PyMol Python Integration

Molecule Tutorials - Herong's Tutorial Examples

∟PyMol Python Integration

This chapter provides quick introductions on PyMol integration with Python to write Python script to launch PyMol and access PyMol commans.

Run Python Statements from PyMol

PyMol Python API

Launch PyMol from Python Interpreter

PyMol Python API Only Functions

Takeaways:

PyMol command interface can interpret Python statements interactively.
PyMol "run" command can load and run a Python script file in a background process.
PyMol has a Python API that provides access to all PyMol command from Python script code.
PyMol can be launched from a Python interpreter.

Table of Contents

About This Book

Introduction of Molecules

Molecule Names and Identifications

Molecule Mass and Weight

Protein and Amino Acid

Nucleobase, Nucleoside, Nucleotide, DNA and RNA

Gene and Chromosome

Protein Kinase (PK)

SDF (Structure Data File)

PyMol Installation

PyMol GUI and CLI

PyMol Selections

PyMol Editing Functions

PyMol Measurement Functions

PyMol Movie Functions

►PyMol Python Integration

PyMol Object Functions

ChEMBL Database - European Molecular Biology Laboratory

PubChem Database - National Library of Medicine

PDB (Protein Data Bank)

INSDC (International Nucleotide Sequence Database Collaboration)

HGNC (HUGO Gene Nomenclature Committee)

Relocated Tutorials

Resources and Tools

Molecule Related Terminologies

Full Version in PDF/EPUB