acemd 4.0.14__tar.gz

acemd-4.0.14/LICENSE

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+ACEMD LICENSE
+=============
+
+Acellera Software Not-for-Profit License Agreement v1.2
+
+The software ("Software") has been developed by the contributing
+researchers from Acellera and made available through Acellera for your
+internal, non-profit research use.
+
+Acellera allows researchers at your institution to run, display, copy and
+modify Software on the following conditions:
+
+1. The Software remains at your institution and is not published, distributed,
+   or otherwise transferred or made available to other than institution employees
+   and students involved in research under your supervision.
+
+2. You agree to make results generated using Software available to other
+   academic researchers for non-profit research purposes. If you wish to obtain
+   Software for any commercial purposes, including fee-based service projects, you
+   will need to execute a separate licensing agreement with Acellera and pay a
+   fee. In that case please contact: info@acellera.com.
+
+3. You retain in Software and any modifications to Software, the copyright,
+   trademark, or other notices pertaining to Software as provided by Acellera.
+
+4. You provide Acellera with feedback on the use of the Software in your
+   research, and that Acellera are permitted to use any information you provide in
+   making changes to the Software. All bug reports and technical questions shall
+   be sent to the email address: info@acellera.com.
+
+5. You acknowledge that Acellera and its licensees may develop modifications to
+   Software that may be substantially similar to your modifications of Software,
+   and that Acellera and its licensees shall not be constrained in any way by you
+   in Acellera's or its licensees' use or management of such modifications. You
+   acknowledge the right of Acellera to prepare and publish modifications to
+   Software that may be substantially similar or functionally equivalent to your
+   modifications and improvements, and if you obtain patent protection for any
+   modification or improvement to Software you agree not to allege or enjoin
+   infringement of your patent by Acellera or by any of Acellera's licensees
+   obtaining modifications or improvements to Software from Acellera .
+
+6. You agree to acknowledge the contribution Software make to your research,
+   and cite appropriate references about the Software in your publications.
+
+7. Any risk associated with using the Software at your institution is with you
+   and your institution. Software is experimental in nature and is made available
+   as a research courtesy "AS IS," without obligation by Acellera to provide
+   accompanying services or support.
+
+8. You consent to allow usage information of this software to be sent
+   to Acellera.
+
+9. ACELLERA EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES REGARDING THE SOFTWARE,
+   WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES PERTAINING
+   TO NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

acemd-4.0.14/MANIFEST.in

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+include acemd/logging.ini
+include acemd/LICENSE
+graft acemd/share
+prune tests 
+prune package
+prune docs
+prune .github
+exclude Makefile conda_deps* pytest.ini update_license_header.py .gitattributes .gitignore

acemd-4.0.14/PKG-INFO

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+Metadata-Version: 2.4
+Name: acemd
+Version: 4.0.14
+Summary: ACEMD is the next generation molecular dynamic simulation software
+Author-email: Acellera <info@acellera.com>
+Project-URL: Homepage, https://github.com/Acellera/acemd
+Project-URL: Bug Tracker, https://github.com/Acellera/acemd/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: openmm==8.2.1rc1
+Requires-Dist: moleculekit>=1.9.35
+Requires-Dist: pyyaml
+Requires-Dist: natsort
+Requires-Dist: requests
+Requires-Dist: openmm-torch
+Requires-Dist: torch
+Requires-Dist: torchmd-net>=2.4.10
+Requires-Dist: torchani
+Requires-Dist: huggingface_hub
+Dynamic: license-file
+
+# ACEMD
+
+Python reimplementation of ACEMD
+
+## Documentation & Installation
+
+https://software.acellera.com/internal/acemd/

acemd-4.0.14/README.md

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+# ACEMD
+
+Python reimplementation of ACEMD
+
+## Documentation & Installation
+
+https://software.acellera.com/internal/acemd/

