diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index e915b6fb958115732dcfc1e9bddbce9b881d4dda..37cf4a28f6744df507aa827042c053274af94b39 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -11,11 +11,13 @@ on:
jobs:
build:
-
- runs-on: ubuntu-latest
strategy:
+ fail-fast: false
matrix:
python-version: [3.6, 3.7, 3.8]
+ os: [ubuntu-latest, macos-11.0]
+
+ runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v2
@@ -25,23 +27,20 @@ jobs:
with:
python-version: ${{ matrix.python-version }}
- - name: Get pip cache dir
- id: pip-cache
+ - name: Install pre-install dependencies
run: |
- echo "::set-output name=dir::$(pip cache dir)"
+ python -m pip install --upgrade pip
+ pip install poetry wheel
+ poetry config virtualenvs.in-project true
- - name: pip cache
+ - name: Cache venv
uses: actions/cache@v2
with:
- path: ${{ steps.pip-cache.outputs.dir }}
- key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
- restore-keys: |
- ${{ runner.os }}-pip-
+ path: .venv
+ key: ${{ matrix.os }}-${{ matrix.python-version }}-venv-${{ hashFiles('poetry.lock') }}
- - name: Install dependencies
+ - name: Install project dependencies
run: |
- python -m pip install --upgrade pip
- pip install poetry wheel
poetry install --no-root --extras docs --extras test
- name: Test with pytest
@@ -59,3 +58,7 @@ jobs:
- name: Check that test coverage is above 80%
run: |
poetry run coverage report --fail-under=80
+
+ - name: Test that distributable package builds
+ run: |
+ poetry build
diff --git a/.gitignore b/.gitignore
index 5ad6c26c8599dd3e7bc1c783061c35923ed5edba..6f36e7c0fc782b69a73352a4a555eca34e5ef4a9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,6 +15,7 @@
# Development and Testing
.cache
.coverage
+.python-version
/cover/
/dist/
/docs/build/
diff --git a/README.md b/README.md
index 978c28ac3f13783e1ba039997faf6e1df58d3462..774ca1750db316566854426b533bc725ed9f37db 100644
--- a/README.md
+++ b/README.md
@@ -35,6 +35,13 @@ PyCGTOOL requires Python 3.6 or higher and may be installed using pip:
pip install pycgtool
```
+### MDTraj on macOS
+
+On some versions macOS, with some versions of the Clang compiler, MDTraj may fail to load GROMACS XTC simulation trajectories.
+If you encounter this issue, make sure you have the latest version of MDTraj.
+
+For more information see [MDTraj/#1572](https://github.com/mdtraj/mdtraj/issues/1572).
+
## Usage
Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND. These files provide the atomistic-to-CG mapping and bonded topology respectively. Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory. The format of these files is described in the [full documentation](https://pycgtool.readthedocs.io/en/master/index.html).
diff --git a/pycgtool/__main__.py b/pycgtool/__main__.py
index dcd24128f415302815306d76ead07383f2398507..bdef110be40aa9127effdd70a9bbdf0e74375eb9 100755
--- a/pycgtool/__main__.py
+++ b/pycgtool/__main__.py
@@ -7,8 +7,6 @@ import pathlib
import sys
import typing
-import tqdm
-
from .frame import Frame
from .mapping import Mapping
from .bondset import BondSet
@@ -76,15 +74,7 @@ def mapping_loop(frame: Frame, config) -> typing.Tuple[Frame, Mapping]:
mapping = Mapping(config.map, config, itp_filename=config.itp)
cg_frame = mapping.apply(frame)
- cg_frame.save(get_output_filepath('gro', config))
-
- logger.info("Beginning analysis of %d frames", config.end - config.begin)
-
- if config.xtc:
- # Main loop - perform mapping on every frame in trajectory
- for _ in tqdm.trange(config.begin, config.end):
- frame.next_frame()
- mapping.apply(frame, cg_frame=cg_frame)
+ cg_frame.save(get_output_filepath('gro', config), frame_number=0)
return cg_frame, mapping
@@ -99,14 +89,8 @@ def full_run(config):
frame = Frame(
topology_file=config.gro,
trajectory_file=config.xtc, # May be None
- frame_start=config.begin)
-
- try:
- config.end = min(config.end, frame.numframes)
-
- except TypeError:
- # Value of args.end was None
- config.end = frame.numframes
+ frame_start=config.begin,
+ frame_end=config.end)
if config.map:
cg_frame, mapping = mapping_loop(frame, config)
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index 511926d9351e54ca8e6512728d8659828c458153..d3bfe79f8d096915e813876b4ae1b2bc985dbd52 100644
--- a/pycgtool/frame.py
+++ b/pycgtool/frame.py
@@ -5,6 +5,7 @@ Both Frame and Residue are iterable. Residue is indexable with either atom numbe
"""
import logging
+import pathlib
import typing
import mdtraj
@@ -34,25 +35,35 @@ class NonMatchingSystemError(ValueError):
class Frame:
"""Load and store data from a simulation trajectory."""
