imdclient 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

imdclient/tests/test_namd.py

@@ -1,11 +1,21 @@
 import MDAnalysis as mda
 import pytest
 import logging
-from .base import IMDv3IntegrationTest
-from .datafiles import NAMD_TOPOL, NAMD_CONF, NAMD_TRAJ, NAMD_PARAMS, NAMD_PSF
+from .base import IMDv3IntegrationTest, assert_allclose_with_logging
+from .datafiles import (
+    NAMD_TOPOL,
+    NAMD_CONF_NST_1,
+    NAMD_CONF_NST_8,
+    NAMD_PARAMS,
+    NAMD_PSF,
+)
+from pathlib import Path
+from numpy.testing import (
+    assert_allclose,
+)
 
 logger = logging.getLogger("imdclient.IMDClient")
-file_handler = logging.FileHandler("test.log")
+file_handler = logging.FileHandler("namd_test.log")
 formatter = logging.Formatter(
     "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 )
@@ -16,23 +26,100 @@ logger.setLevel(logging.DEBUG)
 
 class TestIMDv3NAMD(IMDv3IntegrationTest):
 
+    @pytest.fixture(params=[NAMD_CONF_NST_1, NAMD_CONF_NST_8])
+    def inp(self, request):
+        return request.param
+
+    @pytest.fixture()
+    def simulation_command(self, inp):
+        return f"namd3 {Path(inp).name}"
+
+    @pytest.fixture()
+    def input_files(self, inp):
+        return [NAMD_TOPOL, inp, NAMD_PARAMS, NAMD_PSF]
+
+    @pytest.fixture()
+    def topol(self):
+        return Path(NAMD_TOPOL).name
+
     @pytest.fixture()
-    def command(self):
-        return (
-            f"cp {NAMD_PARAMS} {NAMD_PSF} {NAMD_TOPOL} . && namd3 {NAMD_CONF}"
+    def true_u(self, topol, imd_u, tmp_path):
+        u = mda.Universe(
+            (tmp_path / topol),
+            (tmp_path / "alanin.dcd"),
         )
+        yield u
 
     @pytest.fixture()
-    def match_string(self):
-        return "INTERACTIVE MD AWAITING CONNECTION"
+    def true_u_vel(self, topol, imd_u, tmp_path):
+        u = mda.Universe(
+            (tmp_path / topol),
+            (tmp_path / "alanin.vel.dcd"),
+        )
+        yield u
+
+    @pytest.fixture()
+    def true_u_force(self, topol, imd_u, tmp_path):
+        u = mda.Universe(
+            (tmp_path / topol),
+            (tmp_path / "alanin.force.dcd"),
+        )
+        yield u
+
+    # @pytest.fixture()
+    # def match_string(self):
+    #     return "INTERACTIVE MD AWAITING CONNECTION"
 
     @pytest.fixture()
     def first_frame(self):
         return 0
 
-    @pytest.fixture()
-    def universe(self):
-        return mda.Universe(
-            NAMD_TOPOL,
-            NAMD_TRAJ,
-        )
+    # Compare coords, box, time, dt, step
+    def test_compare_imd_to_true_traj(self, imd_u, true_u, first_frame):
+        for i in range(first_frame, len(true_u.trajectory)):
+            assert_allclose(
+                true_u.trajectory[i].time,
+                imd_u.trajectory[i - first_frame].time,
+                atol=1e-03,
+            )
+            assert_allclose(
+                true_u.trajectory[i].dt,
+                imd_u.trajectory[i - first_frame].dt,
+                atol=1e-03,
+            )
+            assert_allclose(
+                true_u.trajectory[i].data["step"],
+                imd_u.trajectory[i - first_frame].data["step"],
+            )
+            assert_allclose_with_logging(
+                true_u.trajectory[i].dimensions,
+                imd_u.trajectory[i - first_frame].dimensions,
+                atol=1e-03,
+            )
+            assert_allclose_with_logging(
+                true_u.trajectory[i].positions,
+                imd_u.trajectory[i - first_frame].positions,
+                atol=1e-03,
+            )
+
+    # Compare velocities
+    def test_compare_imd_to_true_traj_vel(
+        self, imd_u, true_u_vel, first_frame
+    ):
+        for i in range(first_frame, len(true_u_vel.trajectory)):
+            assert_allclose_with_logging(
+                true_u_vel.trajectory[i].positions,
+                imd_u.trajectory[i - first_frame].velocities,
+                atol=1e-03,
+            )
+
+    # Compare forces
+    def test_compare_imd_to_true_traj_forces(
+        self, imd_u, true_u_force, first_frame
+    ):
+        for i in range(first_frame, len(true_u_force.trajectory)):
+            assert_allclose_with_logging(
+                true_u_force.trajectory[i].positions,
+                imd_u.trajectory[i - first_frame].forces,
+                atol=1e-03,
+            )

