biopandas | Working with molecular structures in pandas DataFrames | Dataset library

by rasbt Python Version: 0.5.1.dev0 License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | biopandas Summary

biopandas is a Python library typically used in Artificial Intelligence, Dataset applications. biopandas has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. However biopandas has 11 bugs. You can install using 'pip install biopandas' or download it from GitHub, PyPI.

Working with molecular structures in pandas DataFrames

Support

Quality

Security

License

Reuse

Support

biopandas has a low active ecosystem.

It has 428 star(s) with 94 fork(s). There are 15 watchers for this library.

It had no major release in the last 12 months.

There are 17 open issues and 25 have been closed. On average issues are closed in 113 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of biopandas is 0.5.1.dev0

Quality

biopandas has 11 bugs (0 blocker, 0 critical, 2 major, 9 minor) and 22 code smells.

Security

biopandas has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

biopandas code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

biopandas is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

biopandas releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

biopandas saves you 4052 person hours of effort in developing the same functionality from scratch.

It has 8614 lines of code, 89 functions and 37 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed biopandas and discovered the below as its top functions. This is intended to give you an instant insight into biopandas implemented functionality, and help decide if they suit your requirements.

Generate API documentation for a package
Convert an object to markdown
Return a list of functions and classes
Convert a docstring to markdown
Read a mmCif file
Construct a dataframe from a cif file
Parse a file - like object
Load CIF data from a file
Read a PDB file
Construct a pandas DataFrame from a pdb file
Parse header and code
Import a package
Convert ipynb to markdown
Generate summary files for each module

Get all kandi verified functions for this library.

biopandas Key Features

No Key Features are available at this moment for biopandas.

biopandas Examples and Code Snippets

No Code Snippets are available at this moment for biopandas.

Community Discussions

Trending Discussions on biopandas

ValueError: Unable to coerce list of to Series/DataFrame

Biopython cannot download .PDB files now

QUESTION

ValueError: Unable to coerce list of to Series/DataFrame

Asked 2021-May-27 at 14:22

I am using distance_df function from biopandas to calculate distance of a bunch of atoms form a reference point. The function is working fine, but I am getting this Value error in one part of my code. Basically I am dividing the CLR into 4 parts to check distance of each part from the interacting amino acids. Everything is working fine, but the code is stuck at the last line, it was working before a month, was there any update to biopandas? It's more biology so if anyone has any question about the code i would be happy to clear them. I haven't encountered this error ever and have no idea what to do. Thank you in advance :)

...

ANSWER

Answered 2021-May-27 at 14:22

Thank you, everyone. I have solved the issue. If anyone gets similar error here is the solution: In my case the error was because these three variables:

Source https://stackoverflow.com/questions/67694889

QUESTION

Biopython cannot download .PDB files now

Asked 2020-Sep-18 at 20:22

I am having trouble with Biopyhton. I used this code to download a set of proteins

...

ANSWER

Answered 2020-Sep-18 at 20:22

By looking at the pages https://www.rcsb.org/structure/2DD6 and https://www.rcsb.org/structure/1lbO I can see: Protein 2DD6 does exist and returns a HTTP 200 result. A protein with ID 1lbO just does not exist so I get a 404 (page not found). And iee7 is not even a valid PDB ID as it does not start with a number. Protein 1EE7 does exist - Maybe a typo?

Source https://stackoverflow.com/questions/63947111

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install biopandas

For more information, please see http://rasbt.github.io/biopandas/installation/.
install the latest version (from GitHub): pip install git+git://github.com/rasbt/biopandas.git#egg=biopandas
install the latest PyPI version: pip install biopandas
install biopandas via conda-forge: conda install biopandas -c conda-forge
Python 2.7, 3.5, or 3.6
NumPy >= 1.11.2
SciPy >= 0.18.1
Pandas >= 0.19.1

Support

If you are a computational biologist, chances are that you cursed one too many times about protein structure files. Yes, I am talking about ye Goode Olde Protein Data Bank format, aka "PDB files." Nothing against PDB, it's a neatly structured format (if deployed correctly); yet, it is a bit cumbersome to work with PDB files in "modern" programming languages -- I am pretty sure we all agree on this.

Find more information at: