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_build/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 81cbf3a88fcf36e1f0829019d8b2d3c6
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_build/_sources/index.rst.txt

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+.. maize-biosimspace documentation master file, created by
+   sphinx-quickstart on Wed Mar  8 17:24:58 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+maize-biosimspace
+=================
+*maize* is a graph-based workflow manager for computational chemistry pipelines. This repository contains a namespace package providing BioSimSpace extensions for *maize*. You can find the core maize documentation `here <https://molecularai.github.io/maize>`_.
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: Examples
+
+   production-md
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: Reference
+
+   steps/index
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: Core
+
+   Steps <https://molecularai.github.io/maize/docs/steps>
+   Maize <https://molecularai.github.io/maize>
+
+Installation
+------------
+To install, simply clone this repository and run:
+
+.. code-block:: bash
+
+   mamba env create -f env-users.yml
+   mamba activate maize-biosimspace
+   pip install --no-deps ./
+
+If you want to keep up-to-date with the latest changes to the core, clone `maize <https://github.com/MolecularAI/maize>`_, switch to the directory, and run (in the same conda environment):
+
+.. code-block:: bash
+
+   pip install --no-deps ./
+
+If you plan on developing, you should use ``env-dev.yml`` instead and use the ``-e`` flag for ``pip``.
+
+Configuration
+-------------
+Each step documentation will contain information on how to setup and run the node, as well as install the required dependencies. Dependencies can be managed in several ways, depending on the node and workflow you are running:
+
+* Through a ``module`` system:
+
+  Specify a module providing an executable in the ``config.toml`` (see `Configuring workflows <https://molecularai.github.io/maize/docs/userguide.html#config-workflow>`_). This module will then be loaded in the process running the node.
+
+* With a separate python environment:
+
+  Some nodes will require custom python environments that are likely to be incompatible with the other environments. In those cases, the node process can be spawned in a custom environment. Note that this environment must still contain *maize*.
+
+* By specifying the executable location and possibly script interpreter. This can also be accomplished using ``config.toml`` (see `Configuring workflows <https://molecularai.github.io/maize/docs/userguide.html#config-workflow>`_).
+
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

_build/_sources/production-md.rst.txt

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+Production MD
+==============
+
+An example of a production molecular dynamics workflow using BioSimSpace Maize nodes:
+
+.. code-block:: python
+
+    """Run production Molecular Dynamics using PMEMD.CUDA through BioSimSpace."""
+
+    from pathlib import Path
+
+    from maize.core.workflow import Workflow
+    from maize.steps.exs.biosimspace import ProductionPmemdCuda
+    from maize.steps.io import LoadData, Return
+    from maize.utilities.execution import JobResourceConfig
+
+    # Build the graph
+    flow = Workflow(name="Prod_BSS_AMBER_Test", cleanup_temp=False, level="debug")
+
+    # Add the nodes
+    load_sys = flow.add(LoadData[list[Path]])
+    prod_pmemd = flow.add(
+        ProductionPmemdCuda,
+        name="Production_Amber",
+        parameters={
+            "runtime": 1.0, # ns
+        },
+    )
+    retu = flow.add(Return[list[Path]])
+
+    # Set parameters
+    load_sys.data.set(
+        [
+            Path(
+                "< path to complex.prm7>" # CHANGEME
+            ),
+            Path(
+                "< path to complex.rst7>" # CHANGEME
+            ),
+        ]
+    )
+
+    # Connect the nodes
+    flow.connect(load_sys.out, prod_pmemd.inp)
+    flow.connect(prod_pmemd.out, retu.inp)
+
+    # Check and run!
+    flow.check()
+    flow.visualize()
+    flow.execute()
+
+    mols = retu.get()
+
+    # Load a BioSimSpace system from the returned paths
+    import BioSimSpace as BSS
+
+    sys = BSS.IO.readMolecules([str(mols[0]), str(mols[1])])
+    print(40 * "#")
+    print(sys)
+    # In reality, you would do something here...
+

_build/_sources/steps/biosimspace.rst.txt

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+BioSimSpace
+==================
+
+.. automodule:: maize.steps.exs.biosimspace
+   :members:
+   :no-value:
+   :noindex:
+   :exclude-members: full_timer, run_timer, logger, target_dir, work_dir, run, build
+   :inherited-members: Node, Component

_build/_sources/steps/index.rst.txt

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+.. _custom-steps:
+
+Steps
+=====
+This is the documentation of all contained steps.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Steps
+
+   biosimspace