ncats / molwitch-cdk Goto Github PK

View Code? Open in Web Editor NEW

0.0 17.0 3.0 273 KB

License: GNU Lesser General Public License v2.1

Java 100.00%

ncats-dpi-ifx

molwitch-cdk's Introduction

Which Internal Toolkit for CHemicals

MolWitch implementation using CDK

Available on Maven Central

Usually, one needs to add 2 dependencies: 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 CDK molwitch implementation (this version uses CDK 2.6):

<dependency>
        <groupId>gov.nih.ncats</groupId>
        <artifactId>molwitch-cdk</artifactId>
        <version>1.0.9</version>
</dependency>

Current API Contract Compliance

Results from running the latest code on Molwitch-cdk using the API Contract

Feature	Compliance Level	Comments
Extended Tetrahedral	PARTIALLY
Fingerprint	FULLY
fullInchi	FULLY ( 998 )
fullInchi	NOT_COMPLIANT ( 2 )
Valence Error	FULLY ( 1 )
Valence Error	PARTIALLY ( 1 )
Valence Error	NOT_COMPLIANT ( 1 )	Hypervalent Hydrogen Incorrect Valence
parse mol wierd parity	FULLY
inchiKey	FULLY ( 998 )
inchiKey	NOT_COMPLIANT ( 2 )
Remove Non Descript Hydrogens	FULLY
Inchi	FULLY
Default Fingerprinter	FULLY
Mol Parser	FULLY
Create Chemical	FULLY
MolSearcher	FULLY
Write Mol	FULLY
Problematic Smiles	FULLY
Chemical Source	FULLY
Clone Chemical	FULLY
Atom Alias	FULLY
mol parser unknown format	FULLY
Hetero Atom Tetrahedral	FULLY
Tetrahedral	FULLY
Atom Path Traversal	FULLY
Atom Coords	FULLY
Isotopes	FULLY
Cis/Trans	FULLY

molwitch-cdk's People

Contributors

Watchers

Forkers

dkatzel-ncats tylerperyea

molwitch-cdk's Issues

CDK AtomContainer2 Survey/Feedback

Hi NCATS!

I am looking for feedback.

It looks like you create all your CDK IAtomContainers via the builder which is prefer way. This also means you've been using AtomContainer2 for some time (there is a Sys Prop to turn it off). Did you have any issues with this/pain points. Our plan was to remove the old one for v3.0 but obviously the smoother we can make this the better.

Some downstream projects (e.g. AMBIT) look to be creating their containers with new AtomContainer so they may have a bigger "shock".

Thanks,
John

Ring combintorial explosion problem causes problems.

molwitch-cdk/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java

Line 126 in 1e5005c

AllRingsFinder arf = new AllRingsFinder();

This can throw an exception:

Caused by: org.openscience.cdk.exception.CDKException: Threshold exceeded for AllRingsFinder

We don't need to find all rings, just need to mark those bonds that are in rings. If CDK has a detector for a more limited number of rings that's certainly preferable. It would be totally acceptable to find rings < 12 atoms as well, if there is no other option. Again, this is only used to find those bonds that are in rings.

A good example of something that fails here if you call "isRingBond()" is this structure:


   JSDraw209182020322D

 78 90  0  0  1  0              0 V2000
   33.2167  -28.5376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.3601  -29.5987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.7264  -28.9972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.3788  -30.5182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   33.5637  -27.0168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   35.0546  -26.5569    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   35.4014  -25.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   36.9224  -24.6891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   37.5990  -23.2836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   36.9224  -21.8780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   35.4014  -21.5310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.1818  -22.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.1818  -24.0638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   37.8013  -20.5892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   39.3567  -20.7060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.2354  -19.4169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   41.7908  -19.5337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   42.4679  -18.1280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   43.9889  -17.7811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   43.9889  -16.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   45.2080  -15.2485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   46.7290  -15.5952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   47.9958  -14.6850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   48.3802  -13.1732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   47.5016  -11.8846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   47.9618  -10.3937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   46.8178   -9.3325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   49.4136   -9.8236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   48.1248   -8.9449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   49.4136   -8.2636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   50.7648   -7.4839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   50.3609   -5.9772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   51.1407   -4.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   50.1913   -3.3886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   52.6473   -4.2221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   53.9985   -5.0025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   55.1015   -3.8992    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   56.6085   -4.3031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   57.0118   -5.8097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   55.9091   -6.9130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   54.4024   -6.5091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   53.6221   -7.8598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   52.1154   -8.2636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   52.1154   -9.8236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   50.7648  -10.6040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   50.9970  -12.1461    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   49.9362  -13.2895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   51.0528  -14.3787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   51.2082  -15.9311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   50.3295  -17.2199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   48.8278  -17.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   47.4061  -17.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   46.7290  -18.4066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   45.2080  -18.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   45.2080  -20.3135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   43.9889  -21.2861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   42.4679  -20.9388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   41.5892  -22.2280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   40.0338  -22.1111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.1550  -23.4003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.8315  -24.8054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   58.4419   -6.4335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   59.8211   -5.7046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   61.0036   -6.7220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   60.7135   -8.2551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   62.4756   -6.2070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   63.6584   -7.2244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   62.7657   -4.6742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   64.0479   -5.5627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   65.2894   -4.6175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   64.7738   -3.1453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   63.2144   -3.1803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   61.5831   -3.6568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   60.1111   -4.1720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   59.0936   -2.9893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   59.7174   -1.5600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   57.5346   -3.0477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   56.8057   -1.6685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  3  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  6  1  1  0  0  0
  8  7  1  0  0  0  0
  7 13  1  0  0  0  0
  9  8  1  1  0  0  0
  9 10  1  0  0  0  0
 60  9  1  0  0  0  0
 10 11  1  0  0  0  0
 10 14  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 15 14  1  6  0  0  0
 15 16  1  0  0  0  0
 15 59  1  0  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 17 57  1  0  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 19 54  1  0  0  0  0
 21 20  2  0  0  0  0
 22 21  1  0  0  0  0
 22 23  1  6  0  0  0
 22 52  1  0  0  0  0
 24 23  1  6  0  0  0
 24 25  1  0  0  0  0
 24 47  1  0  0  0  0
 26 25  1  0  0  0  0
 26 27  1  1  0  0  0
 28 26  1  0  0  0  0
 28 29  1  1  0  0  0
 30 28  1  0  0  0  0
 45 28  1  0  0  0  0
 31 30  1  6  0  0  0
 31 32  1  0  0  0  0
 31 43  1  0  0  0  0
 33 32  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 36 35  1  6  0  0  0
 36 37  1  0  0  0  0
 36 41  1  0  0  0  0
 38 37  1  6  0  0  0
 38 39  1  0  0  0  0
 77 38  1  0  0  0  0
 39 40  1  1  0  0  0
 39 62  1  0  0  0  0
 41 40  1  1  0  0  0
 41 42  1  0  0  0  0
 43 42  1  1  0  0  0
 43 44  1  0  0  0  0
 45 44  1  1  0  0  0
 45 46  1  0  0  0  0
 47 46  1  1  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  2  0  0  0  0
 50 51  1  0  0  0  0
 52 51  1  0  0  0  0
 52 53  1  1  0  0  0
 54 53  1  1  0  0  0
 54 55  1  0  0  0  0
 55 56  2  0  0  0  0
 57 56  1  0  0  0  0
 57 58  1  1  0  0  0
 59 58  1  1  0  0  0
 59 60  1  0  0  0  0
 60 61  1  6  0  0  0
 63 62  1  1  0  0  0
 63 64  1  0  0  0  0
 74 63  1  0  0  0  0
 64 65  1  6  0  0  0
 64 66  1  0  0  0  0
 66 67  1  1  0  0  0
 66 68  1  0  0  0  0
 68 69  1  0  0  0  0
 68 72  1  0  0  0  0
 68 73  1  6  0  0  0
 69 70  1  0  0  0  0
 70 71  1  0  0  0  0
 72 71  1  0  0  0  0
 74 73  1  6  0  0  0
 75 74  1  0  0  0  0
 75 76  1  6  0  0  0
 75 77  1  0  0  0  0
 77 78  1  1  0  0  0
M  END

Stderr Stacktrace on stdinchikey sometimes

org.openscience.cdk.exception.CDKException: Cannot assign Kekulé structure, non-sigma bond order has already been assigned?
at org.openscience.cdk.aromaticity.Kekulization.kekulize(Kekulization.java:113)
at gov.nih.ncats.molwitch.cdk.CdkChemicalImpl.lambda$kekulize$15(CdkChemicalImpl.java:979)
at gov.nih.ncats.molwitch.cdk.CdkChemicalImpl.doWithQueryFixes(CdkChemicalImpl.java:772)
at gov.nih.ncats.molwitch.cdk.CdkChemicalImpl.kekulize(CdkChemicalImpl.java:977)
at gov.nih.ncats.molwitch.Chemical.kekulize(Chemical.java:540)
at gov.nih.ncats.molwitch.cdk.CdkChemicalInchiImplFactory.asStdInchi(CdkChemicalInchiImplFactory.java:94)
at gov.nih.ncats.molwitch.inchi.Inchi.asStdInchi(Inchi.java:48)
at gov.nih.ncats.molwitch.Chemical.toInchi(Chemical.java:579)
at gov.nih.ncats.molvec.internal.algo.experimental.InChIKeySetScorer.score(InChIKeySetScorer.java:98)
at gov.nih.ncats.molvec.internal.algo.experimental.ModifiedMolvecPipel

I don't know that it should actually throw the exception, but it should probably have a global flag for whether it swallows, throws, or prints. I don't think printing is the right default.

Error when processing some non-most abundant isotopes

"org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 43"

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.