imdclient/tests/test_stream_analysis.py

@@ -15,7 +15,7 @@ from numpy.testing import (
 )
 import numpy as np
 import pytest
-from imdclient.IMDREADER import IMDReader
+from imdclient.IMD import IMDReader
 
 
 class TestStreamAnalysis:

imdclient/tests/utils.py

@@ -1,6 +1,5 @@
 from imdclient.IMDProtocol import *
 import socket
-from imdclient.IMDProtocol import *
 import logging
 
 

imdclient-0.1.3.dist-info/LICENSE

@@ -0,0 +1,5 @@
+Copyright 2024 Lawson Woods
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

imdclient-0.1.3.dist-info/METADATA

@@ -0,0 +1,132 @@
+Metadata-Version: 2.1
+Name: imdclient
+Version: 0.1.3
+Summary: Receiver for IMD v2 and v3 data from simulation engines like Gromacs, LAMMPS, and NAMD
+Author-email: Lawson <ljwoods2@asu.edu>
+Maintainer-email: Lawson <ljwoods2@asu.edu>
+License: Copyright 2024 Lawson Woods
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+Keywords: molecular simulations
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: MDAnalysis>=2.7.0
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-xdist>=2.5; extra == "test"
+Requires-Dist: pytest-cov>=3.0; extra == "test"
+Requires-Dist: MDAnalysisTests>=2.7.0; extra == "test"
+Requires-Dist: docker-py; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+
+IMDClient
+==============================
+[//]: # (Badges)
+
+| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since]  [![Documentation Status][badge_docs]][url_docs]|
+| :----------------- | :------- |
+| **Status**         | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
+| **Community**      | [![License: MIT][badge_license]][url_license]  [![Powered by MDAnalysis][badge_mda]][url_mda]|
+
+[badge_actions]: https://github.com/becksteinlab/imdclient/actions/workflows/gh-ci.yaml/badge.svg
+[badge_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main/graph/badge.svg
+[badge_commits_since]: https://img.shields.io/github/commits-since/becksteinlab/imdclient/latest
+[badge_docs]: https://readthedocs.org/projects/imdclient/badge/?version=latest
+[badge_license]: https://img.shields.io/badge/License-MIT-blue.svg
+[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
+[badge_release]: https://img.shields.io/github/release-pre/becksteinlab/imdclient.svg
+[url_actions]: https://github.com/becksteinlab/imdclient/actions?query=branch%3Amain+workflow%3Agh-ci
+[url_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main
+[url_docs]: https://imdclient.readthedocs.io/en/latest/?badge=latest
+[url_latest_release]: https://github.com/becksteinlab/imdclient/releases
+[url_license]: https://opensource.org/license/mit
+[url_mda]: https://www.mdanalysis.org
+
+Receiver for [IMDv3 protocol](https://imdclient.readthedocs.io/en/latest/protocol_v3.html) from simulation engines like Gromacs, LAMMPS, and NAMD.
+
+IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdreader/blob/main/CODE_OF_CONDUCT.md).
+
+### Installation
+
+IMDClient is available via PyPi and can be installed with pip:
+```bash
+pip install imdclient
+```
+
+To build IMDClient from source,
+we highly recommend using virtual environments.
+If possible, we strongly recommend that you use
+[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
+Below we provide instructions both for `conda` and
+for `pip`.
+
+#### With conda
+
+Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
+
+Create a virtual environment and activate it:
+
+```
+conda create --name imdclient
+conda activate imdclient
+```
+
+<!-- Install the development and documentation dependencies:
+
+```
+conda env update --name imdreader --file devtools/conda-envs/test_env.yaml
+conda env update --name imdreader --file docs/requirements.yaml
+``` -->
+
+Build this package from source:
+
+```
+pip install -e .
+```
+
+If you want to update your dependencies (which can be risky!), run:
+
+```
+conda update --all
+```
+
+And when you are finished, you can exit the virtual environment with:
+
+```
+conda deactivate
+```
+
+#### With pip
+
+To build the package from source, run:
+
+```
+pip install .
+```
+
+If you want to create a development environment, install
+the dependencies required for tests and docs with:
+
+```
+pip install ".[test,doc]"
+```
+
+### Copyright
+
+The IMDClient source code is hosted at https://github.com/becksteinlab/imdclient
+and is available under the MIT license (see the file [LICENSE](https://github.com/becksteinlab/imdclient/blob/main/LICENSE)).
+
+Copyright (c) 2024, Lawson
+
+
+#### Acknowledgements
+ 
+Project based on the 
+[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
+<!-- Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using IMDReader in published work. --> 

