Introduction
Installation
Conda
UV
Integration Testing
Available Scripts
Outline of Recipes
Image Manipulation
Adding Logo to PNG Image
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
🔄 Depicting Molecule in JPG
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
See also in OEChem manual
See also in OEDepict manual
🆕 Depicting Molecule in Jupyter Notebook
Problem
Difficulty level
Download
2D Depiction
Generating Transparent PNG
Problem
Ingredients
Difficulty Level
Solution
Discussion
See also in OEDepict TK manual
Depicting Polar Hydrogens
Problem
Ingredients
Difficulty Level
Solution
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting Tripos Atom Types
Problem
Ingredients
Difficulty Level
Solution
Discussion
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting Molecule with Various Styles
Problem
Ingredients
Difficulty Level
Solution
Default
Aromaticity Style
Atom Color Style
Super Atom Style
Atom Stereo Style
Bond Stereo Style
Title Style
Border Style
Display Atom Index
Display Bond Index
Display Atom Property
Display Bond Property
Hover Atom Property
Hover Bond Property
Toggle Atom Property
Toggle Bond Property
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting Atom Contributions of XLogP
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage (xlogp2img)
Discussion
Usage (xlogp2pdf)
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in MolProp TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Depicting Fragment Contributions of XLogP
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage (fragxlogp2img)
Discussion
Usage (fragxlogp2pdf)
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in MolProp TK manual
See also in Quacpac TK manual
See also in OEMedChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Depicting Atom Properties
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Discussion
Atom Partial Charge
Atom XLogP Contribution
Usage
Usage (partial charge)
Usage (XLogP)
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Depicting Molecule Similarity Based on Fingerprints
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage (simcalc2img)
Discussion
Usage (simcalc2pdf)
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in GraphSim TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Depicting Topological Polar Surface Area
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Discussion
Usage (psa2img)
Usage (psa2pdf)
See also in OEChem TK manual
See also in MolProp TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Depicting Activities of Molecules
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Depicting Reaction Components
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Related Python Cookbook Recipes
See also
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting Library Generation
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting CSV or SDF in PDF
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting CSV or SDF in HTML
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting CSV or SDF in XLSX (Excel)
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Related Python Cookbook Recipes
See also
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting CSV or SDF in PPTX (PowerPoint)
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
See also
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
Highlighting Fragments
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Discussion
Usage (frags2img)
Usage (frags2pdf)
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEMedChem TK manual
See also in OEDepict TK manual
See also
Depicting Fragment Combinations
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEMedChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
🆕 Depict SMILES in Interactive Web Application
Problem
Ingredients
Difficulty Level
Source Code
Usage
See also in OEDepict TK manual
Depicting Multiple Matches
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting Molecular Graph Symmetry
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
See also in OEChem TK manual
See also in OEDepict TK manual
Depicting Molecular Properties
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
See also in OEChem TK manual
See also in MolProp TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing 3D Information
Visualizing Torsional Angle Distribution
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Visualizing Torsion Flexibility
Visualizing Torsional Angle Distribution with Reference
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
🆕 Visualizing the Variability in Torsional Angle Sampling
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing Molecular Dipole Moment
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing Electron Density
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
See also
Visualizing Protein-Ligand B-factor
