dimer-builder-step 2026.6.30__tar.gz

dimer_builder_step-2026.6.30/AUTHORS.rst

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+Development Team
+----------------
+
+* Paul Saxe <psaxe@molssi.org> (Lead)
+* Why don't you join the team? Become a contributor!

dimer_builder_step-2026.6.30/CONTRIBUTING.rst

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+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/molssi-seamm/dimer_builder_step/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Dimer Builder Step could always use more documentation, whether as part of the
+official Dimer Builder Step docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/molssi-seamm/dimer_builder_step/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `dimer_builder_step` for local development.
+
+1. Fork the `dimer_builder_step` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/dimer_builder_step.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv dimer_builder_step
+    $ cd dimer_builder_step/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 dimer_builder_step tests
+    $ python setup.py test or py.test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
+   https://travis-ci.org/molssi-seamm/dimer_builder_step/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+    $ py.test tests.test_dimer_builder_step

dimer_builder_step-2026.6.30/HISTORY.rst

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+=======
+History
+=======
+
+2026.6.30 -- Initial release
+    * Generates sets of dimer (molecule-pair) configurations across a range of
+      separations and relative orientations, for building interaction-energy data
+      sets and training sets for machine-learned force fields.
+    * Two ways to provide the input structures:
+
+        - two sets of monomer conformers, which are assembled into dimers at
+          random relative orientations; or
+        - prepared complexes, each scanned along the axis between a "fixed" and a
+          "movable" group (taken from subsets if present, otherwise the last
+          molecule is movable and the rest are fixed).
+    * For each orientation, scans the center-to-center separation from just inside
+      the van der Waals contact distance out to a chosen maximum, with geometric
+      (default), linear, or explicit spacing.
+    * Records the scan geometry on every configuration as properties -- separation,
+      gap beyond contact, the approach-direction angles, and the movable group's
+      orientation angles -- and marks the two molecules as "fixed" and "movable"
+      subsets, so the pieces are easy to find downstream.
+    * Stores all the generated structures as conformers of a new system, named by
+      orientation and point (1/1, 1/2, ...) by default.

dimer_builder_step-2026.6.30/LICENSE

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+
+BSD 3-Clause License
+
+Copyright (c) 2026, Paul Saxe
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

dimer_builder_step-2026.6.30/MANIFEST.in

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+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+include requirements*
+include versioneer.py
+
+recursive-include dimer_builder_step/data *
+recursive-include tests *
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

dimer_builder_step-2026.6.30/PKG-INFO

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+Metadata-Version: 2.4
+Name: dimer_builder_step
+Version: 2026.6.30
+Summary: A SEAMM plug-in for Dimer Builder
+Home-page: https://github.com/molssi-seamm/dimer_builder_step
+Author: Paul Saxe
+Author-email: psaxe@molssi.org
+License: BSD-3-Clause
+Keywords: SEAMM,SEAMMplugin,flowchart
+Platform: Linux
+Platform: Mac OS-X
+Platform: Unix
+Platform: Windows
+Classifier: Environment :: Plugins
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: seamm
+Requires-Dist: seamm-util
+Requires-Dist: seamm-widgets
+Requires-Dist: molsystem
+Requires-Dist: mendeleev
+Requires-Dist: numpy
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: requires-dist
+Dynamic: summary
+
+===========================
+SEAMM Dimer Builder Plug-in
+===========================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/dimer_builder_step
+   :target: https://github.com/molssi-seamm/dimer_builder_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/dimer_builder_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/dimer_builder_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/dimer_builder_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/dimer_builder_step
+   :alt: Code Coverage
+
+.. image:: https://github.com/molssi-seamm/dimer_builder_step/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/dimer_builder_step/security/code-scanning
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/dimer_builder_step/workflows/Release/badge.svg
+   :target: https://molssi-seamm.github.io/dimer_builder_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/v/dimer_builder_step.svg
+   :target: https://pypi.python.org/pypi/dimer_builder_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for Dimer Builder
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/dimer_builder_step/index.html
+* Code: https://github.com/molssi-seamm/dimer_builder_step
+
+Features
+--------
+
+* Please edit this section!
+
+Acknowledgements
+----------------
+
+This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
+is based on the excellent Cookiecutter_.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
+
+Developed by the Molecular Sciences Software Institute (MolSSI_),
+which receives funding from the `National Science Foundation`_ under
+award CHE-2136142.
+
+.. _MolSSI: https://molssi.org
+.. _`National Science Foundation`: https://www.nsf.gov
+
+
+=======
+History
+=======
+
+2026.6.30 -- Initial release
+    * Generates sets of dimer (molecule-pair) configurations across a range of
+      separations and relative orientations, for building interaction-energy data
+      sets and training sets for machine-learned force fields.
+    * Two ways to provide the input structures:
+
+        - two sets of monomer conformers, which are assembled into dimers at
+          random relative orientations; or
+        - prepared complexes, each scanned along the axis between a "fixed" and a
+          "movable" group (taken from subsets if present, otherwise the last
+          molecule is movable and the rest are fixed).
+    * For each orientation, scans the center-to-center separation from just inside
+      the van der Waals contact distance out to a chosen maximum, with geometric
+      (default), linear, or explicit spacing.
+    * Records the scan geometry on every configuration as properties -- separation,
+      gap beyond contact, the approach-direction angles, and the movable group's
+      orientation angles -- and marks the two molecules as "fixed" and "movable"
+      subsets, so the pieces are easy to find downstream.
+    * Stores all the generated structures as conformers of a new system, named by
+      orientation and point (1/1, 1/2, ...) by default.

