Comments (4)
Hi,
This is simple - RDKit does not support pdbqt files. The solution is simple, you should use OpenBabel instead.
If you wish to use RDKit you should convert pdbqt to PDB which is supported by RDKit. Unfortunately not all features are available with RDKit, such as Vina docking, due to limited support of file formats.
If it still does not work for you I will need some more information on which part/method of ODDT is failing for you.
from oddt.
Hi,
Thank you for the reply.
One more question: how can I use openbabel instead of rdkit (using that same script)?
from oddt.
Actually if OpenBabel is installed it should be preferred over RDKit. Please verify if you have openbabel installed by:
import pybel
If you fail to import Pybel then you have to properly install Openbabel to your environment.
On the ODDT part you can explicitly set the toolkit to one you desire at the top of your script, right after import oddt
:
oddt.toolkit = oddt.toolkits.ob
OR
oddt.toolkit = oddt.toolkits.rdk
from oddt.
Hi,
That worked but I had to reinstall openbabel using conda.
Thank you!
from oddt.
Related Issues (20)
- Calculating PLEC by bypassing completely OpenBabel HOT 6
- Could there be a new release? HOT 2
- Ring normal vector is calculated incorrectly in pip package HOT 1
- Please do not install tests into the 'test' directory
- failure in completing HOT 4
- Protein structure used does not change when using autodock_vina_descriptor.build()
- PIP distribution does not correspond to github version HOT 1
- Installing oddt from poetry is not possible HOT 3
- TypeError: in method 'new_OBMol' HOT 2
- RDKIT molecule HOT 1
- Training scoring functions and updated version of PDBBind HOT 2
- oodt syntax error HOT 1
- pip installation failed -
- you have a mol2 parser in there? HOT 3
- Docking Issues Between MacOS and Windows HOT 1
- AttributeError: module 'openbabel.openbabel' has no attribute 'OBElementTable' HOT 1
- toolkit not being recognised
- rf = RFScore() TypeError: 'module' object is not callable HOT 2
- for mol in ligands: TypeError: 'NoneType' object is not iterable
- Question about retrain your model on PDBbind-2016 by modifying the 'act' column
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 oddt.