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing Protein-Ligand B-factor Map
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing Protein-Ligand B-factor Heat Map
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
🔄 Visualizing Protein-Ligand Interactions
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
complex2img
🚧 complexes2pdf
Discussion
Interaction perception
Interaction depiction
Hydrogen position optimization
🚧 Custom Ligand Alignment
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in Spruce TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
🔄 Visualizing Protein-Ligand Contacts
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in Spruce TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing Protein-Ligand Unpaired Interactions
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Interaction Perception
Unpaired Interaction Depiction
Hydrogen Position Optimization
Unpaired Map vs Active Site Interaction Map
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing Protein-Ligand Maps
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Visualizing Shape and Color Overlap
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in GraphSim TK manual
See also in Shape TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Plotting (not the evil kind)
🔄 Ramachandran Plot
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
See also
See also in OEChem TK manual
See also in OEDepict TK manual
See also in Grapheme
TM
TK manual
Drawing ROC Curve
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in matplotlib documentation
See also in sklearn documentation
See also
Plotting ROC Curves of Fingerprint Similarity
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Related Python Cookbook Recipes
See also in numpy documentation
See also in sklearn documentation
See also in matplotlib documentation
See also in GraphSim TK manual
Drawing Fingerprint Score Histogram
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Performance
Related Python Cookbook Recipes
See also in GraphSim TK manual
See also in matplotlib documentation
Cheminformatics
Identifying Acceptor and Donor Atoms
Ingredients
Difficulty Level
Solution
Discussion
See also in OEChem TK manual
See also in OEMolProp TK manual
See also
Manipulating Large Molecule Files
Problem
Ingredients
Difficulty Level
Solution
Creating Molecule Database Index File
Counting Molecules
Output Molecule Titles
Extracting Molecules by Title
Extracting Random Set of Molecules
Splitting Molecule Database
Sorting Molecules
Discussion
See also in Python documentation
See also in OEChem TK manual
See also in OEMedChem TK manual
Rapid Similarity Searching of Large Molecule Files
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Generating Fingerprints
Usage (makefastfp)
Searching Fingerprints
Usage (searchfastfp)
Discussion
Performance of fingerprint generation
Fingerprint search options
Performance of fingerprint search
Memory-Mapped vs In-Memory Search
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in GraphSim TK manual
Enumerating Fragment Combinations
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Related Python Cookbook Recipes
See also in Python documentation
See also in OEChem TK manual
See also in OEMedChem TK manual
See also
Finding Core Fragment of a Molecule Series
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Discussion
Usage
See also in OEChem TK manual
See also in GraphSim TK manual
See also
🔄 Ring Perception
Problem
Ingredients
Difficulty level
Download
Source Code
Solution
Usage
Discussion
Identifying Spiro Atoms of a Molecule
Identifying Macro-cycle Atoms of a Molecule
Identifying Ring Systems of a Molecule
Identifying Aromatic Ring Systems of a Molecule
Identifying Atom in Certain Ring Size
Identifying Atom in Certain Aromatic Ring Size
Identifying Atoms’ Smallest Ring Size
See also in OEChem TK manual
Enumerating Atom Substitutions
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Discussion
See also in Python documentation
See also in OEChem TK manual
🔄 Accessing Interaction Hint Information
Ingredients
Difficulty Level
Solution
Perceiving Interaction Hints
Accessing Interactions
Accessing Interaction Atoms
Retrieving Interacting Residues
Accessing Calculated Interaction Hint Geometries
Serializing Interaction
Discussion
Overview of OEChem TK Interaction API
Atom predicates
Interaction predicates
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Print Protein-Ligand Interactions to Console
Problem
Ingredients
Difficulty Level
Download
Source Code
Discussion
Usage
Input Ligand-Protein Complex
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Print the Summary of Protein-Ligand Interactions for a Set of Molecules
Problem
Ingredients
Difficulty Level
Download
Source Code
Discussion
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Serialize Protein-Ligand Interactions
