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Charlles Abreu
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Changes plugin name (#5)
* Changed file content * Changed file names * Fixed bugs
1 parent b9c32cf commit fb8e284

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-101
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CMakeLists.txt

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#---------------------------------------------------
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# OpenMM CustomCPPForces Plugin
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# OpenMM OpenMMCPPForces Plugin
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#----------------------------------------------------
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CMAKE_MINIMUM_REQUIRED(VERSION 3.17)
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PROJECT(OpenMMCustomCPPForces VERSION 0.0.0)
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PROJECT(OpenMMCPPForces VERSION 0.0.0)
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IF(DEFINED ENV{CONDA_PREFIX})
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SET(OPENMM_DIR $ENV{CONDA_PREFIX} CACHE PATH "Where OpenMM is installed")
@@ -35,14 +35,14 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
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# The source is organized into subdirectories, but we handle them all from
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# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
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SET(PLUGIN_SOURCE_SUBDIRS customcppforces serialization)
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SET(PLUGIN_SOURCE_SUBDIRS openmmcppforces serialization)
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# Set the library name
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SET(PLUGIN_LIBRARY_NAME CustomCPPForces)
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SET(PLUGIN_LIBRARY_NAME OpenMMCPPForces)
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SET(SHARED_CUSTOM_CPP_FORCES_TARGET ${PLUGIN_LIBRARY_NAME})
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# These are all the places to search for header files which are to be part of the API.
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SET(API_INCLUDE_DIRS "customcppforces/include")
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SET(API_INCLUDE_DIRS "openmmcppforces/include")
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# Locate header files.
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SET(API_INCLUDE_FILES)
@@ -75,7 +75,7 @@ TARGET_LINK_LIBRARIES(${SHARED_CUSTOM_CPP_FORCES_TARGET} OpenMM)
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INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_CUSTOM_CPP_FORCES_TARGET})
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# install headers
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FILE(GLOB API_ONLY_INCLUDE_FILES "customcppforces/include/*.h")
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FILE(GLOB API_ONLY_INCLUDE_FILES "openmmcppforces/include/*.h")
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INSTALL (FILES ${API_ONLY_INCLUDE_FILES} DESTINATION include)
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# Enable testing

README.md

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CustomCPPForces Plugin
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OpenMMCPPForces Plugin
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========================
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[![Linux](https://github.com/craabreu/customcppforces/actions/workflows/Linux.yml/badge.svg)](https://github.com/craabreu/customcppforces/actions/workflows/Linux.yml)
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[![MacOS](https://github.com/craabreu/customcppforces/actions/workflows/MacOS.yml/badge.svg)](https://github.com/craabreu/customcppforces/actions/workflows/MacOS.yml)
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[![Doc](https://github.com/craabreu/customcppforces/actions/workflows/Doc.yml/badge.svg)](https://github.com/craabreu/customcppforces/actions/workflows/Doc.yml)
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[![Linux](https://github.com/craabreu/openmm-cpp-forces/actions/workflows/Linux.yml/badge.svg)](https://github.com/craabreu/openmm-cpp-forces/actions/workflows/Linux.yml)
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[![MacOS](https://github.com/craabreu/openmm-cpp-forces/actions/workflows/MacOS.yml/badge.svg)](https://github.com/craabreu/openmm-cpp-forces/actions/workflows/MacOS.yml)
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[![Doc](https://github.com/craabreu/openmm-cpp-forces/actions/workflows/Doc.yml/badge.svg)](https://github.com/craabreu/openmm-cpp-forces/actions/workflows/Doc.yml)
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[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
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This [OpenMM] plugin is a laboratory for low-level code implementation.
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Documentation
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=============
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Documentation for this plugin is available at [Github Pages](https://craabreu.github.io/customcppforces/).
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Documentation for this plugin is available at [Github Pages](https://craabreu.github.io/openmm-cpp-forces/).
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Installing from Source
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======================
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```py
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import openmm as mm
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import customcppforces as nbs
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import openmmcppforces as nbs
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system = mm.System()
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force = nbs.SlicedNonbondedForce(2)
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system.addForce(force)

