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‎.gitignore

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ChimAARON*
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build
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ChimAARON*
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build
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*.pxd
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*.pyc
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*.egg*

‎ChimAARONX.png

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‎README.md

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### Chimera
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The Chimera version of ChimAARON can be found on the [Chimera branch](https://github.com/QChASM/ChimAARON/tree/Chimera).
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### ChimeraX Daily
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### ChimeraX Daily
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For the latest features and bugs, go to the [development branch](https://github.com/QChASM/ChimAARON/tree/dev)

‎SEQCROW.png

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‎bundle_info.xml

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<BundleInfo name="SEQCROW"
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customInit="true"
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minSessionVersion="1"
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maxSessionVersion="1"
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package="SEQCROW"
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purePython="true"
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version="0.1">
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<Author>QChASM</Author>
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<Email>[email protected]</Email>
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<URL>catalysttrends.org</URL>
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<License>license.txt</License>
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<Synopsis>Structure Editing and Quantum Chemical Representation and Organization for Workflows</Synopsis>
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<Description>An AaronTools-based plugin for ChimeraX.
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SEQCROW adds the following to ChimeraX:
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I/O:
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read XYZ, Gaussian COM, Gaussian LOG files, and ORCA output files
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save models to XYZ files
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tools:
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AaronTools
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Add to Personal Library - add substituents, ligands, or rings to your personal AaronTools library
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Browse AaronTools - browse substituents, ligands, and rings in the AaronTools library
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Process Thermochemistry - compute thermal corrections for models with vibrational mode information
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Structure Modification - modify your structure using pieces from the AaronTools library
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Visualize Normal Modes - display normal modes for models with vibrational mode information as vectors or an animation
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SEQCROW
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Managed Models - restore models opened through SEQCROW to their original state
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Build QM Input - build Gaussian input file
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selectors:
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tm - select all transition metals
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presets:
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ball-stick-endcap - all non-H atoms are represented as balls and sticks; H atoms are represented as sticks/endcaps
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index labels - label each atom with its index (1-indexed)
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sticks - all atoms are represented as sticks/endcaps
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</Description>
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<Dependencies>
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<Dependency name="ChimeraX-Core" version=">=0.93"/>
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<Dependency name="scipy"/>
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<Dependency name="numpy"/>
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</Dependencies>
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<Categories>
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<Category name="General"/>
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<Category name="Input/Output"/>
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</Categories>
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<Managers>
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<Manager name="filereader_manager" uiOnly="true"/>
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<Manager name="seqcrow_ordered_selection_manager" uiOnly="true"/>
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</Managers>
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<Providers manager="data formats">
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<Provider name="Gaussian input file"
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category="Molecular structure"
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suffixes=".com,.gjf"
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encoding="utf-8"
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nicknames="com"
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synopsis="Gaussian input file"/>
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<Provider name="Gaussian output file"
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category="Molecular structure"
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suffixes=".log"
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encoding="utf-8"
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nicknames="log"
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synopsis="Gaussian output file"/>
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<Provider name="ORCA output file"
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category="Molecular structure"