def __init__(self,
- topology_file: typing.Optional[str] = None,
- trajectory_file: typing.Optional[str] = None,
- frame_start: int = 0):
- self.frame_number = frame_start
-
- if topology_file:
+ topology_file: typing.Optional[typing.Union[pathlib.Path,
+ str]] = None,
+ trajectory_file: typing.Optional[typing.Union[pathlib.Path,
+ str]] = None,
+ frame_start: int = 0,
+ frame_end: typing.Optional[int] = None):
+ """Load a simulation trajectory.
+
+ :param topology_file: File containing system topology
+ :param trajectory_file: File containing simulation trajectory
+ :param frame_start: First frame of trajectory to use
+ :param frame_end: Last frame of trajectory to use
+ """
+ if topology_file is not None:
try:
- self._trajectory = mdtraj.load(topology_file)
+ self._trajectory = mdtraj.load(str(topology_file))
self._topology = self._trajectory.topology
- if trajectory_file:
+ if trajectory_file is not None:
try:
- self._trajectory = mdtraj.load(trajectory_file,
+ self._trajectory = mdtraj.load(str(trajectory_file),
top=self._topology)
+ self._slice_trajectory(frame_start, frame_end)
+
except ValueError as exc:
raise NonMatchingSystemError from exc
- self._load_trajectory_frame(self.frame_number)
+ self._load_trajectory()
except OSError as exc:
if 'no loader' in str(exc):
@@ -64,39 +75,44 @@ class Frame:
# No topology - we're probably building a CG frame
self._topology = mdtraj.Topology()
- def _load_trajectory_frame(self, frame_number) -> None:
- """Load a trajectory frame into the frame attributes."""
+ def _slice_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
+ :param frame_end: Last frame of trajectory to use
+ """
+ traj = self._trajectory
+
+ if frame_start != 0:
+ if frame_end is not None:
+ traj = traj[frame_start:frame_end]
+
+ else:
+ traj = traj[frame_start:]
+
+ return traj
+
+ def _load_trajectory(self) -> None:
+ """Load a trajectory into the frame attributes."""
# Improve performance by not double indexing repeatedly
traj = self._trajectory
- xyz_frame = traj.xyz[frame_number]
for atom in self._topology.atoms:
- atom.coords = xyz_frame[atom.index]
+ atom.coords = traj.xyz[:, atom.index]
# TODO handle non-cubic boxes
try:
- self.unitcell_lengths = traj.unitcell_lengths[frame_number]
- self.unitcell_angles = traj.unitcell_angles[frame_number]
+ self.unitcell_lengths = traj.unitcell_lengths
+ self.unitcell_angles = traj.unitcell_angles
except TypeError:
self.unitcell_lengths = None
self.unitcell_angles = None
- self.time = traj.time[frame_number]
-
- def next_frame(self) -> bool:
- """Load the next trajectory frame into the frame attributes.
-
- :return: Loading next frame was successful?
- """
- try:
- self._load_trajectory_frame(self.frame_number + 1)
-
- except IndexError:
- return False
-
- self.frame_number += 1
- return True
+ self.time = traj.time
@property
def residues(self):
@@ -122,10 +138,9 @@ class Frame:
return self._topology.n_atoms
@property
- def numframes(self) -> int:
- """Number of frames in the frame trajectory."""
- # The MDTraj trajectory has the topology file as frame 0
- return self._trajectory.n_frames - 1
+ def n_frames(self) -> int:
+ """Number of frames in the trajectory."""
