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com.simolecule.centres

Perception and labelling of stereogenic centres in chemical structures

https://github.com/simolecule/centres

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (10.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Perception and labelling of stereogenic centres in chemical structures

Basic Info
  • Host: GitHub
  • Owner: SiMolecule
  • License: bsd-2-clause
  • Language: Java
  • Default Branch: develop
  • Size: 686 KB
Statistics
  • Stars: 18
  • Watchers: 7
  • Forks: 4
  • Open Issues: 0
  • Releases: 2
Created over 13 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

Stereochemistry Labelling Done Good

Centres is an Open Source Java library for that allows perception and labelling of stereogenic centres in chemical structures using the Cahn-Ingold-Prelog priority rules.

How to Use

You can use Centres interactively at http://www.simolecule.com/cdkdepict by selecting the annotation "CIP Stereo Label". Alternatively you can download the centres.jar (built on CDK) from the releases page. This JAR can be used to label and test an SD or SMILES file.

java -jar centres.jar input.sdf

To run the benchmark tests pressented by Hanson et al (note limitations below) run the following commands. The files can be downloaded from https://cipvalidationsuite.github.io/ValidationSuite/.

java -jar centres.jar compounds_2d.sdf -e CIP_LABELS java -jar centres.jar compounds_3d.sdf -e CIP_LABELS java -jar centres.jar compounds.smi -e 1

Key Features

  • Generic library allowing dependency injection of any molecule/atom object representation. Currently supported 'endpoints':
  • Perception and labelling of tetrahedral (R/S/r/s) and geometric double bonds (Z/E).
  • Implementation of the Cahn-Ingold-Prelog (CIP) priority rules as they appear in Prelog and Helmchen, 1982
  • Implementation of the Cahn-Ingold-Prelog (CIP) priority rules as they appear in Nomenclature of Organic Chemistry, IUPAC Recommendations and Preferred Names 2013

Install

jchem and opsin backends do not currently pass the internal validation tests and should be skipped when running tests.

mvn install -pl '!jchem,!opsin'

alternatively skip the tests:

mvn install -DskipTests

License

BSD 2-Clause

Authors

John Mayfield (né May)

Limitations

  • Helicene and chirality planes are not supported
  • SMILES does not capture axial atropisomerism but this is supported in 2D/3D
  • When using CDK the 3D SDfile must find stereocentres with little information available, the current algorithm does not find all centres in the test sets by default. To prevent this a modified version of CDK is used in Centres that captures all possible tetrahedral/double bond stereochemistries.

References

  • Robert M. Hanson John Mayfield Mikko J. Vainio Andrey Yerin Dmitry Redkin Sophia Musacchio. Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. Submitted preprint.
  • Prelog and Helmchen. Basic Principles of the CIP-System and Proposals for a Revision. Angewandte Chemie International Edition 21 (1982) 567-683
  • Perdih and Rmzinger. Stereo-chemistry and Sequence Rules A Proposal for Modification of Cahn-Ingold-Prelog System. Tetrahedron: Asymmetry Vol 5 (1994) 835-861

Owner

  • Name: Silicon Molecule
  • Login: SiMolecule
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "John"
  given-names: "Mayfield"
  orcid: "https://orcid.org/0000-0001-7730-2646"
title: "centres"
version: 1.0
doi: 10.1021/acs.jcim.8b00324
date-released: 2018-06-28
url: "https://github.com/SiMolecule/centres"

GitHub Events

Total
  • Fork event: 2
Last Year
  • Fork event: 2

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 7
  • Total pull requests: 2
  • Average time to close issues: 12 days
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 4.29
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 6
  • Pull requests: 1
  • Average time to close issues: 15 days
  • Average time to close pull requests: about 9 hours
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 4.83
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • iclkevin (6)
  • egonw (1)
  • greglandrum (1)
  • shubbey (1)
Pull Request Authors
  • dependabot[bot] (1)
  • nobkd (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 4
  • Total downloads: unknown
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 16
repo1.maven.org: com.simolecule.centres:centres-core

Library of Labelling Stereochemistry

  • Versions: 4
  • Dependent Packages: 2
  • Dependent Repositories: 1
Rankings
Dependent repos count: 20.8%
Dependent packages count: 23.2%
Average: 33.8%
Stargazers count: 42.8%
Forks count: 48.3%
Last synced: 7 months ago
repo1.maven.org: com.simolecule.centres:centres

Library of Labelling Stereochemistry

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Stargazers count: 29.9%
Dependent repos count: 32.0%
Forks count: 33.1%
Average: 36.0%
Dependent packages count: 48.9%
Last synced: 6 months ago
repo1.maven.org: com.simolecule.centres:centres-opsin

Library of Labelling Stereochemistry

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Stargazers count: 29.9%
Dependent repos count: 32.0%
Forks count: 33.1%
Average: 36.0%
Dependent packages count: 48.9%
Last synced: 6 months ago
repo1.maven.org: com.simolecule.centres:centres-cdk

Library of Labelling Stereochemistry

  • Versions: 4
  • Dependent Packages: 1
  • Dependent Repositories: 1
Rankings
Dependent repos count: 20.8%
Dependent packages count: 33.0%
Average: 36.2%
Stargazers count: 42.8%
Forks count: 48.3%
Last synced: 6 months ago

Dependencies

cdk/pom.xml maven
  • com.simolecule.centres:centres-core 1.2-SNAPSHOT
  • junit:junit
  • org.openscience.cdk:cdk-ctab 2.7.1
  • org.openscience.cdk:cdk-interfaces 2.7.1
  • org.openscience.cdk:cdk-io 2.7.1
  • org.openscience.cdk:cdk-silent 2.7.1
  • org.openscience.cdk:cdk-smiles 2.7.1
  • org.openscience.cdk:cdk-standard 2.7.1
  • com.simolecule.centres:centres-core 1.2-SNAPSHOT test
core/pom.xml maven
  • com.google.guava:guava 30.0-jre
  • junit:junit
  • org.hamcrest:hamcrest-all
jchem/pom.xml maven
  • com.chemaxon:chemaxon-common 14.11.10.0 provided
  • com.chemaxon:chemaxon-concurrent 14.11.10.0 provided
  • com.chemaxon:chemaxon-concurrent-utils 14.11.10.0 provided
  • com.chemaxon:chemaxon-core 14.11.10.0 provided
  • com.chemaxon:chemaxon-io 14.11.10.0 provided
  • com.chemaxon:chemaxon-io-smiles 14.11.10.0 provided
  • com.chemaxon:chemaxon-license 14.11.10.0 provided
  • com.simolecule.centres:centres-core 1.0
opsin/pom.xml maven
  • ${project.groupId}:centres-core 1.2-SNAPSHOT
  • junit:junit
  • uk.ac.cam.ch.opsin:opsin-core 2.6.0
  • ${project.groupId}:centres-core 1.2-SNAPSHOT test
pom.xml maven
  • junit:junit 4.13.1 test
  • org.hamcrest:hamcrest-all 1.3 test