imdclient-0.1.3.dist-info/RECORD

@@ -0,0 +1,42 @@
+imdclient/IMD.py,sha256=-ySUiRBumVEKyZU3UXXNywajtVnERQhtP4ama3guCR4,3767
+imdclient/IMDClient.py,sha256=6p8nLe70d-eUdsJ6QNcpc8V1Mp-ozD7mhB35_p6Owuc,33330
+imdclient/IMDProtocol.py,sha256=jm7ehwfDCcs-zWHjZ2V2KpAWdGhD4JSy7RVtCSF0818,4045
+imdclient/__init__.py,sha256=Pa5h6Fjyvyxf3ECzO43pcmLm3Vk-vOuEb5Gi6TDWhds,339
+imdclient/backends.py,sha256=QmHjwYbmvFVHz-uFgpSOA0UmZTZqiMGqWMO7B8wr1zs,10368
+imdclient/results.py,sha256=2MyjFdQMW7BfiHhG5X6wQwMVrF_0mKYFnv907lgLMas,9920
+imdclient/streamanalysis.py,sha256=Qq0h_WPO-wb0_lP8jTRHe0HX7UDZNgJFA6C4PZdUmK8,38385
+imdclient/streambase.py,sha256=rwhdyC2V3_9pSz_6rNwjSc4MNToI9S318OH7AH0arHA,6176
+imdclient/utils.py,sha256=VWxk4vQ6hzxoYRu-8Ge8fJG-EitJwgJR93wOWCvzY-0,3308
+imdclient/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+imdclient/data/gromacs/md/gromacs_struct.gro,sha256=kt4vE10iF_1RbeyTogmYmIY9yKJacofrzNT-hPHGyL8,1459301
+imdclient/data/gromacs/md/gromacs_v3.top,sha256=AXFEDjvz5Qqq-VECffimdeEvhD6L-H0SFPILW-6Sums,348329
+imdclient/data/gromacs/md/gromacs_v3_nst1.mdp,sha256=3ZStLxoeQo7k5R3C6EY2oRxet_FAccDEIwVsymbN8f4,3053
+imdclient/data/gromacs/md/gromacs_v3_nst8.mdp,sha256=CYz5gKFApeJMrJyCmd3kgPFzRjahgaLRNyIomuVyY0w,3053
+imdclient/data/lammps/md/lammps_topol.data,sha256=u4osSkn7yG9p2Egz9ovLW4eVmdaThPxeZ0L218J3-V0,172948
+imdclient/data/lammps/md/lammps_v3_nst_1.in,sha256=AcvkgNNDtTkB7RlFZwpUEKKp6W_7o_UFgrX_LwC3HXI,2586
+imdclient/data/lammps/md/lammps_v3_nst_8.in,sha256=gpdAp1dDhJbG06wZVDtBGUs6biJNz8EStV341S0uJ2s,2594
+imdclient/data/namd/md/alanin.params,sha256=zWw-UfqYD3-xpdA_8R8T-0OYBbUM6py7jKAq_uyu8HE,17389
+imdclient/data/namd/md/alanin.pdb,sha256=eccDD-ledUXjbB2s1fxY40lmAKWWDpxkxANbsOkqjHc,5615
+imdclient/data/namd/md/alanin.psf,sha256=VhCZeGFhpUa8yN5iEL19zlVjqIJg2JIdPzhazpRForY,12953
+imdclient/data/namd/md/namd_v3_nst_1.namd,sha256=EZU7PGyytZdGixrBnmpAcwonN0n_JTk9U-Q82FoqO7k,983