+ return self._trajectory.n_frames
def add_residue(self,
name,
@@ -168,28 +183,39 @@ class Frame:
return self._topology.add_atom(name, element, residue)
- def save(self, filename, **kwargs) -> None:
+ def save(self,
+ filename: str,
+ frame_number: typing.Optional[int] = None,
+ **kwargs) -> None:
"""Write trajctory to file.
:param filename: Name of output file
"""
- self._trajectory.save(str(filename), **kwargs)
+ traj = self._trajectory
+ if frame_number is not None:
+ traj = traj.slice(frame_number)
- def add_frame_to_trajectory(self) -> None:
- """Add a new trajectory frame from the values stored as attributes on this frame."""
+ traj.save(str(filename), **kwargs)
+
+ def build_trajectory(self) -> None:
+ """Build an MDTraj trajectory from atom coordinates and the values stored as attributes on this frame."""
xyz = np.array([atom.coords for atom in self._topology.atoms])
+ # We currently have axes: 0 - each atom, 1 - timestep, 2 - xyz coords
+ # Need to convert to axes: 0 - timestep, 1 - each atom, 2 - xyz coords
+ xyz = xyz.swapaxes(0, 1)
+
optional_values = {
- attr: None if getattr(self, attr) is None else [getattr(self, attr)]
+ attr: getattr(self, attr, None)
for attr in {'time', 'unitcell_lengths', 'unitcell_angles'}
} # yapf: disable
- new_frame = mdtraj.Trajectory(xyz,
- topology=self._topology,
- **optional_values)
+ new_trajectory = mdtraj.Trajectory(xyz,
+ topology=self._topology,
+ **optional_values)
if hasattr(self, '_trajectory'):
- self._trajectory += new_frame
+ self._trajectory += new_trajectory
else:
- self._trajectory = new_frame
+ self._trajectory = new_trajectory
diff --git a/pycgtool/mapping.py b/pycgtool/mapping.py
index 1197d501f8c0ba39d0f7f5c1076bf138403ba01d..7046654d48de7aec3d11e78ea76e02df3d50db9b 100644
--- a/pycgtool/mapping.py
+++ b/pycgtool/mapping.py
@@ -378,7 +378,6 @@ class Mapping:
# Frame needs initialising
cg_frame = self._cg_frame_setup(frame.residues)
- cg_frame.frame_number = frame.frame_number
cg_frame.time = frame.time
cg_frame.unitcell_lengths = frame.unitcell_lengths
cg_frame.unitcell_angles = frame.unitcell_angles
@@ -417,7 +416,7 @@ class Mapping:
bmap.weights,
unitcell_lengths)
- cg_frame.add_frame_to_trajectory()
+ cg_frame.build_trajectory()
return cg_frame
@@ -437,7 +436,7 @@ def calc_coords_weight(ref_coords, coords, weights, box=None):
vectors -= box * np.rint(vectors / box)
# Reshape weights array to match atom positions
- weights_t = weights[np.newaxis].T
+ weights_t = weights[np.newaxis, np.newaxis].T
result = np.sum(weights_t * vectors, axis=0)
result += ref_coords
return result
diff --git a/pycgtool/util.py b/pycgtool/util.py
index 5b6b2c375cd63bc3e658e58bc08342df68aa523c..82aff29f650f8bbff2b95f78b2e26a550119a073 100644
--- a/pycgtool/util.py
+++ b/pycgtool/util.py
@@ -1,6 +1,4 @@
-"""
-This module contains some general purpose utility functions used in PyCGTOOL.
-"""
+"""This module contains some general purpose utility functions used in PyCGTOOL."""