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suffixes=".out"
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encoding="utf-8"
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nicknames="out"
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synopsis="ORCA output file"/>
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<Provider name="XYZ file"
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category="Molecular structure"
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suffixes=".xyz"
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encoding="utf-8"
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nicknames="xyz"
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synopsis="XYZ coordinate file"/>
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</Providers>
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<Providers manager="open command">
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<Provider name="Gaussian input file" want_path="true"/>
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<Provider name="Gaussian output file" want_path="true"/>
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<Provider name="ORCA output file" want_path="true"/>
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<Provider name="XYZ file" want_path="true"/>
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</Providers>
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<!--we can save Gaussian input files, but not with the save command-->
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<Providers manager="save command">
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<Provider name="XYZ file"/>
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</Providers>
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<Classifiers>
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<PythonClassifier>Development Status :: 2 - Pre-Alpha</PythonClassifier>
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<PythonClassifier>License :: OSI Approved :: GNU General Public License v3 (GPLv3)</PythonClassifier>
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<PythonClassifier>Environment :: Win32 (MS Windows)</PythonClassifier>
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<PythonClassifier>Environment :: MacOS X</PythonClassifier>
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<PythonClassifier>Environment :: X11 Applications :: Qt</PythonClassifier>
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<PythonClassifier>Framework :: ChimeraX</PythonClassifier>
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<PythonClassifier>Intended Audience :: Science/Research</PythonClassifier>
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<PythonClassifier>Natural Language :: English</PythonClassifier>
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<PythonClassifier>Operating System :: MacOS</PythonClassifier>
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<PythonClassifier>Operating System :: Microsoft :: Windows</PythonClassifier>
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<PythonClassifier>Operating System :: POSIX :: Linux</PythonClassifier>
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<PythonClassifier>Programming Language :: Python :: 3</PythonClassifier>
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<PythonClassifier>Topic :: Scientific/Engineering :: Chemistry</PythonClassifier>
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<PythonClassifier>Topic :: Scientific/Engineering :: Visualization</PythonClassifier>
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<!-- TODO: move tools to appropriate menus -->
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<!--NOTE:
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including my own Bundle line will prevent anything after it from being loaded
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ChimeraX's devel build
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ChimeraXClassifier>ChimeraX :: Bundle :: General,Input/Output,Structure Editing,External Program :: 1,1 :: SEQCROW :: ChimAARON,SEQCRO,SEQCROW :: true</ChimeraXClassifier-->
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<ChimeraXClassifier>ChimeraX :: Tool :: Build QM Input :: SEQCROW :: Create Gaussian input file</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Tool :: Structure Modification :: AaronTools :: Modify substituents, swap ligands, and close rings</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Tool :: Browse AaronTools Libraries :: AaronTools :: Browse the AaronTools ligand, substituent, and ring libraries"</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Tool :: Process QM Thermochemistry :: AaronTools :: Compute the free energy of a molecule with frequency data</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Tool :: Managed Models :: SEQCROW :: see models managed by SEQCROW</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Tool :: Add to Personal Library :: AaronTools :: Add to your personal ligand, substituent, and ring libraries</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Tool :: Visualize Normal Modes :: AaronTools :: Visualize normal modes from a Gaussian output file as displacement vectors or as an animation</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Selector :: tm :: Transition metals</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: DataFormat :: XYZ :: XYZ :: Molecular structure :: .xyz :: :: :: :: :: XYZ Format :: utf-8</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Open :: XYZ :: AaronTools :: false :: coordsets:Bool</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: DataFormat :: COM :: COM :: Molecular structure :: .com,.gjf :: :: :: :: :: Gaussian input file :: utf-8</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Open :: COM :: COM ::</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: DataFormat :: LOG :: LOG :: Molecular structure :: .log :: :: :: :: :: Gaussian output file :: utf-8</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Open :: LOG :: LOG :: false :: coordsets:Bool</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: DataFormat :: OUT :: OUT :: Molecular structure :: .out :: :: :: :: :: ORCA output file :: utf-8</ChimeraXClassifier>
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<ChimeraXClassifier>ChimeraX :: Open :: OUT :: OUT :: false :: coordsets:Bool</ChimeraXClassifier>
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</Classifiers>
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</BundleInfo>
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‎dist/ChimAARON-0.1-py3-none-any.whl

