mols2grid

mols2grid is a Python chemical viewer for 2D structures of small molecules, based on RDKit.

Installation

mols2grid was developped for Python 3.6+ and requires rdkit, pandas and jinja2 as dependencies.

To install mols2grid from a clean conda environment:

conda install -c conda-forge rdkit
pip install mols2grid

Usage

You can setup the grid from various inputs:

• a pandas DataFrame (with a SMILES column),
• a list of RDKit molecules (with properties accessible through the mol.GetPropsAsDict() method),
• or an SDF file:

from mols2grid import MolGrid

# pandas
mg = MolGrid(df)

# List of molecules
mg = MolGrid.from_mols([Chem.MolFromSmiles(smi) for smi in smiles])

# SDF
mg = MolGrid.from_sdf("/path/to/molecules.sdf")

This first step sets up the internal dataframe that will be used by mols2grid (which you can access and sort/rename with mg.dataframe) and creates the drawings of each molecule. Here, you can set up how the drawings should look:

• useSVG=True: use SVG images or PNG
• coordGen=True: use the coordGen library instead of the RDKit one to depict the molecules in 2D
• size=(160, 120): size of each image
• and all the arguments available in RDKit's MolDrawOptions, like addStereoAnnotation=True.
• Additionally, if you're using the from_mols and from_sdf classmethods, you can rename the property fields using the mapping={"old_name": "new_name"} parameter.

Two columns are automatically added to the mg.dataframe after this operation: img and SMILES. If a SMILES column already existed in your molecules' properties or SDF file, it will not be overwritten.

You can then call the mg.display or mg.save methods to render and display/save the HTML document.

You can control which template is used through the template argument:

• template="pages" (default) which is displayed above. It integrates nicely with notebooks
• template="table", which displays the full list of molecules (no pages). Useful if you ever need to print the full list of molecules on paper (or print to PDF)

Both templates can be configured with the same parameters (a lot of which are CSS declarations):

• subset=None: list or None
  Columns to be displayed in each cell of the grid. Each column's value will be displayed from top to bottom in the same order given here. Use "img" for the image of the molecule. Default: all columns (with "img" in first position)
• tooltip=None: list or None
  Columns to be displayed as a tooltip when hovering/clicking on the image of a cell. Use None for no tooltip.
• tooltip_fmt="<strong>{key}</strong>: {value}": str
  Format string of each key/value pair in the tooltip
• tooltip_trigger="click hover": str
  Sequence of triggers for the tooltip: (click, hover, focus)
• tooltip_placement="bottom": str
  Position of the tooltip: auto, top, bottom, left, right
• cell_width=160: int
  Max width of each cell, in pixels
• n_cols=5: int
  Number of columns per page
• border="1px solid #cccccc": str
  Styling of the border around each cell (CSS)
• gap=0: int or str
  Size of the margin around each cell (CSS)
• fontsize="12pt": str
  Font size of the text displayed in each cell (CSS)
• fontfamily"'DejaVu', sans-serif": str
  Font used for the text in each cell (CSS)
• textalign="center": str
  Alignment of the text in each cell (CSS)
• hover_color="#e7e7e7": str
  Background color when hovering a cell (CSS)
• style=None: dict or None
  CSS styling applied to each item in a cell. The dict must follow a key: function structure where the key must correspond to one of the columns in subset or tooltip. The function takes the item's value as input, and outputs a valid CSS styling. For example, if you want to color the text corresponding to the "Solubility" column in your dataframe:

  style={"Solubility": lambda x: "color: red" if x < -5 else "color: black"}
  

The pages template comes with additional parameters:

• n_rows=3 : int
  Number of rows per page

License

Unless otherwise noted, all files in this directory and all subdirectories are distributed under the Apache License, Version 2.0:

    Copyright 2021 Cédric BOUYSSET

    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
    You may obtain a copy of the License at

        http://www.apache.org/licenses/LICENSE-2.0

    Unless required by applicable law or agreed to in writing, software
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.