import filecmp
import functools
@@ -293,21 +291,37 @@ def any_starts_with(iterable: typing.Iterable, char: str) -> bool:
return any(map(recurse, iterable))
-def compare_trajectories(*trajectory_files: typing.Iterable[typing.Union[
- str, pathlib.Path]],
- topology_file: typing.Union[str, pathlib.Path],
- rtol: float = 0.001) -> bool:
+def load_optional_topology(
+ 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
+ :param topfile: Corresponding topology file
+ :return: MDTraj trajectory
+ """
+ if topfile is None:
+ return mdtraj.load(str(trajfile))
+
+ return mdtraj.load(str(trajfile), top=str(topfile))
+
+
+def compare_trajectories(
+ *trajectory_files: typing.Iterable[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
:param topology_file: Topology file path
:param coords_only: Only compare coordinates from trajectory - e.g. not box size
"""
- ref_traj = mdtraj.load(str(trajectory_files[0]), top=str(topology_file))
+ ref_traj = load_optional_topology(trajectory_files[0], topology_file)
for traj_file in trajectory_files[1:]:
try:
- traj = mdtraj.load(str(traj_file), top=str(topology_file))
+ traj = load_optional_topology(traj_file, topology_file)
except ValueError as exc:
raise ValueError('Topology does not match') from exc
diff --git a/test/test_bondset.py b/test/test_bondset.py
index 08d56298f2f7102107b0f9d427cf33fc3a754cc2..aa34785b9403dc91d49d76a6f71c6762cf3f0ba0 100644
--- a/test/test_bondset.py
+++ b/test/test_bondset.py
@@ -2,6 +2,8 @@ import unittest
import math
import os
+import pathlib
+import tempfile
from pycgtool.bondset import BondSet
from pycgtool.frame import Frame
@@ -31,6 +33,9 @@ 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
invert_test_ref_data = [
( 0.220474419132, 72658.18163, 1250),
@@ -104,8 +109,6 @@ class BondSetTest(unittest.TestCase):
mapping = Mapping('test/data/sugar.map', DummyOptions)
cg_frame = mapping.apply(frame)
- while frame.next_frame():
- cg_frame = mapping.apply(frame, cg_frame=cg_frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
@@ -121,8 +124,6 @@ class BondSetTest(unittest.TestCase):
mapping = Mapping('test/data/sugar.map', DefaultOptions)
cg_frame = mapping.apply(frame)
- while frame.next_frame():
- cg_frame = mapping.apply(frame, cg_frame=cg_frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
@@ -140,8 +141,6 @@ class BondSetTest(unittest.TestCase):
mapping = Mapping('test/data/sugar.map', DummyOptions)
cg_frame = mapping.apply(frame)
- while frame.next_frame():
- cg_frame = mapping.apply(frame, cg_frame=cg_frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
@@ -180,17 +179,23 @@ class BondSetTest(unittest.TestCase):
measure = BondSet('test/data/sugar.bnd', DummyOptions)
frame = Frame('test/data/sugar.gro', 'test/data/sugar.xtc')
mapping = Mapping('test/data/sugar.map', DummyOptions)
- cg_frame = mapping.apply(frame)
- while frame.next_frame():
- cg_frame = mapping.apply(frame, cg_frame=cg_frame)
+ cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
- measure.write_itp('sugar_out.itp', mapping)
- self.assertTrue(cmp_file_whitespace_float('sugar_out.itp', 'test/data/sugar_out.itp',
- rtol=0.005, verbose=True))
+ with tempfile.TemporaryDirectory() as tmpdir:
+ tmp_path = pathlib.Path(tmpdir)
+
+ 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'),
+ rtol=0.005,
+ verbose=True))
def test_full_itp_vsites(self):
"""Test full operation to output of .itp file for molecule with vsites."""
