DebiChem Cheminformatics packages

The CDK is a library of Java classes used in computational and information chemistry and in bioinformatics. It includes renderers, file IO, SMILES generation/parsing, maximal common substructure algorithms, fingerprinting and much, much more.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

• babel: Convert between various chemical file formats
• obenergy: Calculate the energy for a molecule
• obminimize: Optimize the geometry, minimize the energy for a molecule
• obgrep: Molecular search program using SMARTS pattern
• obprop: Print standard molecular properties
• obfit: Superimpose two molecules based on a pattern
• obrotamer: Generate conformer/rotamer coordinates
• obchiral: Print molecular chirality information
• obrotate: Rotate dihedral angle of molecules in batch mode *

Cinfoy provides a common Python interface to various cheminformatics toolkits. This makes it possible to use the complementary features of cheminformatics toolktis using a common interface. If functionality is provided by more than one toolkit, the Cinfony user can choose the implementation they prefer.

Cinfony supports the following toolkits:

• OpenBabel
• RDKit
• CDK

Cinfony also provides the Webel web services module.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package contains the Python binding.

RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include:

• Chemical reaction handling and transforms
• Substructure searching with SMARTS
• Canonical SMILES
• Molecule-molecule alignment
• Large number of descriptors
• Fragmentation using RECAP rules
• 2D coordinate generation and depiction
• 3D coordinate generation using geometry embedding
• UFF forcefield
• Calculation of (R/S) stereochemistry codes
• Pharmacophore searching
• Calculation of shape similarity
• Atom pairs and topological torsions fingerprints
• Feature maps and feature-maps vectors
• Machine-learning algorithms
• Gasteiger-Marsili partial charge calculation

File formats RDKit supports include MDL Mol, SDF, TDT, SMILES and RDKit binary format.