simonboothroyd/plotmol

Interactive plotting of data annotated with molecule structures.

plotmol's Issues

Pass extra arguments to `ColumnDataSource` for more customized tooltips

It would be great to expose other sources of data that get passed to ColumnDataSource like some sort of molecule title, so that a custom tooltip_template could take advantage of them.

plotmol/plotmol/plotmol.py

Line 103 in 19a0aa8

source = ColumnDataSource(data={"x": x, "y": y, "smiles": smiles, "image": images})

def custom_tooltip_template() -> str:
    """Returns the a custom html based template to use for the figure hover pop-up with the molecule image and name."""

    return """
    <div>
        <div>
            <img src="@image" ></img>
        </div>
        <div>
            <span style="font-size: 10px; color: #696;">$molecule_name</span>
        </div>

    </div>
"""

Only works with Python 3.8+

I believe this'll only work with Python 3.8+ due to Literal:

ImportError: cannot import name 'Literal' from 'typing' 

Can't `pip install` from Github

The library can no longer be installed with pip, directly from GitHub. It's probably related to the latest changes to the pyproject.toml file.

How to reproduce

mkdir plotmol-pip-install-test && cd plotmol-pip-install-test
python -m venv .venv
source .venv/bin/activate
pip install git+https://github.com/SimonBoothroyd/plotmol.git

And we get:

Collecting git+https://github.com/SimonBoothroyd/plotmol.git
  Cloning https://github.com/SimonBoothroyd/plotmol.git to /tmp/pip-req-build-c7b87b4s
  Running command git clone --filter=blob:none --quiet https://github.com/SimonBoothroyd/plotmol.git /tmp/pip-req-build-c7b87b4s
  Resolved https://github.com/SimonBoothroyd/plotmol.git to commit 4490e2c4aea4a035357049e0598cecd2a00c02e0
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [93 lines of output]
      Traceback (most recent call last):
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 80, in __getattr__
          return next(
                 ^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 81, in <genexpr>
          ast.literal_eval(value)
        File "/usr/lib/python3.11/ast.py", line 110, in literal_eval
          return _convert(node_or_string)
                 ^^^^^^^^^^^^^^^^^^^^^^^^
        File "/usr/lib/python3.11/ast.py", line 109, in _convert
          return _convert_signed_num(node)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/usr/lib/python3.11/ast.py", line 83, in _convert_signed_num
          return _convert_num(node)
                 ^^^^^^^^^^^^^^^^^^
        File "/usr/lib/python3.11/ast.py", line 74, in _convert_num
          _raise_malformed_node(node)
        File "/usr/lib/python3.11/ast.py", line 71, in _raise_malformed_node
          raise ValueError(msg + f': {node!r}')
      ValueError: malformed node or string on line 10: <ast.Subscript object at 0x7fe73052b400>
      
      The above exception was the direct cause of the following exception:
      
      Traceback (most recent call last):
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 192, in read_attr
          return getattr(StaticModule(module_name, spec), attr_name)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 86, in __getattr__
          raise AttributeError(f"{self.name} has no attribute {attr}") from e
      AttributeError: plotmol has no attribute __version__
      
      During handling of the above exception, another exception occurred:
      
      Traceback (most recent call last):
        File "/home/whoeverest/Code/plotmol-test/.venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/whoeverest/Code/plotmol-test/.venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/whoeverest/Code/plotmol-test/.venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 1, in <module>
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 103, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 159, in setup
          dist.parse_config_files()
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 627, in parse_config_files
          pyprojecttoml.apply_configuration(self, filename, ignore_option_errors)
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 66, in apply_configuration
          config = read_configuration(filepath, True, ignore_option_errors, dist)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 131, in read_configuration
          return expand_configuration(asdict, root_dir, ignore_option_errors, dist)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 156, in expand_configuration
          return _ConfigExpander(config, root_dir, ignore_option_errors, dist).expand()
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 204, in expand
          self._expand_all_dynamic(dist, package_dir)
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 249, in _expand_all_dynamic
          version=self._obtain_version(dist, package_dir),
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 298, in _obtain_version
          return _expand.version(self._obtain(dist, "version", package_dir))
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 287, in _obtain
          return self._expand_directive(
                 ^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py", line 281, in _expand_directive
          return _expand.read_attr(directive["attr"], package_dir, root_dir)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 195, in read_attr
          module = _load_spec(spec, module_name)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-v7yxd7wt/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 215, in _load_spec
          spec.loader.exec_module(module)  # type: ignore
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<frozen importlib._bootstrap_external>", line 940, in exec_module
        File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
        File "/tmp/pip-req-build-c7b87b4s/plotmol/__init__.py", line 8, in <module>
          from ._plotmol import InputSizeError, default_tooltip_template, scatter
        File "/tmp/pip-req-build-c7b87b4s/plotmol/_plotmol.py", line 4, in <module>
          import bokeh.models
      ModuleNotFoundError: No module named 'bokeh'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Side by side multi molecules

Plotmol will currently draw multiple molecules in the tooltip image above each other it would be great to have the option to draw the molecules side by side as well. For this we could try and split the molecule using Chem.GetMolFrags(rdkit_mol, asMols=True) and if we have more than one molecule we can break up the SVG into a grid and rdkit should work out where to place the molecules automatically.

rdkit_mol = Chem.RemoveHs(Chem.MolFromSmiles(smiles))
rdkit_mol = Draw.PrepareMolForDrawing(rdkit_mol, forceCoords=True)
mols = Chem.GetMolFrags(rdkit_mol, asMols=True)
if len(mols) == 2:
    drawer = Draw.rdMolDraw2D.MolDraw2DSVG(400, 200, 200, 200)
    drawer.DrawMolecules(mols)
else:
    drawer = Draw.rdMolDraw2D.MolDraw2DSVG(400, 200)
    drawer.DrawMolecule(rdkit_mol)