mols2grid
mols2grid is an interactive chemical viewer for 2D structures of small molecules, based on RDKit.
? Installation
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
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
andmol_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 PNGcoordGen=True
: use the coordGen library instead of the RDKit one to depict the molecules in 2Dsize=(160, 120)
: size of each imageuse_coords=True
: use the coordinates of the input molecules if availableMolDrawOptions=None
: RDKit's MolDrawOptions class. Useful for making highly customized drawings. You can also leave this toNone
, and directly use the attributes of this class as parameters likeaddStereoAnnotation=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 bartemplate="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. UseNone
for no tooltip.tooltip_fmt="<strong>{key}</strong>: {value}"
: str
Format string of each key/value pair in the tooltiptooltip_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, rightn_cols=5
: int
Number of columns per pageborder="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 akey: function
structure where the key must correspond to one of the columns insubset
ortooltip
. 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 akey: function
structure where the key must correspond to one of the columns insubset
. 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:
These transformations only affect columns intransform={"Solubility": lambda x: f"{x:.2f}", "Melting point": lambda x: f"MP: {5/9*(x-32):.1f}°C"}
subset
(nottooltip
) and are applied independantly fromstyle
.
The pages
template comes with additional parameters:
n_rows=3
: int
Number of rows per pageselection=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) throughmols2grid.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
)