• 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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 GraphemeTM 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
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© Copyright 2026, Cadence Design Systems, Inc. Last updated on Aug 13, 2026.