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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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 Grapheme
TM
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
All OpenEye Documentation
»
Contents
»
Miscellaneous
Miscellaneous
Reordering
CSV
File