ncats / molwitch

Which Internal Toolkit for CHemicals

MolWitch

MolWitch is a Bridge Pattern wrapper around various Cheminformatics Toolkits so that users can change the underlying toolkit at runtime without changing any client code.

Available on Maven Central

Usually, one needs to add multiple dependencies for both molwitch as well as the underlying toolkit: This adds the API.

<dependency>
  <groupId>gov.nih.ncats</groupId>
  <artifactId>molwitch</artifactId>
  <version>0.6.1</version>
</dependency>

There also needs to be a molwitch implementation

To add molwitch-CDK :

<dependency>
        <groupId>gov.nih.ncats</groupId>
        <artifactId>molwitch-cdk</artifactId>
        <version>1.0.8</version>
</dependency>

License

This project is Open Sourced under the Apache 2.0 However the underlying molwitch implementations may use different licences depending on the license of the underlying toolkit.

molwitch's Issues

Support / require reading unspecified SMARTS bonds as single-or-aromatic on query atoms

From Daylight's SMARTS page:
https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

4.2 Bond Primitives

Various bond symbols are available to match connections between atoms. A missing bond symbol is interpreted as "single or aromatic".

In practice, most tools don't really honor this daylight convention, per se. And that's mostly okay. By a strict reading of the Daylight resource a SMARTS query of c1ccccc1 (benzene) would actually be interpreted as having single-or-aromatic bonds between each atom with each atom itself having at least one aromatic bond somewhere. This is impractical to specify in a molfile.

Typically when a tool produces a SMARTS/SMILES pattern with aromatic atoms (e.g. c) but non-specific bonds between those aromatic atoms (e.g. cc), the common interpretation is that the unspecified bond is aromatic (e.g. c:c). Similarly, when a tool produces a SMARTS/SMILES pattern with aliphatic atoms (e.g. C), but a non-specific bond (e.g. CC), the common interpretation is an implied single bond (e.g. C-C). These conventions are widely used even if they present some problems.

The compromise solution requires a modification to Daylight's statement:

A missing bond symbol BETWEEN ATOMS WHERE AT LEAST ONE ATOM HAS A QUERY FEATURE is interpreted as "single or aromatic".

That is, it's fine to have explicit non-query atoms imply the bonds between them. But if at least one atom is a query atom, AND the SMARTS pattern does not specify a bond type, it should get interpreted as single-or-aromatic. For example:

Ambiguous SMARTS	Equivalent to
cc	c:c
CC	C-C
C[#6]	C-,:[#6]
C[*]	C-,:[*]
[#6,#7][#6]	[#6,#7]-,:[#6]

Here a "query atom" is any atom specified as an atom list (including a list of 1 element) or an atom wildcard.

System identified diazo group as a E/Z center

System identified the double bond in diazo group as a E/Z center; EX 6-DIAZO-5-OXO-L-NORLEUCINE

https://cnigsllc.atlassian.net/browse/GSRS-1323