acemd-4.0.14/acemd/LICENSE

@@ -0,0 +1,52 @@
+Acellera Software Not-for-Profit License Agreement v1.2
+
+The software ("Software") has been developed by the contributing
+researchers from Acellera and made available through Acellera for your
+internal, non-profit research use.
+
+Acellera allows researchers at your institution to run, display, copy and
+modify Software on the following conditions:
+
+1. The Software remains at your institution and is not published, distributed,
+   or otherwise transferred or made available to other than institution employees
+   and students involved in research under your supervision.
+
+2. You agree to make results generated using Software available to other
+   academic researchers for non-profit research purposes. If you wish to obtain
+   Software for any commercial purposes, including fee-based service projects, you
+   will need to execute a separate licensing agreement with Acellera and pay a
+   fee. In that case please contact: info@acellera.com.
+
+3. You retain in Software and any modifications to Software, the copyright,
+   trademark, or other notices pertaining to Software as provided by Acellera.
+
+4. You provide Acellera with feedback on the use of the Software in your
+   research, and that Acellera are permitted to use any information you provide in
+   making changes to the Software. All bug reports and technical questions shall
+   be sent to the email address: info@acellera.com.
+
+5. You acknowledge that Acellera and its licensees may develop modifications to
+   Software that may be substantially similar to your modifications of Software,
+   and that Acellera and its licensees shall not be constrained in any way by you
+   in Acellera's or its licensees' use or management of such modifications. You
+   acknowledge the right of Acellera to prepare and publish modifications to
+   Software that may be substantially similar or functionally equivalent to your
+   modifications and improvements, and if you obtain patent protection for any
+   modification or improvement to Software you agree not to allege or enjoin
+   infringement of your patent by Acellera or by any of Acellera's licensees
+   obtaining modifications or improvements to Software from Acellera .
+
+6. You agree to acknowledge the contribution Software make to your research,
+   and cite appropriate references about the Software in your publications.
+
+7. Any risk associated with using the Software at your institution is with you
+   and your institution. Software is experimental in nature and is made available
+   as a research courtesy "AS IS," without obligation by Acellera to provide
+   accompanying services or support.
+
+8. You consent to allow usage information of this software to be sent
+   to Acellera.
+
+9. ACELLERA EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES REGARDING THE SOFTWARE,
+   WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES PERTAINING
+   TO NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

acemd-4.0.14/acemd/__init__.py

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+# (c) 2015-2024 Acellera Ltd http://www.acellera.com
+# All Rights Reserved
+# Distributed under HTMD Software License Agreement
+# No redistribution in whole or part
+#
+import os
+import logging.config
+import sys
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("acemd")
+except PackageNotFoundError:
+    pass
+
+
+dirname = os.path.dirname(__file__)
+
+try:
+    logging.config.fileConfig(
+        os.path.join(dirname, "logging.ini"), disable_existing_loggers=False
+    )
+except Exception:
+    print("acemd: Logging setup failed")
+
+from acemd.acemd import acemd, get_acemd_system
+
+_skip_checks = False
+if len(sys.argv) > 0 and sys.argv[0].endswith("acemd_register"):
+    _skip_checks = True
+if (
+    len(sys.argv) == 2
+    and sys.argv[0].endswith("acemd")
+    and sys.argv[1] in ("-h", "--help", "--version", "--license")
+):
+    _skip_checks = True
+
+if (
+    not _skip_checks  # Don't run when the user is executing acemd_register or acemd --help/license/version
+    and not os.getenv("CI")  # Don't run in CI
+    and not os.getenv("ACEMD_NONINTERACTIVE")  # Don't run in non-interactive mode
+    and not os.getenv("APPTAINER_CONTAINER")  # Don't run in Apptainer
+):
+    from acemd.versionwarnings import _check_for_updates, _print_news
+    from acemd.licensing import (
+        _is_registered,
+        _check_registration,
+        _check_license,
+        _print_license_file,
+        _send_telemetry,
+    )
+    import time
+
+    licensed = _check_license()
+
+    if not licensed:
+        # Don't send telemetry for licensed users
+        _send_telemetry("ACEMD", __version__)
+
+    _check_for_updates()
+    _print_news()
+
+    # Check if user has an ACEMD license. If not check if they are registered
+    if not licensed and (not _is_registered() or not _check_registration()):
+        _print_license_file()
+        print(
+            "By continuing to use ACEMD you are automatically accepting the above license agreement.\n"
+            "For commercial licenses please contact info@acellera.com\n"
+            "To remove the above license message for non-commercial purposes please register ACEMD by calling acemd_register from command line.\n"
+            "Resuming in 5 seconds..."
+        )
+        time.sleep(5)