bundle_info.xml

<!--
ChimeraX bundle names must start with "ChimeraX-"
to avoid clashes with package names in pypi.python.org.
When uploaded to the ChimeraX toolshed, the bundle
will be displayed without the ChimeraX- prefix.
-->

<BundleInfo name="ChimeraX-check"
	    version="0.11" package="chimerax.check1"
  	    minSessionVersion="1" maxSessionVersion="1">

  <!-- Additional information about bundle source -->
  <Author>Aryan Tajmir Riahi</Author>
  <Email>artajmir3@gmail.come</Email>
  <URL></URL>

  <!-- Synopsis is a one-line description
       Description is a full multi-line description -->
  <Synopsis>An implementation of two Optimal Transport based density map alignment methods</Synopsis>
  <Description>Based on the methods introduced in the following papers:

    Aryan Tajmir Riahi, Geoffrey Woollard, Frédéric Poitevin, Anne Condon, and Khanh Dao Duc. "AlignOT: An optimal transport based algorithm for fast 3D alignment with applications to cryogenic electron microscopy density maps." IEEE/ACM Transactions on Computational Biology and Bioinformatics (2023).

    Aryan Tajmir Riahi, Chenwei Zhang, James Chen, Anne Condon, and Khanh Dao Duc. "EMPOT: partial alignment of density maps and rigid body fitting using unbalanced Gromov-Wasserstein divergence." arXiv preprint arXiv:2311.00850 (2023).
  </Description>

  <!-- Categories is a list where this bundle should appear -->  <Categories>
    <Category name="General"/>
  </Categories>

  <!-- Dependencies on other ChimeraX/Python packages -->
  <Dependencies>
    <Dependency name="ChimeraX-Core" version=">=0.1"/>
    <Dependency name="mrcfile" version=">=0.1"/>
    <Dependency name="numpy" version=">=0.1"/>
    <Dependency name="pandas" version=">=0.1"/>
    <Dependency name="POT" version=">=0.1"/>
    <Dependency name="scipy" version=">=0.1"/>
    <Dependency name="matplotlib" version=">=0.1"/>
    <Dependency name="seaborn" version=">=0.1"/>
    <Dependency name="numba" version=">=0.1"/>
    <Dependency name="unbalancedgw" version=">=0.1"/>
    <Dependency name="Bio" version=">=0.1"/>
    <Dependency name="shapely" version=">=0.1"/>
  </Dependencies>

  <!-- Python and ChimeraX-specific classifiers
       From https://pypi.python.org/pypi?%3Aaction=list_classifiers
       Some Python classifiers are always inserted by the build process.
       These include the Environment and Operating System classifiers
       as well as:
         Framework :: ChimeraX
         Intended Audience :: Science/Research
         Programming Language :: Python :: 3
         Topic :: Scientific/Engineering :: Visualization
         Topic :: Scientific/Engineering :: Chemistry
         Topic :: Scientific/Engineering :: Bio-Informatics
       The "ChimeraX :: Bundle" classifier is also supplied automatically.  -->
  <Classifiers>
    <!-- Development Status should be compatible with bundle version number -->
    <PythonClassifier>Development Status :: 3 - Alpha</PythonClassifier>
    <PythonClassifier>License :: Freeware</PythonClassifier>
    <!-- ChimeraX classifiers describe supplied functionality -->
    <ChimeraXClassifier>ChimeraX :: Command :: ot_alignment show_points :: General ::
	Print "hello world" in the log</ChimeraXClassifier>
    <ChimeraXClassifier>ChimeraX :: Command :: ot_alignment EMPOT :: General ::
  Print "hello world" in the log</ChimeraXClassifier>
    <ChimeraXClassifier>ChimeraX :: Command :: ot_alignment AlignOT :: General ::
  Print "hello world" in the log</ChimeraXClassifier>
  </Classifiers>

</BundleInfo>