Comments (6)
I believe the RDKit now has a complete C++ implementation of the functionality provided by MolVS, including picking a canonical tautomer.
An aside: the python code in https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/MolStandardize is legacy and should be removed.
from molvs.
I think that the part that does tautomer choosing is not part of rdkit.
from molvs.
@UnixJunkie, which part do you mean exactly?
If I compare https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/MolStandardize and https://github.com/mcs07/MolVS/tree/master/molvs, it seems like all modules (except for the commandline interface in cli.py) have been copied into RDKit. Does this also mean that the RDKit repository is the primary location for further development. @mcs07 or @greglandrum , can you comment on this?
I agree with @jvansan that it would be good to mention this in the documentation of this project.
from molvs.
@susanhleung should know if this has been completely integrated into rdkit
from molvs.
@msteijaert the CLI is in rdkit/Contrib/MolVS/molvs_cli.py
from molvs.
Thanks for the clarification! So, if I understand correctly, the recommended python interface is now documented here: http://www.rdkit.org/docs/source/rdkit.Chem.MolStandardize.rdMolStandardize.html? Indeed I see most of the MolVS functionality there. However, I do not see the Standardizer.isotope_parent
reflected there. As an alternative, I use the the following to remove all isotope from my rdchem.Mol
object: _ = [atom.SetIsotope(0) for atom in mol.GetAtoms()]
from molvs.
Related Issues (20)
- Triazole tautomers not normalized
- Tautomer patterns should be referenced to their original research paper.
- Molecule did not standardise overnight HOT 4
- error standardizing ionization HOT 1
- Is there salt removal implemented in there? HOT 3
- TautomerCanonicalizer gives unexpected/forbidden form of phosphoric acid HOT 3
- molvs hugs on some molecules HOT 2
- MolVS 0.1.0 Standardization fails on Python 3 HOT 6
- Fluorine considered metal HOT 1
- stdout=False - output is still printed
- Propagate the warning 'Tautomer enumeration stopped at maximum... '
- test_tautomer.py extended results in C++ implementation HOT 1
- Only one molecule from the input SMILES file is processed... HOT 7
- Tautomer canonicalization bug
- standardize should unsalt
- standardize script of mol file without rdkit or openbabel HOT 2
- tautomer.TautomerEnumerator() function HOT 6
- Unable to standardize some PubChem molecules HOT 1
- Missing preferred citation format in the documentation.
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.
from molvs.