chemimg 2026.2.10

Draw 2d molecule representation easily. Change colors, increase size, make a background cover

Chemimg

Overview

A very light package that makes Rdkit's molecule drawing simple for quick usage. It comes with 4 main core attributes.

• With one line of code create a 2D representation of a molecule from its SMILES representation.
• Change the color, size and thickness of the strokes of your molecule.
• Create a background cover (collage) of a group of molecules by randomly placing and rotating your 2D images.
  
• Do all these 3 easily and also for only the molecule scaffolds.

Installation

This project relies on RDKit and Cairo, which are best installed via conda.

Cairo must be installed separately.
System Requirements (Required for CairoSVG)

• Windows: Install the GTK Runtime.
• macOS: brew install cairo
• Linux: sudo apt-get install libcairo2

Install from PyPI

pip install chemimg

With conda

git clone https://github.com/bsaldivaremc2/chemimg
cd chemimg
conda env create -f environment.yml  
conda activate chemimg310
pip install .

OR

pip install git+https://github.com/bsaldivaremc2/chemimg.git

Usage

Check demo.ipynb for examples.

Load the package

import os
import chemimg

Generate one example of the complete molecule or only the scaffold

border_width: thicker strokes
increase_factor: default 1, makes the image bigger proportionately
scaffold_only: only plot the molecule scaffold

ismiles = "CC(C)Cc1ccc(cc1)C(C)C(=O)O"
fo1 = "imgs/demo.png"
scaffold_only = False
chemimg.chem.scaffolds.draw_transparent_mol(ismiles, fo1,increase_factor=100,scaffold_only=scaffold_only,border_width=1)

fo2 = "imgs/demo_scaffold.png"
scaffold_only = True
chemimg.chem.scaffolds.draw_transparent_mol(ismiles, fo2,increase_factor=100,scaffold_only=scaffold_only,border_width=1)

ismiles = "CC(C)Cc1ccc(cc1)C(C)C(=O)O"
border_widths = [1, 3, 5]  # N rows
scales = [50, 100, 150]   # M cols
output_dir = "imgs"

# Molecule grid
prefix = "mol"
mol_grid = chemimg.imgproc.demo.generate_grid(ismiles, output_dir, border_widths, scales, scaffold_only=False, prefix=prefix)
#mol_grid.show() #Open the image in the default image viewer

# Scaffold grid
prefix = "scaffold"
scaffold_grid = chemimg.imgproc.demo.generate_grid(ismiles, output_dir, border_widths, scales, scaffold_only=True, prefix=prefix)
#scaffold_grid.show() #Open the image in the default image viewer

Change colors

fname = "mol_bw5_scale150.png"
input_path=f"imgs/{fname}"
new_fname = fname.replace(".png","_blue.png")
output_path=f"imgs/{new_fname}"
chemimg.imgproc.colors.change_color_to_color_fast(input_path, output_path, 
                               original_color=(0,0,0), replacement_color=(0,0,255),any_color=False)

nf1 = output_path
new_fname = fname.replace(".png","_allblue.png")
output_path=f"imgs/{new_fname}"
chemimg.imgproc.colors.change_color_to_color_fast(input_path, output_path, 
                               original_color=(0,0,0), replacement_color=(0,0,255),any_color=True)

Make a collage/background cover

for the listed 20 molecules create their 2d representations as:

• Normal molecules
• Scaffolds only
• Normal molecules but blue
• Scaffolds only but red

# A collection of 20 diverse SMILES strings 
smiles_list = [
    "CC(=O)Oc1ccccc1C(=O)O",                # Aspirin
    "CC(=O)Nc1ccc(O)cc1",                   # Paracetamol
    "CN1C=NC2=C1C(=O)N(C(=O)N2C)C",         # Caffeine
    "CN(C)C(=N)N=C(N)N",                    # Metformin
    "CC1(C(N2C(S1)C(C2=O)NC(=O)Cc3ccccc3)C(=O)O)C", # Penicillin G
    "CCO",                                  # Ethanol
    "CC(=O)O",                              # Acetic Acid
    "CC(=O)C",                              # Acetone
    "c1ccccc1",                             # Benzene
    "C(C1C(C(C(C(O1)O)O)O)O)O",             # Glucose
    "C1=CC(=C(C=C1CCN)O)O",                 # Dopamine
    "C1=CC2=C(C=C1O)C(=CN2)CCN",            # Serotonin
    "CNC[C@H](C1=CC(=C(C=C1)O)O)O",         # Adrenaline
    "C(C(=O)O)N",                           # Glycine
    "C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N", # ATP
    "COc1cc(C=O)ccc1O",                     # Vanillin
    "CC1=CCC(CC1)C(=C)C",                   # Limonene
    "C1=CC=C(C=C1)C=CC=O",                  # Cinnamaldehyde
    "CC(C)/C=C/CCCCC(=O)NCC1=CC(=C(C=C1)O)OC", # Capsaicin
    "CC1CCC(C(C1)O)C(C)C"                   # Menthol
]

odir="imgs/imgs4collage/"
for i,ismiles in enumerate(smiles_list):
    ofname = os.path.join(odir,f"mol_{i:03d}.png")
    chemimg.chem.scaffolds.draw_transparent_mol(ismiles, ofname,increase_factor=10,scaffold_only=False,border_width=5,verbose=False)

odir="imgs/imgs4collageScaffold/"
for i,ismiles in enumerate(smiles_list):
    ofname = os.path.join(odir,f"mol_{i:03d}.png")
    chemimg.chem.scaffolds.draw_transparent_mol(ismiles, ofname,increase_factor=10,scaffold_only=True,border_width=5,verbose=False)

# Change colors for collage, to blue for the full molecules, and red for the scaffolds. The any_color=True option will change all non-white pixels to the replacement color, which is useful for images with anti-aliasing or slight variations in color.
input_path="imgs/imgs4collage/"
output_path="imgs/imgs4collageBlue/"
chemimg.imgproc.colors.change_color_to_color_fast(input_path, output_path, 
                               original_color=(0,0,0), replacement_color=(0,0,255),any_color=True)

input_path="imgs/imgs4collageScaffold/"
output_path="imgs/imgs4collageScaffoldRed/"
chemimg.imgproc.colors.change_color_to_color_fast(input_path, output_path, 
                               original_color=(0,0,0), replacement_color=(255,0,0),any_color=True)

Create 4 collage images

• Normal molecules
• Scaffolds only
• Normal molecules but blue
• Scaffolds only but red

folder_paths = ["imgs/imgs4collage/", "imgs/imgs4collageScaffold/", "imgs/imgs4collageBlue/", "imgs/imgs4collageScaffoldRed/"]
output_files = ["imgs/collage_simple.png", "imgs/collage_scaffold.png", "imgs/collage_simple_blue.png", "imgs/collage_scaffold_red.png"]
for folder_path, output_file in zip(folder_paths, output_files):
    chemimg.imgproc.collage.create_collage_randomNoCollapse(output_size=(1024, 1024), folder_path=folder_path, 
                                                            max_time_seconds=10, max_images=1000,
                       output_file=output_file, min_scale_factor=-1, max_scale_factor=-1,
                       lower_alpha=0.5, upper_alpha=1.0,rotate_only_if_vertical=False)

License

This project is licensed under the Creative Commons Attribution–NonCommercial 4.0 International License.