+imdclient/data/namd/md/namd_v3_nst_8.namd,sha256=WJmwj0E4nJVhYRr_ALBlTax6kyNkdRE1krPsmY-QFLM,984
+imdclient/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+imdclient/tests/base.py,sha256=CoU6oZanTnWrASxY5aRJdICtj4yz5PfYwh9iqQ_o8WE,6461
+imdclient/tests/conftest.py,sha256=ERj5d4roxWGqpXS8-W-LFB_INEkb_4oz5ous92u2yK4,1377
+imdclient/tests/datafiles.py,sha256=NtLuk1P4vk1h4b5Hb71vne2RMmWKGRV9RaIfRvLOfIc,1262
+imdclient/tests/server.py,sha256=7KqzDg74d7Oe617jctB-rDGvEUNSaT9agkp9SiEtiME,6978
+imdclient/tests/test_gromacs.py,sha256=rXkabRB40xX7LRdF2_nrPgeNpfFF9J7m-5LeRNMA5TM,1454
+imdclient/tests/test_imdclient.py,sha256=hhfvI1wGocE5e38tfbsNW9w2uotUXtedhq3FOQC68EM,7030
+imdclient/tests/test_imdreader.py,sha256=bD2we7TBJwM4wcHJh9ob6Ap8hNsGu1KTkc_tQ_5IzrU,23532
+imdclient/tests/test_lammps.py,sha256=hwZBVvhclN1mtPuYLyODUaWjlaZaAkhAFqX-mpQvWk4,2244
+imdclient/tests/test_manual.py,sha256=BR8MCdCUxcaDKSFyR-jLhJ4mk9s9CIS5MIAf5dR4PBE,3557
+imdclient/tests/test_namd.py,sha256=dFOJUQl9ByekuuYgUOIirf6qFj5_qaKfgQq4Qimtotw,3671
+imdclient/tests/test_stream_analysis.py,sha256=qqsm_Bv8qCXyNwgdSKZM8bLyiEO5nlpqJ-XtEn-YKew,1723
+imdclient/tests/utils.py,sha256=_x1gVQ3AmhaMurpcEPLKBG5BTGu4ZMy5EGUpr0P6D6g,854
+imdclient/tests/docker_testing/docker.md,sha256=SxHEpSA1mXAvzYzsxL0EesGqPCVC8qdRMbvxGz5R0Yo,840
+imdclient-0.1.3.dist-info/AUTHORS.md,sha256=R4JTI7mrgL1WYgfyuAv4quw0e0oLQGVjWcMQa-UXJlE,652
+imdclient-0.1.3.dist-info/LICENSE,sha256=28aS5DC2LCwcOVe3VN0g2L-Dooqof34T9TMGJ6jqMig,593
+imdclient-0.1.3.dist-info/METADATA,sha256=6Vl27FFPSTPCa1MDlSDCsk9rrGCdGY6wKGJ1G1pvHJM,6531
+imdclient-0.1.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+imdclient-0.1.3.dist-info/top_level.txt,sha256=40W62GWiXUT2CbDm-No7GTeJG160wyIMpk1hBNrdkkE,10
+imdclient-0.1.3.dist-info/RECORD,,

{imdclient-0.1.2.dist-info → imdclient-0.1.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.2.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any