@@ -200,17 +205,23 @@ class BondSetTest(unittest.TestCase):
measure = BondSet('test/data/martini3/naphthalene.bnd', options)
frame = Frame('test/data/martini3/naphthalene.gro')
mapping = Mapping('test/data/martini3/naphthalene.map', options)
+
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
- measure.write_itp('naphthalene_out.itp', mapping)
- self.assertTrue(
- cmp_file_whitespace_float('naphthalene_out.itp',
- 'test/data/martini3/naphthalene_out.itp',
- rtol=0.005,
- verbose=True))
+ with tempfile.TemporaryDirectory() as tmpdir:
+ tmp_path = pathlib.Path(tmpdir)
+ 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'),
+ rtol=0.005,
+ verbose=True))
def test_duplicate_atoms_in_bond(self):
with self.assertRaises(ValueError):
@@ -220,19 +231,21 @@ class BondSetTest(unittest.TestCase):
measure = BondSet('test/data/sugar.bnd', DummyOptions)
frame = Frame('test/data/sugar.gro', 'test/data/sugar.xtc')
mapping = Mapping('test/data/sugar.map', DummyOptions)
- cg_frame = mapping.apply(frame)
- while frame.next_frame():
- cg_frame = mapping.apply(frame, cg_frame=cg_frame)
+ cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
measure.dump_values()
+ data_dir = pathlib.Path('test/data')
filenames = ('ALLA_length.dat', 'ALLA_angle.dat', 'ALLA_dihedral.dat')
for filename in filenames:
- self.assertTrue(cmp_file_whitespace_float(os.path.join('test/data', filename), filename,
- rtol=0.008, verbose=True))
+ self.assertTrue(
+ cmp_file_whitespace_float(data_dir.joinpath(filename),
+ filename,
+ rtol=0.008,
+ verbose=True))
os.remove(filename)
def test_get_lines_for_bond_dump(self):
diff --git a/test/test_frame.py b/test/test_frame.py
index fd340ddf252a084e54690dd90894bbe1f278fb71..0b073668c2c79affb47cd20c1edf8fa5f981de8e 100644
--- a/test/test_frame.py
+++ b/test/test_frame.py
@@ -1,11 +1,14 @@
import filecmp
import os
+import pathlib
import unittest
+import tempfile
import numpy as np
from pycgtool.frame import NonMatchingSystemError, UnsupportedFormatException
from pycgtool.frame import Frame
+from pycgtool import util
def try_remove(filename) -> None:
@@ -18,6 +21,9 @@ 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')
+
def check_reference_topology(self, frame, skip_names=True):
self.assertEqual(663, frame.natoms)
@@ -33,8 +39,8 @@ class FrameTest(unittest.TestCase):
def check_reference_frame(self, frame):
self.check_reference_topology(frame)
- atom0_coords = np.array([0.696, 1.330, 1.211])
- box_vectors = np.array([1.89868, 1.89868, 1.89868])
+ atom0_coords = np.array([[0.696, 1.330, 1.211]])
+ box_vectors = np.array([[1.89868, 1.89868, 1.89868]])
np.testing.assert_allclose(atom0_coords, frame.atom(0).coords)
np.testing.assert_allclose(box_vectors, frame.unitcell_lengths,
@@ -43,18 +49,38 @@ class FrameTest(unittest.TestCase):
def check_reference_trajectory(self, frame):
self.check_reference_topology(frame)
- atom0_coords_array = np.array([[1.176, 1.152, 1.586],
- [1.122, 1.130, 1.534]])
-
- box_vectors_array = np.array([[1.9052, 1.9052, 1.9052],
- [1.90325272, 1.90325272, 1.90325272]])
+ 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
- for _, (atom0_coords, box_vectors) in enumerate(
- zip(atom0_coords_array, box_vectors_array)):
- np.testing.assert_allclose(atom0_coords, frame.atom(0).coords)
- np.testing.assert_allclose(box_vectors, frame.unitcell_lengths,
- rtol=1e-4) # PDB files are f9.3
- frame.next_frame()
+ 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
def test_frame_create(self):
Frame()
@@ -85,25 +111,43 @@ class FrameTest(unittest.TestCase):
def test_frame_output_gro(self):
frame = Frame('test/data/water.gro')
- frame.save('water-out.gro')
- self.assertTrue(filecmp.cmp('test/data/water.gro', 'water-out.gro'))
- try_remove('water-out.gro')
+ with tempfile.TemporaryDirectory() as tmpdir:
+ tmp_path = pathlib.Path(tmpdir)
+
+ frame.save(tmp_path.joinpath('water-out.gro'))
+ self.assertTrue(
+ filecmp.cmp(self.data_dir.joinpath('water.gro'),
+ tmp_path.joinpath('water-out.gro')))
def test_frame_read_xtc_numframes(self):
frame = Frame('test/data/water.gro', 'test/data/water.xtc')
- self.assertEqual(10, frame.numframes)
+ self.assertEqual(11, frame.n_frames)
def test_frame_read_xtc(self):
frame = Frame('test/data/water.gro', 'test/data/water.xtc')