dimer_builder_step-2026.6.30/README.rst

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+===========================
+SEAMM Dimer Builder Plug-in
+===========================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/dimer_builder_step
+   :target: https://github.com/molssi-seamm/dimer_builder_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/dimer_builder_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/dimer_builder_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/dimer_builder_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/dimer_builder_step
+   :alt: Code Coverage
+
+.. image:: https://github.com/molssi-seamm/dimer_builder_step/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/dimer_builder_step/security/code-scanning
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/dimer_builder_step/workflows/Release/badge.svg
+   :target: https://molssi-seamm.github.io/dimer_builder_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/v/dimer_builder_step.svg
+   :target: https://pypi.python.org/pypi/dimer_builder_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for Dimer Builder
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/dimer_builder_step/index.html
+* Code: https://github.com/molssi-seamm/dimer_builder_step
+
+Features
+--------
+
+* Please edit this section!
+
+Acknowledgements
+----------------
+
+This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
+is based on the excellent Cookiecutter_.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
+
+Developed by the Molecular Sciences Software Institute (MolSSI_),
+which receives funding from the `National Science Foundation`_ under
+award CHE-2136142.
+
+.. _MolSSI: https://molssi.org
+.. _`National Science Foundation`: https://www.nsf.gov

dimer_builder_step-2026.6.30/dimer_builder_step/__init__.py

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+# -*- coding: utf-8 -*-
+
+"""
+dimer_builder_step
+A SEAMM plug-in for Dimer Builder
+"""
+
+# Bring up the classes so that they appear to be directly in
+# the dimer_builder_step package.
+
+from .dimer_builder import DimerBuilder  # noqa: F401, E501
+from .dimer_builder_parameters import DimerBuilderParameters  # noqa: F401, E501
+from .dimer_builder_step import DimerBuilderStep  # noqa: F401, E501
+from .tk_dimer_builder import TkDimerBuilder  # noqa: F401, E501
+
+from .metadata import metadata  # noqa: F401
+
+# Handle versioneer
+from ._version import get_versions
+
+__author__ = "Paul Saxe"
+__email__ = "psaxe@molssi.org"
+versions = get_versions()
+__version__ = versions["version"]
+__git_revision__ = versions["full-revisionid"]
+del get_versions, versions

dimer_builder_step-2026.6.30/dimer_builder_step/_version.py

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+
+# This file was generated by 'versioneer.py' (0.18) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2026-06-30T21:41:48-0400",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "0f7ee6983409f7564c08ee718371c490bb17d613",
+ "version": "2026.6.30"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

dimer_builder_step-2026.6.30/dimer_builder_step/data/properties.csv

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+Property,Type,Units,Description,URL
+dimer separation#DimerBuilder#scan,float,Å,The center-to-center separation of the fixed and movable groups,
+dimer gap#DimerBuilder#scan,float,Å,The gap beyond the van der Waals contact distance (negative is overlap),
+dimer orientation#DimerBuilder#scan,int,,The index of the random relative orientation this configuration belongs to,
+approach theta#DimerBuilder#scan,float,degree,The polar angle of the fixed-to-movable displacement vector,
+approach phi#DimerBuilder#scan,float,degree,The azimuthal angle of the fixed-to-movable displacement vector,
+movable alpha#DimerBuilder#scan,float,degree,The first ZYZ Euler angle of the movable group relative to its principal axes,
+movable beta#DimerBuilder#scan,float,degree,The second ZYZ Euler angle of the movable group relative to its principal axes,
+movable gamma#DimerBuilder#scan,float,degree,The third ZYZ Euler angle of the movable group relative to its principal axes,

dimer_builder_step-2026.6.30/dimer_builder_step/data/references.bib

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+This is an initial library of BibTex references for the dimer_builder_step plug-in for SEAMM,
+generated automatically by the cookiecutter. You may wish to edit the first entry to correct some
+of the information.
+
+Add other references to the end of the file and add code in the plug-in to cite the references as
+appropriate. This is done with code like this:
+
+        self.references.cite(
+            raw=self._bibliography['doi:10.1002/jcc.21224'],
+            alias='packmol',
+            module='packmol_step',
+            level=1,
+            note='The principle PACKMOL citation.'
+        )
+
+which is typically in the run() method of the plug-in.
+
+The base node class in SEAMM automatically reads this list of references into a dictionary in
+self._bibliography with the key being the key of the BibTex entry -- usually the name on the
+first line of the entry after the 'article' or 'misc' (for software) keyword.
+
+See the documentation for the Reference Handler for the other arguments to cite().
+
+# End of initial comments #
+
+# This is the citation for this plug-in, generated and used automatically.
+# You might need to edit the author, address, etc. The month, year and version fields
+# are automatically filled in with information about current version of the plug-in.
+# This is handled in seamm/nody.py, the run() method.
+
+@Misc{dimer_builder_step,
+	author = {Paul Saxe},
+	title = {Dimer Builder plug-in for SEAMM},
+	month = {$month},
+	year = {$year},
+	organization = {molssi-seamm},
+	url = {https://github.com/molssi-seamm/dimer_builder_step },
+	address = {USA},
+	version = {$version}
+}
+
+# mendeleev provides the van der Waals radii used to estimate the contact
+# distance for the radial scan.
+
+@Misc{mendeleev,
+	author = {Mentel, Łukasz},
+	title = {mendeleev -- A Python resource for properties of chemical elements, ions and isotopes},
+	year = {2014},
+	url = {https://github.com/lmmentel/mendeleev}
+}