trendingtechnology / mols2grid

Interactive chemical viewer for 2D structures of small molecules

👀 mols2grid

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

➡️ Try the demo notebook on Google Colab

🐍 Installation

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mols2grid was developped for Python 3.6+ and requires rdkit (>=2019.09.1), pandas and jinja2 as dependencies.

To install mols2grid from a clean conda environment:

conda install -c conda-forge 'rdkit>=2019.09.1'
pip install mols2grid

It is compatible with Jupyter Notebook and Google Colab (Visual Studio notebooks and Jupyterlab are not supported) and can run on Streamlit.

📜 Usage

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import mols2grid

mols2grid.display("path/to/molecules.sdf",
                  # RDKit's MolDrawOptions parameters
                  fixedBondLength=25,
                  # rename fields for the output document
                  mapping={"SOL": "Solubility",
                           "SOL_classification": "Class",
                           "NAME": "Name"},
                  # set what's displayed on the grid
                  subset=["ID", "img", "Solubility"],
                  # set what's displayed on the tooltips
                  tooltip=["Name", "smiles", "Class", "Solubility"],
                  # style for the grid labels and tooltips
                  style={"Solubility": lambda x: "color: red" if x < -3 else "color: black"},
                  # change the precision and format (or other transformations)
                  transform={"Solubility": lambda x: f"{x:+.2f}"})

Input parameters

You can setup the grid from various inputs:

• a pandas DataFrame (with a column of SMILES or RDKit molecules, controlled by the smiles_col and mol_col parameters),
• a list of RDKit molecules (with properties accessible through the mol.GetPropsAsDict() method),
• or an SDF file

You can also rename each field of your input with the mapping parameter. Please note that 3 fields are automatically added regardless of your input: mols2grid-id, SMILES and img. If a "SMILES" field already exists, it will not be overwritten.

Parameters for the drawing of each molecule

• 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
• use_coords=True: use the coordinates of the input molecules if available
• MolDrawOptions=None: RDKit's MolDrawOptions class. Useful for making highly customized drawings. You can also leave this to None, and directly use the attributes of this class as parameters like addStereoAnnotation=True

Parameters for the grid

You can control the general look of the document through the template argument:

• template="pages" (default) which is displayed above. It integrates nicely with Jupyter notebooks and has a search bar
• 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
• 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 < -3 else "color: black"}

• transform=None: dict or None Functions applied to specific items in all cells. The dict must follow a key: function structure where the key must correspond to one of the columns in subset. The function takes the item's value as input and transforms it. For example, to round the "Solubility" to 2 decimals, and display the "Melting point" in Celsius instead of Fahrenheit with a single digit precision and some text before ("MP") and after ("°C") the value:

  transform={"Solubility": lambda x: f"{x:.2f}",
             "Melting point": lambda x: f"MP: {5/9*(x-32):.1f}°C"}

  These transformations only affect columns in subset (not tooltip) and are applied independantly from style.

The pages template comes with additional parameters:

• n_rows=3 : int
  Number of rows per page
• selection=True : bool Enables the selection of molecules using a checkbox. Only usefull in the context of a Jupyter notebook. You can retrieve your selection of molecules (index and SMILES) through mols2grid.selection

The pages template also allows searching (by text or SMARTS) and sorting the grid.

Output parameters

You can either:

• save the grid with mols2grid.save(output_path, ...). The file that is generated is a standalone HTML document that should work with most web browsers.
• display it directly in a Jupyter notebook with mols2grid.display(...) (optionnal argument: width="100%", height=None)

⚖ License

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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.