The Mychem Handbook

Jérôme PANSANEL

0.9.3

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Abstract

The Mychem Handbook is a documentation for the Mychem software. The Mychem software provides a set of functions for handling chemical data within MySQL. Mychem v0.9.3 is based on Open Babel version 2.3.0 (or any later version).


Table of Contents

1. Introduction
1.1. Mychem
1.2. MySQL
1.3. Open Babel
2. Using Mychem
2.1. The Database
2.1.1. Database Creation with SQL and Python Scripts
2.1.2. Database creation with mychemdb-manager.py
2.2. Examples
2.2.1. Calculate the Molecular Weight
2.2.2. Search a Substructure
3. Command Reference
3.1. The molecule Type
3.2. Conversion Commands
3.3. Helper Commands
3.4. Modification Commands
3.5. Molmatch Commands
3.6. Property Commands
4. Credits and License
4.1. Contributions
4.1.1. Developers
4.1.2. Contributors
4.2. Copyright
4.3. License
A. Installation
A.1. How to Obtain Mychem
A.1.1. Source Package
A.1.2. GIT Repository
A.2. Requirements
A.3. Compilation and Installation
A.3.1. Compiling and Installing Mychem on GNU/Linux
A.3.2. Installing Mychem on Mac OS X
A.3.3. Installing Mychem on Microsoft Windows
A.4. Mychem API
B. Troubleshooting
B.1. MySQL-Related Errors
B.1.1. ERROR 2013 (HY000): Lost connection to MySQL server during query
B.2. AppArmor
B.3. Other Errors
C. Loading MDL SDFFile with Python
D. Chemical Database Manager
D.1. Introduction
D.2. mychemdb-manager.py
E. Molecule Formats
E.1. Serialized OBMol
E.2. CML
E.3. Fingerprints
E.3.1. FP2
E.3.2. FP3
E.3.3. FP4
E.4. InChI
E.5. Sybyl Mol2
E.6. MDL Molfile
E.6.1. V2000
E.6.2. V3000
E.7. PDB
E.8. SMILES
E.8.1. Canonical SMILES