• Introduction
    • Outline of Recipes
  • Image Manipulation
    • Adding Logo to PNG Image
      • Problem
      • Ingredients
      • Difficulty Level
      • Download
      • Solution
      • Usage
      • Discussion
    • Depicting Molecule in JPG
      • Problem
      • Ingredients
      • Difficulty level
      • Download
      • Solution
      • Usage
      • See also in OEChem manual
      • See also in OEDepict manual
  • 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
      • Discussion
      • 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
      • Solution
      • Usage (xlogp2img)
        • Command Line Parameters
      • Discussion
      • Usage (xlogp2pdf)
        • Command Line Parameters
      • 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
      • Solution
      • Usage (fragxlogp2img)
        • Command Line Parameters
      • Discussion
      • Usage (fragxlogp2pdf)
        • Command Line Parameters
      • 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
      • Solution
      • Discussion
        • Atom Partial Charge
        • Usage (Partial Charge)
        • Atom XLogP Contribution
        • 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
      • Solution
      • Discussion
      • 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
      • Solution
      • Discussion
      • 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
      • Solution
      • 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
      • Solution
      • 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
      • Solution
      • Discussion
      • See also in OEChem TK manual
      • See also in OEDepict TK manual
    • Depicting CSV or SDF in PDF
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
      • 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
      • Solution
      • 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
      • Solution
      • Discussion
      • 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
      • Solution
      • 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
      • Solution
      • Discussion
      • 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
      • Solution
      • 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
    • OEViz - A Simple Depiction Web Service
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
      • Discussion
      • See also in Flask manual
      • See also in OEDepict TK manual
    • Depicting Multiple Matches
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
      • Discussion
      • See also in OEChem TK manual
      • See also in OEDepict TK manual
    • Depicting Molecular Graph Symmetry
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
      • Discussion
      • See also in OEChem TK manual
      • See also in OEDepict TK manual
    • Depicting Peptides
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
      • Discussion
      • See also in OEDepict TK Manual
      • See also in GraphemeTM TK Manual
    • Depicting Molecular Properties
      • Problem
      • Ingredients
      • Difficulty level
      • Download
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • Discussion
        • Visualizing Torsion Flexibility
        • Visualizing Torsional Angle Distribution with Reference
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • Discussion
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • Discussion
        • Command Line Parameters
      • 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
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • 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 Contacts
      • Problem
      • Ingredients
      • Difficulty level
      • Download
      • Solution
      • Usage
        • Command Line Parameters
      • 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 Unpaired Interactions
      • Problem
      • Ingredients
      • Difficulty level
      • Download
      • Solution
      • Usage
        • Command Line Parameters
      • 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 Interactions
      • Problem
      • Ingredients
      • Difficulty level
      • Download
      • Solution
      • Usage
        • Command Line Parameters
      • Discussion
        • Interaction perception
        • Interaction depiction
        • Hydrogen position optimization
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • 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
      • 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
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • 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
      • Solution
      • Usage
        • Command Line Parameters
      • Discussion
        • Performance
      • Related Python Cookbook Recipes
      • See also in GraphSim TK manual
      • See also in matplotlib documentation
  • Cheminformatics
    • Identifying Acceptor and Donor Atoms
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
      • Discussion
      • See also in OEChem TK manual
      • See also in OEMolProp TK manual
      • See also
    • Accessing Interaction Hint Information
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
        • Perceiving Interaction Hints
        • Accessing Interactions
        • Accessing Interaction Atoms
      • Discussion
        • Overview of OEChem TK Interaction API
        • Atom predicates
        • Interaction predicates
      • See also in OEChem TK manual
    • 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
      • 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
    • Similarity Searching of Large Molecule Files
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
        • Pre-generating Fingerprints
        • Creating Molecule Database Index File
        • Searching Fingerprints
      • Discussion
      • See also in OEChem TK manual
      • See also in GraphSim TK manual
    • Enumerating Fragment Combinations
      • Problem
      • Ingredients
      • Difficulty Level
      • Solution
      • 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
      • Solution
      • Discussion
      • See also in OEChem TK manual
      • See also in GraphSim TK manual
      • See also
    • Ring Perception
      • Problem
      • Ingredients
      • Difficulty level
      • Download
      • Solution
      • Usage
      • Discussion
        • 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
      • Solution
      • Discussion
      • See also in Python documentation
      • See also in OEChem TK manual
  • Molecular Modeling
    • Generating Canonical AM1-BCC Charges
      • Problem
      • Ingredients
      • Difficulty level
      • Download
      • Solution
      • Usage
      • See also in Omega TK manual
      • See also in Quacpac TK manual
  • Miscellaneous
    • Reordering CSV File
      • Problem
      • Ingredients
      • Difficulty Level
      • Download
      • Solution
      • Usage
        • Command Line Parameters
      • Related Python Cookbook Recipes
      • See also in OEChem TK manual
  • Just for Fun
    • Dalton
    • Picasso
    • OELove
    • Flag of New Mexico
    • OEHolidays
    • Depicting OpenEye Logo
    • Depicting molecule with shadow
    • OETree
    • OEAnime
    • Christmas Card
  • OpenEye Glossary of Terms
  • Bibliography
    • Fingerprint Similarity Search
    • Interaction Perception
    • Drug-likeness
    • Maximum Common Substructure Search
    • Validating Protein-Ligand Structures
    • Ramachandran Plot
    • Color References
  • Legal Notices
    • Copyright and Trademarks
    • Sample Code
    • Citation
      • Orion ® Floes
      • Toolkits and Applications
      • OpenEye Web Services
    • Technology Licensing
    • GCC
      • GCC RUNTIME LIBRARY EXCEPTION
      • GNU GENERAL PUBLIC LICENSE
Python Cookbook
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  • Contents »
  • Legal Notices

Legal Notices

  • Copyright and Trademarks
  • Sample Code
  • Citation
    • Orion ® Floes
    • Toolkits and Applications
    • OpenEye Web Services
  • Technology Licensing
  • GCC
    • GCC RUNTIME LIBRARY EXCEPTION
    • GNU GENERAL PUBLIC LICENSE
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© Copyright 2025, Cadence Design Systems, Inc. Last updated on Jun 06, 2025.