Comments (5)
from teachopencadd.
I installed biopython=1.77, but it generated the same error. As a pure biologist, I read the installation instructions but was unable to reproduce them, therefore, I tried this way, open a new Jupyter notebook, and install the following stuff one by one.
'!pip install biopython==1.77'
'!pip install rdkit'
'!pip install biotite'
'!pip install pypdb'
'!pip install nglview'
'!pip install requests-cache'
'!pip install ipywidgets'
'!pip install git+https://github.com/volkamerlab/opencadd.git'
'!pip install MDAnalysis'
'!pip install redo'
Then, I used the import scripts mentioned there, and all the scripts till,
'results = align(complexes, method=METHODS["mda"])' worked properly.
How I installed these packages?
I run the import script, and following the error, took help from google and keep installing each package as mentioned above.
I thought I am doing good.
Best Regards,
from teachopencadd.
Hi Ash, thanks for your reply!
It looks like the environment that you are using for running T008 is not the one where you installed biopython==1.77 as the error AttributeError: module 'Bio' has no attribute 'Alphabet'
should only occur from 1.78 on (see here). Are you sure that the environment that you installed all these packages into, is the one that Jupyter Lab is using to run T008?
We cannot easily debug your custom installation, but we can try to help you get the installation as shown on our website to work for you, as that way, you should have all the correct package versions for all talktorials in place.
Can you tell us (a) where you got stuck in the instructions here and (b) which operating system you are using?
An alternative would be to run T008 in the cloud via Binder:
https://mybinder.org/v2/gh/volkamerlab/TeachOpenCADD/master
(installation setup might take a while though)
from teachopencadd.
Thank you for your response. As I mentioned earlier, I do not have in-depth knowledge of programming, therefore, I opened a notebook and run the installation scripts (mentioned by you) directly, but that did not work either. Then, I found my local way, and first run the import script mentioned in T008. I knew it will generate an error because nothing was installed. I read all the errors one by one, and from there i figure out what packages I will require, and thus I installed all these packages in notebook individually (mentioned above).
You have asked for the environment, I installed "!pip install biopython==1.77", and it said, successfully installed. Also I am working on Win10, Chrome Browser.
ok, i will try to figure out, how to install those scripts on a notebook. Thank you so much once again
from teachopencadd.
I have confirmed the version with,
'print(Bio.version)' that is perfectly fine 1.77.
I included
'from Bio.Alphabet import IUPAC'
'from Bio.Alphabet import Alphabet'
'from Bio.Alphabet import generic_dna, generic_rna, generic_protein'
But now I am having
TypeError: read() got an unexpected keyword argument 'alphabet'
from teachopencadd.
Related Issues (20)
- CI: Cache the conda environment
- [DL Edition] ignore unresponsive sites
- [DL Edition] Add missing thumbnail for T038 HOT 1
- T018: CI fail
- Strategy for data set handling in ML notebooks
- Env: Package ordering
- Conda packaging: env failure HOT 6
- 'no thumb nail' warning on website HOT 1
- Refer to nextAID in the new talktorials HOT 2
- T020: Problem with RMSD Calculation for Resname 03P
- teachopencadd.utils error not found HOT 2
- T019 ยท Molecular dynamics simulation - problems installing dependencies in Colab
- T010: Changed REST API
- T001: Pandas deprecation warnings HOT 1
- T011: Wikipedia scraping fails
- T024: Pandas/jinja import error HOT 1
- Broken docs links
- CI: `black` fails HOT 2
- CI: T006 output fail
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ 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. ๐๐๐
-
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 โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from teachopencadd.