self.check_reference_trajectory(frame)
- def test_frame_write_xtc(self):
- try_remove('water_test2.xtc')
+ 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 = Frame('test/data/water.gro', 'test/data/water.xtc')
- frame.save('water_test2.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'))
+
+ with tempfile.TemporaryDirectory() as tmpdir:
+ tmp_path = pathlib.Path(tmpdir)
+
+ 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')))
def test_raise_nonmatching_system_mdtraj(self):
with self.assertRaises(NonMatchingSystemError):
diff --git a/test/test_mapping.py b/test/test_mapping.py
index fa1d6caaf2182fb7c1192ede1d1ed39f4e0221d6..d6f987bab9759a17efc19e35e02823ee9a0dd404 100644
--- a/test/test_mapping.py
+++ b/test/test_mapping.py
@@ -110,7 +110,7 @@ class MappingTest(unittest.TestCase):
mapping = Mapping("test/data/two.map", DummyOptions)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([1.5, 1.5, 1.5]),
+ 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):
@@ -119,7 +119,7 @@ class MappingTest(unittest.TestCase):
mapping = Mapping("test/data/martini3/four.map", DummyOptions)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([2.5, 2.5, 2.5]),
+ 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):
@@ -130,7 +130,7 @@ class MappingTest(unittest.TestCase):
mapping = Mapping("test/data/two.map", options, itp_filename="test/data/two.itp")
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([2., 2., 2.]),
+ np.testing.assert_allclose(np.array([[2., 2., 2.]]),
cg_frame.residue(0).atom(0).coords)
def test_virtual_mapping_weights_mass(self):
@@ -141,7 +141,7 @@ class MappingTest(unittest.TestCase):
mapping = Mapping("test/data/martini3/four.map", options, itp_filename="test/data/martini3/four.itp")
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([3.0, 3.0, 3.0]),
+ 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):
@@ -152,7 +152,7 @@ class MappingTest(unittest.TestCase):
mapping = Mapping("test/data/two.map", options)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([1.922575, 1.922575, 1.922575], dtype=np.float32),
+ 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):
@@ -163,7 +163,7 @@ class MappingTest(unittest.TestCase):
mapping = Mapping("test/data/martini3/four.map", options)
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([2.83337, 2.83337, 2.83337], dtype=np.float32),
+ 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):
@@ -174,7 +174,7 @@ class MappingTest(unittest.TestCase):
mapping = Mapping("test/data/two.map", options, itp_filename="test/data/two.itp")
cg_frame = mapping.apply(frame)
- np.testing.assert_allclose(np.array([1., 1., 1.]),
+ np.testing.assert_allclose(np.array([[1., 1., 1.]]),
cg_frame.residue(0).atom(0).coords)
def test_mapping_itp_multi(self):
diff --git a/test/test_pycgtool.py b/test/test_pycgtool.py
index 820449650cbc7669f61cf25af9c6eef862f9e27d..a2b9813a5c6ee9e4132a33aeaa47a2e6f758b75a 100644
--- a/test/test_pycgtool.py
+++ b/test/test_pycgtool.py
@@ -91,7 +91,6 @@ class PycgtoolTest(unittest.TestCase):
util.compare_trajectories(
self.data_dir.joinpath('sugar_out.gro'),
tmp_path.joinpath('out.gro'),
- topology_file=self.data_dir.joinpath('sugar_out.gro'),
rtol=0.001))
def test_full_no_traj(self):
@@ -109,7 +108,6 @@ class PycgtoolTest(unittest.TestCase):
util.compare_trajectories(
self.data_dir.joinpath('sugar_out.gro'),
tmp_path.joinpath('out.gro'),
- topology_file=self.data_dir.joinpath('sugar_out.gro'),
rtol=0.001))
def test_measure_only(self):
diff --git a/test/test_util.py b/test/test_util.py
index 8c3b1ef3d51bc1a4cf0cc5c3bbff4c75cd0d844c..7e5cbc7350185f67b7ba2ebc7ba95a62605df48c 100644
--- a/test/test_util.py
+++ b/test/test_util.py
@@ -172,16 +172,14 @@ class CompareTrajectoryTest(unittest.TestCase):
def test_compare_trajectory_single(self):
self.assertTrue(util.compare_trajectories(
'test/data/sugar.gro',
- 'test/data/sugar.gro',
- topology_file='test/data/sugar.gro'
+ 'test/data/sugar.gro'
))
def test_compare_trajectory_single_false(self):
with self.assertRaises(ValueError):
util.compare_trajectories(
'test/data/sugar.gro',
- 'test/data/water.gro',
- topology_file='test/data/sugar.gro'
+ 'test/data/water.gro'
)
def test_compare_trajectory(self):