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‎dist/ChimAARON-0.1.tar.gz

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‎dist/SEQCROW-0.1-py3-none-any.whl

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‎LICENSE ‎license.txt

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‎old_setup.py

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#this is no longer used
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#all info should be in bundle_info.xml
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"""
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python3 setup.py sdist bdist_wheel
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cp dist/SEQCROW-0.1-py3-none-any.whl $desktop/
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"""
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from setuptools import setup, find_packages
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import os
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synopsis = "Structure Editing and Quantum Chemical Representation and Organization"
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description = """
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An AaronTools-based plugin for ChimeraX.
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17+
SEQCROW adds the following to ChimeraX:
18+
I/O:
19+
read XYZ, Gaussian COM, Gaussian LOG files, and Orca output files
20+
save models to XYZ files
21+
22+
tools:
23+
AaronTools
24+
Add to Personal Library - add substituents, ligands, or rings to your personal AaronTools library
25+
Browse AaronTools - browse substituents, ligands, and rings in the AaronTools library
26+
Process Thermochemistry - compute thermal corrections for models with vibrational mode information
27+
Structure Modification - modify your structure using pieces from the AaronTools library
28+
Visualize Normal Modes - display normal modes for models with vibrational mode information as vectors or an animation
29+
30+
SEQCROW
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Managed Models - restore models opened through SEQCROW to their original state
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selectors:
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tm - select all transition metals
35+
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presets:
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ball-stick-endcap - all non-H atoms are represented as balls and sticks; H atoms are represented as sticks/endcaps
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index labels - label each atom with its index (1-indexed)
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sticks - all atoms are represented as sticks/endcaps
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"""
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# ChimeraX classifiers are put in the code as comments
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# go find those comments so I don't have to remember to update setup.py
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chimerax_classifiers = []
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xml_mods = {}
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d = os.path.dirname(os.path.realpath(__file__))
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src_dir = "src"
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ext_mods = []
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#pure python hopefully works everywhere
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#windows users may have to set USERPROFILE environment variable
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environments = [
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"Environment :: MacOS X :: Aqua",
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"Environment :: Win32 (MS Windows)",
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"Environment :: X11 Applications",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows :: Windows 10",
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"Operating System :: POSIX :: Linux",
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]
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setup(
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name="SEQCROW",
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version="0.1",
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description=synopsis,
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long_description=description,
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author="QChASM",
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author_email="[email protected]",
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url="https://github.com/QChASM",
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python_requires=">= 3.5",
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package_dir={
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"SEQCROW": src_dir,
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},
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packages=[
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"SEQCROW",
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"SEQCROW.tools",
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"SEQCROW.managers",
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],
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ext_modules=ext_mods,
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install_requires=[
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#TODO: add AaronTools (AaronTools should require scipy)
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"ChimeraX-Core >= 0.93",
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"scipy",
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"numpy",
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],
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classifiers=[
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# https://pypi.python.org/pypi?%3Aaction=list_classifiers
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# https://www.rbvi.ucsf.edu/chimerax/docs/devel/tutorials/bundle_info.html#chimerax-metadata-classifiers
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"Development Status :: 2 - Pre-Alpha", # TODO: update as appropriate
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"Framework :: ChimeraX",
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"Intended Audience :: Science/Research",
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"License :: Free for non-commercial use",
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"Programming Language :: Python :: 3",
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"Topic :: Scientific/Engineering :: Visualization",
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"Topic :: Scientific/Engineering :: Chemistry",
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"ChimeraX :: Bundle :: General,Input/Output,Structure Editing,External Program :: 1,1 :: SEQCROW :: ChimAARON,SEQCRO,SEQCROW :: true ",
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"ChimeraX :: Tool :: Build QM Input :: SEQCROW :: Create input file for Gaussian or Orca",
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"ChimeraX :: Tool :: Structure Modification :: AaronTools :: Modify substituents, swap ligands, and close rings, all for the one-time fee of an arm and a leg!",
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"ChimeraX :: Tool :: Browse AaronTools Libraries :: AaronTools :: Browse the AaronTools ligand, substituent, and ring libraries",
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"ChimeraX :: Tool :: Process Thermochemistry :: AaronTools :: Compute the free energy of a molecule with frequency data",
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"ChimeraX :: Tool :: Managed Models :: SEQCROW :: see models managed by SEQCROW",
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"ChimeraX :: Tool :: Add to Personal Library :: AaronTools :: Add to your personal ligand, substituent, and ring libraries",
102+
"ChimeraX :: Tool :: Visualize Normal Modes :: AaronTools :: Visualize normal modes from a Gaussian output file as displacement vectors or as an animation",
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"ChimeraX :: DataFormat :: XYZ :: XYZ :: Molecular structure :: .xyz :: :: :: :: :: XYZ Format :: utf-8",
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"ChimeraX :: Open :: XYZ :: AaronTools :: false :: coordsets:Bool",
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"ChimeraX :: DataFormat :: COM :: Gaussian input file :: Molecular structure :: .com,.gjf :: :: :: :: :: Gaussian input file :: utf-8",
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"ChimeraX :: Open :: COM :: Gaussian input file ::",
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"ChimeraX :: DataFormat :: LOG :: Gaussian output file :: Molecular structure :: .log :: :: :: :: :: Gaussian output file :: utf-8",
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"ChimeraX :: Open :: LOG :: Gaussian output file :: false :: coordsets:Bool",
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"ChimeraX :: DataFormat :: OUT :: Orca output file :: Molecular structure :: .out :: :: :: :: :: Orca output file :: utf-8",
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"ChimeraX :: Open :: OUT :: Orca output file :: false :: coordsets:Bool",
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"ChimeraX :: Manager :: filereader_manager",
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"ChimeraX :: Manager :: seqcrow_ordered_selection_manager",
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] + environments,
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)

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