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PhD project work with Sheffield University. Variety of MCS algorithms coded in Java

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chemcs_suite's Introduction

Java_MCS_algorithms

Description

PhD project work with Sheffield University (Under supervision of Professor Peter Willett and Doctor John Holliday). Variety of Maximum Common Substructure (MCS) algorithms for use with chemical graphs/structures. Coded in Java 1.6.

Usage

Please compile using Eclipse IDE (I used Mars.2). Usage examples revolve around the ExtendedIsomorphism class, in MCSMethodsTest.java

Citing
Please cite the article below when using this code:

Duesbury et al, 2017, Comparison of Maximum Common Subgraph Isomorphism Algorithms for the Alignment of 2D Chemical Structures, ChemMedChem. Available at [http://onlinelibrary.wiley.com/doi/10.1002/cmdc.201700482/abstract]

Java Library Requirements

Chemistry Development Kit (CDK) 1.5 - molecule handling
Ambit Core and SMARTS libraries (2.4.13) - fast SMARTS parsing and generation used in MCS representation
Colt (1.0) - Eigenvector calculations
Java-getopt (1.0.13) - command line options
guava (18.0) - alternative list handling
SMSD (2015 04 01) - additional graph theory tools and MCS handling

Author Information

Dr Edmund Duesbury (eduece99 AT g mail DOT com)

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chemcs_suite's Issues

Accessiblity

Currently only works with KNIME (though inconsistently). Having a more generic mode of usage, like command line application, would be more suitable

Threading for parallel calculations

Currently single core

Similarity coefficients

Tanimoto and Tversky (allow alpha and beta as option input for CLI)

Piping in Linux

To allow connections to other applications in command line. Database molecules should be pipeable (assumably as SMILES)

Depiction errors in molecule image outputs (CH3 in rings)

Is this from how the molecules were inputted, processed or depicted?

Switching on/off of heuristics

Ring and non-ring heuristics currently not toggleable in the CLI

Result tabulation

CSV or tab delimited

GUI

to allow for display of MCS ad hoc, rather than saving images. Also to support multiple molecule MCS rather than just 2.

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