devtools/conda-recipes/anaconda/meta.yaml

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{% set plugin_version = environ['PLUGIN_VERSION'].lstrip('v') %}
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package:
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name: customcppforces
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name: openmmcppforces
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version: {{ plugin_version }}
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source:
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test:
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imports:
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- customcppforces
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- openmmcppforces
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about:
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home: https://github.com/craabreu/customcppforces
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home: https://github.com/craabreu/openmm-cpp-forces
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summary: Platform-agnostic OpenMM Forces
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license: MIT
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license_file: LICENSE.md
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doc_url: https://craabreu.github.io/customcppforces
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dev_url: https://github.com/craabreu/customcppforces
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doc_url: https://craabreu.github.io/openmm-cpp-forces
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dev_url: https://github.com/craabreu/openmm-cpp-forces
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extra:
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recipe-maintainers:

docs/conf.py

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# -*- coding: utf-8 -*-
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from __future__ import unicode_literals
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import os
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import customcppforces
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import openmmcppforces
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import openmm
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])
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create_rst_file(customcppforces.ConcertedRMSDForce)
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create_rst_file(openmmcppforces.ConcertedRMSDForce)
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extensions = [
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'sphinx.ext.autodoc',
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source_suffix = '.rst'
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master_doc = 'index'
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project = 'OpenMM Custom CPP Forces'
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project = 'OpenMM OpenMM CPP Forces'
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copyright = ('2024, Charlles Abreu. Project based on OpenMM')
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author = 'Charlles Abreu'
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pygments_style = 'trac'
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templates_path = ['.']
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extlinks = {
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'issue': ('https://github.com/craabreu/customcppforces/issues/%s', '#'),
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'pr': ('https://github.com/craabreu/customcppforces/pull/%s', 'PR #'),
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'issue': ('https://github.com/craabreu/openmm-cpp-forces/issues/%s', '#'),
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'pr': ('https://github.com/craabreu/openmm-cpp-forces/pull/%s', 'PR #'),
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}
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# on_rtd is whether we are on readthedocs.org
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'logo_name': True,
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'github_button': False,
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'github_user': 'craabreu',
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'github_repo': 'customcppforces',
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'github_repo': 'openmmcppforces',
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}
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html_sidebars = {
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'**': ['about.html', 'globaltoc.html', 'searchbox.html'],

docs/contributing.rst

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Bug reports
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===========
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When `reporting a bug <https://github.com/craabreu/customcppforces/issues>`_ please include:
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When `reporting a bug <https://github.com/craabreu/openmm-cpp-forces/issues>`_ please include:
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* Your operating system name and version.
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* Any details about your local setup that might be helpful in troubleshooting.
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Documentation improvements
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==========================
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CustomCPPForces could always use more documentation, whether as part of the
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official CustomCPPForces docs, in docstrings, or even on the web in blog posts,
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OpenMMCPPForces could always use more documentation, whether as part of the
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official OpenMMCPPForces docs, in docstrings, or even on the web in blog posts,
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articles, and such.
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Feature requests and feedback
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=============================
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The best way to send feedback is to file an issue at https://github.com/craabreu/customcppforces/issues.
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The best way to send feedback is to file an issue at https://github.com/craabreu/openmm-cpp-forces/issues.
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If you are proposing a feature:
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Development
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===========
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To set up `customcppforces` for local development:
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To set up `openmmcppforces` for local development:
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1. Fork `customcppforces <https://github.com/craabreu/customcppforces>`_
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1. Fork `openmmcppforces <https://github.com/craabreu/openmm-cpp-forces>`_
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(look for the "Fork" button).
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2. Clone your fork locally::
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git clone git@github.com:your_name_here/customcppforces.git
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git clone git@github.com:your_name_here/openmmcppforces.git
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3. Create a branch for local development::
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4. Add yourself to ``docs/authors.rst``.
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.. [1] If you don't have all the necessary python versions available locally you can rely on Github Actions - it will
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`run the tests <https://travis-ci.org/craabreu/customcppforces/pull_requests>`_ for each change you add in the pull request.
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`run the tests <https://travis-ci.org/craabreu/openmm-cpp-forces/pull_requests>`_ for each change you add in the pull request.

