testfile.2#'),
+ tmp_dir.joinpath("testfile"),
+ tmp_dir.joinpath("#testfile.1#"),
+ tmp_dir.joinpath("#testfile.2#"),
]
path = paths[0]
@@ -168,27 +168,31 @@ class UtilTest(unittest.TestCase):
def test_cmp_whitespace_float_diff_lengths(self):
"""Test that lists of different lengths are considered different."""
- ref = ['1']
- test = ['1', '2']
+ ref = ["1"]
+ test = ["1", "2"]
self.assertFalse(cmp_whitespace_float(ref, test))
def test_circular_mean(self):
values = np.deg2rad(np.array([-175, 165], dtype=np.float32))
- test = np.deg2rad(175.)
- self.assertAlmostEqual(circular_mean(values), test, delta=test / 500.)
+ test = np.deg2rad(175.0)
+ self.assertAlmostEqual(circular_mean(values), test, delta=test / 500.0)
values = np.deg2rad(np.array([165, 145], dtype=np.float32))
- test = np.deg2rad(155.)
- self.assertAlmostEqual(circular_mean(values), test, delta=test / 500.)
+ test = np.deg2rad(155.0)
+ self.assertAlmostEqual(circular_mean(values), test, delta=test / 500.0)
def test_circular_variance(self):
values = np.deg2rad(np.array([165, 145], dtype=np.float32))
test_var = np.var(values)
- self.assertAlmostEqual(circular_variance(values), test_var, delta=test_var / 500.)
+ self.assertAlmostEqual(
+ circular_variance(values), test_var, delta=test_var / 500.0
+ )
values = np.deg2rad(np.array([-175, 165], dtype=np.float32))
- self.assertAlmostEqual(circular_variance(values), test_var, delta=test_var / 500.)
+ self.assertAlmostEqual(
+ circular_variance(values), test_var, delta=test_var / 500.0
+ )
class UtilFileWriteLinesTest(unittest.TestCase):
@@ -224,36 +228,38 @@ class UtilFileWriteLinesTest(unittest.TestCase):
class CompareTrajectoryTest(unittest.TestCase):
base_dir = pathlib.Path(__file__).absolute().parent
- data_dir = base_dir.joinpath('data')
+ data_dir = base_dir.joinpath("data")
def test_compare_trajectory_single(self):
- self.assertTrue(util.compare_trajectories(
- self.data_dir.joinpath('sugar.gro'),
- self.data_dir.joinpath('sugar.gro')
- ))
+ self.assertTrue(
+ util.compare_trajectories(
+ self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.gro")
+ )
+ )
def test_compare_trajectory_single_false(self):
with self.assertRaises(ValueError):
util.compare_trajectories(
- self.data_dir.joinpath('sugar.gro'),
- self.data_dir.joinpath('water.gro')
+ self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("water.gro")
)
def test_compare_trajectory(self):
- self.assertTrue(util.compare_trajectories(
- self.data_dir.joinpath('sugar.xtc'),
- self.data_dir.joinpath('sugar.xtc'),
- topology_file=self.data_dir.joinpath('sugar.gro')
- ))
+ self.assertTrue(
+ util.compare_trajectories(
+ self.data_dir.joinpath("sugar.xtc"),
+ self.data_dir.joinpath("sugar.xtc"),
+ topology_file=self.data_dir.joinpath("sugar.gro"),
+ )
+ )
def test_compare_trajectory_false(self):
with self.assertRaises(ValueError):
util.compare_trajectories(
- self.data_dir.joinpath('sugar.xtc'),
- self.data_dir.joinpath('water.xtc'),
- topology_file=self.data_dir.joinpath('sugar.gro')
+ self.data_dir.joinpath("sugar.xtc"),
+ self.data_dir.joinpath("water.xtc"),
+ topology_file=self.data_dir.joinpath("sugar.gro"),
)
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/tox.ini b/tox.ini
index ee519819c0d54f96e76e6c839f382e464edb6614..6a14acffd70fad11f629fa6bf4477da950ec9c34 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,8 +4,10 @@ envlist = lint,py3
[testenv:lint]
deps =
+ black
flake8
commands =
+ black --check pycgtool/ tests/
flake8 pycgtool/ tests/
[testenv]