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Serialization
Deserialization
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Peptide Informatics
🆕 Theory
Monomers
Monomers with
Peptide
Polymer Type
Monomers with
Chem
Polymer Type
Monomers with Unspecified Stereochemistry
Defining Monomer Connection Points
OEChem TK Built-in Monomer Sets
HELM
HELM Parsing
Embedded SMILES
Helm Generation
Tautomer Handling
Handling Charged Molecules
Handling Molecules with Unspecified Stereochemistry
Peptide Cyclization and Cross-links
🆕 Generating Custom Monomer Set
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Discussion
Usage
🆕 Convert Monomers to OpenEye JSON Format
Problem
Ingredients
Difficulty Level
Download
Source Code
Usage
See also in OEChem TK manual
🆕 Substructure Search in Monomer Set
Problem
Ingredients
Difficulty Level
Download
Source Code
Usage
See also in OEChem TK manual
🆕 Similarity Search in Monomer Set
Problem
Ingredients
Difficulty Level
Download
Source Code
Discussion
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in GraphSim TK manual
🆕 Depict Monomer
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
See also in OEChem TK manual
See also in OEGrapheme TK manual
🆕 Depict Peptide
Problem
Ingredients
Difficulty Level
Download
Source Code
Usage
Peptide Input
Depiction Options
Monomer Set Options
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in OEGrapheme TK manual
🆕 Convert HELM to SMILES
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Monomer Set Options
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Convert SMILES to HELM
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Monomer Set Options
Helm Generation Options
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Convert HELM File to Molecule File
Problem
Ingredients
Difficulty Level
Download
Source Code
Usage
Monomer Set Options
Verbose Options
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Convert Molecule File to HELM File
Problem
Ingredients
Difficulty Level
Download
Source Code
Usage
Monomer Set Options
Verbose Options
Helm Generation Options
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Print Monomer Set Information to Console
Problem
Ingredients
Difficulty Level
Download
Source Code
Usage
See also in OEChem TK manual
🆕 Plot Similarities in a Monomer Set
Problem
Ingredients
Difficulty Level
Download
Source Code
Discussion
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
See also in GraphSim TK manual
See also in OEGrapheme TK manual
🆕 Print Monomer Sequence of HELMS to Console
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Convert Peptides File to XLSX (Excel) with Monomer Sequence
Problem
Ingredients
Difficulty Level
Download
Source Code
Usage
Monomer Set Options
Helm Generation Options
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Generate HELM in Interactive Web Application
Problem
Ingredients
Difficulty Level
Source Code
Usage
See also in OEChem TK manual
See also in OEGrapheme TK manual
🆕 Generate Random Peptides
Problem
Ingredients
Difficulty Level
Solution
Download
Source Code
Usage
Output Options
Peptide Generation Options
Monomer Set Options
Related Python Cookbook Recipes
See also in OEChem TK manual
🆕 Mutate Peptide
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Output Options
Peptide Generation Options
Replacement Codes
Monomer Set Options
Related Python Cookbook Recipes
See also in OEChem TK manual
Molecular Modeling
Generating Canonical AM1-BCC Charges
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
See also in Omega TK manual
See also in Quacpac TK manual
Miscellaneous
Reordering
CSV
File
Problem
Ingredients
Difficulty Level
Download
Source Code
Solution
Usage
Related Python Cookbook Recipes
See also in OEChem TK manual
API References
Predicates
IsLipinskiAcceptor
IsLipinskiAcceptor
IsLipinskiDonor
IsLipinskiDonor
Functions
num_lipinsky_acceptors
num_lipinsky_acceptors()
num_lipinsky_donors
num_lipinsky_donors()
Just for Fun
Dalton
Picasso
OELove
Flag of New Mexico
OEHolidays
Depicting OpenEye Logo
Depicting molecule with shadow
OEAnime
Christmas Card
📝 2026.1.0
OpenEye Glossary of Terms
Bibliography
Fingerprint Similarity Search
Interaction Perception
Drug-likeness
Maximum Common Substructure Search
Validating Protein-Ligand Structures
Peptide Informatics
Ramachandran Plot
Color References
Legal Notices
Copyright and Trademarks
Sample Code
Citation
Orion
®
Orion Floes
Toolkits and Applications
Publications for Bibliographies
Orion
AFITT and FLYNN Applications
OEDocking Application and Toolkit
OMEGA Application and Toolkit
ROCS Application
OpenEye MMDS Web Service
Technology Licensing
GCC
GCC RUNTIME LIBRARY EXCEPTION
GNU GENERAL PUBLIC LICENSE
Index
Python Cookbook
All OpenEye Documentation
»
Contents
»
Overview: module code
All modules for which code is available
oecookbook.acceptor_atom
oecookbook.donor_atom