docs/index.rst

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========================
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CustomCPPForces
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OpenMMCPPForces
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========================
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.. image:: https://badgen.net/badge/icon/github?icon=github&label
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:target: https://github.com/craabreu/customcppforces
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:target: https://github.com/craabreu/openmm-cpp-forces
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.. image:: https://img.shields.io/badge/License-MIT-green.svg
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:target: https://github.com/craabreu/customcppforces/blob/main/LICENSE.md
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:target: https://github.com/craabreu/openmm-cpp-forces/blob/main/LICENSE.md
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.. raw:: html
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<a class="github-button" href="https://github.com/craabreu/customcppforces" data-show-count="true" aria-label="Star craabreu/customcppforces on GitHub">Star</a>
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<a class="github-button" href="https://github.com/craabreu/openmm-cpp-forces" data-show-count="true" aria-label="Star craabreu/openmm-cpp-forces on GitHub">Star</a>
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Contents

docs/pythonapi/index.rst

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.. code-block:: python
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import openmm as mm
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import customcppforces
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import openmmcppforces
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force = customcppforces.ConcertedRMSDForce()
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force = openmmcppforces.ConcertedRMSDForce()
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This is the implemented subclass of :OpenMM:`Force`:
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.. testsetup::
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from customcppforces import *
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from openmmcppforces import *

customcppforces/include/ConcertedRMSDForce.h renamed to openmmcppforces/include/ConcertedRMSDForce.h

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#define OPENMM_CONCERTEDRMSDFORCE_H_
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/* -------------------------------------------------------------------------- *
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* OpenMM Custom CPP Forces *
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* ======================== *
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* OpenMM CPP Forces *
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* ================= *
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* *
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* A plugin for distributing OpenMM CustomCPPForce instances *
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* A plugin for distributing platform-agnostic OpenMM Forces *
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* *
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* Copyright (c) 2024 Charlles Abreu *
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* https://github.com/craabreu/customcppforces *
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* https://github.com/craabreu/openmm-cpp-forces *
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* -------------------------------------------------------------------------- */
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#include "internal/windowsExportCustomCPPForces.h"
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#include "internal/windowsExportOpenMMCPPForces.h"
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#include "openmm/Force.h"
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#include "openmm/Vec3.h"
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using namespace OpenMM;
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using namespace std;
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namespace CustomCPPForces {
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namespace OpenMMCPPForces {
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/**
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* This is a force whose energy equals a special type of root mean squared deviation
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vector<vector<int>> groups;
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};
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} // namespace CustomCPPForces
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} // namespace OpenMMCPPForces
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#endif /*OPENMM_CONCERTEDRMSDFORCE_H_*/

customcppforces/include/internal/ConcertedRMSDForceImpl.h renamed to openmmcppforces/include/internal/ConcertedRMSDForceImpl.h

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#define OPENMM_CONCERTEDRMSDFORCEIMPL_H_
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/* -------------------------------------------------------------------------- *
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* OpenMM Custom CPP Forces *
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* ======================== *
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* OpenMM CPP Forces *
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* ================= *
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* *
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* A plugin for distributing OpenMM CustomCPPForce instances *
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* A plugin for distributing platform-agnostic OpenMM Forces *
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* *
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* Copyright (c) 2024 Charlles Abreu *
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* https://github.com/craabreu/customcppforces *
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* https://github.com/craabreu/openmm-cpp-forces *
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* -------------------------------------------------------------------------- */
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#include "ConcertedRMSDForce.h"
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using namespace OpenMM;
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using namespace std;
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namespace CustomCPPForces {
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namespace OpenMMCPPForces {
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/**
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* This is the internal implementation of ConcertedRMSDForce.
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vector<Vec3> referencePos;
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};
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} // namespace CustomCPPForces
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} // namespace OpenMMCPPForces
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#endif /*OPENMM_CONCERTEDRMSDFORCEIMPL_H_*/

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