forlilab / scrubber Goto Github PK
View Code? Open in Web Editor NEWEnumerate conformational, protomeric, and pH-related microstates for docking with AutoDock
License: GNU General Public License v3.0
scrubber's People
Contributors
Stargazers
Watchers
scrubber's Issues
Issues with --out_fname
--out_fname decoys_.sdf:
Observed behavior:
(scrubber) althea@pixar:~/Documents/dev/cryokit/ALK$ scrub.py --in_fname decoys.smi --out_mode split --out_naming name --out_fname decoys_.sdf
[ initializing multiprocessing pipeline ]
[ storage initialized in FILE MODE ]
[ 32 geometry workers initialized ]
[ ▇|▅|▆|▆|▄|▃|▄|▁|▆|▅|▇|▃|▆|▆|▄|▄|▄|█|▇|▁|▃|▅|▇|▅|▅|▇|▄|▄|▄|▅|▆|▄ processing input mol. 4 ] Process MoleculeStorage:
Traceback (most recent call last):
File "/home/althea/programs/miniconda3/envs/scrubber/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/althea/programs/scrubber/scrubber/storage.py", line 374, in run
outfname = self._get_outfname(mol)
File "/home/althea/programs/scrubber/scrubber/storage.py", line 416, in _get_outfname
os.makedirs(dirname)
File "/home/althea/programs/miniconda3/envs/scrubber/lib/python3.10/os.py", line 225, in makedirs
mkdir(name, mode)
FileNotFoundError: [Errno 2] No such file or directory: ''
[ ▄|▇|▄|▄|█|▃|▆|▅|▃|▃|▄|▇|▃|▃|▄|▄|▄|▅|▆|▄|▅|▁|▃|▅|▁|▆|▄|▆|▃|█|▆|▇ processing input mol. 116 ] ( 23.587 mol/sec.)
- program freezes
Expected behavior: - program runs and places files in directory named "decoys"
--out_fname ./decoys_.sdf:
Observed behavior:
- program completes, all expected file written
- written in working directory
Expected behavior:
- program runs and places files in directory named "decoys"
Isomers scrubbed from .smi into sdfs have identical ligand names and are rejected by prepare_reactive_ibm.py
Scrubber working great to create SDF file!
However, the prepare_reactive_ibm.py script rejects the file due to isomers generated with identical ligand names:
SDF file looks like this (identical ligand name highlighted):
--out_mode {split} & -out_naming name currently not working either? Gets stuck here: (image 4)
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.