biotite | A comprehensive library for computational molecular biology | Genomics library

by biotite-dev Python Version: 0.40.0 License: BSD-3-Clause

X-Ray Key Features Code Snippets(3)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | biotite Summary

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

A comprehensive library for computational molecular biology

Support

Quality

Security

License

Reuse

Support

biotite has a low active ecosystem.

It has 405 star(s) with 64 fork(s). There are 16 watchers for this library.

There were 2 major release(s) in the last 6 months.

There are 10 open issues and 95 have been closed. On average issues are closed in 65 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of biotite is 0.40.0

Quality

biotite has no bugs reported.

Security

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

License

biotite 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

biotite releases are available to install and integrate.

Deployable package is available in PyPI.

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

Top functions reviewed by kandi - BETA

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

Plot a nucleotide secondary structure
Repeate the atoms at the given coordinate
The number of frames in the stack
Returns the length of the array
Get a structure from the file
Generates a unit cell vectors from a unit cell
Get atoms from CONECT file
Returns the length of the model
Plot a tree
Annotate the SSE
Plot a plasmid map
Align the atoms to the given direction
Get the structure of the GRO file
Plot alignment similarity based on given axes
Compute the Glycosidic bond vectors for each basis pair
Set a PDBx Structure object from an array
Get assembly
Repeat a box
Get the coordinates of a given model
R Compute the stacking of the given atoms
Get a Structure object for a given model
Get the length of the model
Fetch a file from the database
Translate this sequence to a protein sequence
Given an array of atoms return a numpy array of molecule masks
Compute the edge of a given atom array
Plot an alignment type

Get all kandi verified functions for this library.

biotite Key Features

No Key Features are available at this moment for biotite.

biotite Examples and Code Snippets

How do I do multiple pairwise alignments from a FASTA file and print the percentage similarity?

Python

Lines of Code : 46

License : Strong Copyleft (CC BY-SA 4.0)

Copy

import numpy as np
import biotite
import biotite.sequence as seq
import biotite.sequence.io.fasta as fasta
import biotite.sequence.align as align
import biotite.database.entrez as entrez


# 5 example sequences (bacterial luciferase varian

Is there a way to separate the chains belong to each Biological assembly in a PDB file?(python Script)

Python

Lines of Code : 86

License : Strong Copyleft (CC BY-SA 4.0)

Copy

loop_
_pdbx_struct_assembly_gen.assembly_id 
_pdbx_struct_assembly_gen.oper_expression 
_pdbx_struct_assembly_gen.asym_id_list 
1 1 A,D,G,J 
2 1 B,E,H,K 
3 1 C,F,I,L

import biotite.database.rcsb as rcsb
import bio

Download all the heteroComplex protein PDB IDs in RCSB Protein Data Bank

Python

Lines of Code : 4

License : Strong Copyleft (CC BY-SA 4.0)

Copy

import biotite.database.rcsb as rcsb
pdb_ids = rcsb.search(rcsb.EntityCountQuery(min=2, entity_type="protein"))
rcsb.fetch(pdb_ids, format="pdb", target_path="some/directory", verbose=True)

Community Discussions

Trending Discussions on biotite

What does 'PYVERNODOTS' in Python C-extension modules mean?

QUESTION

What does 'PYVERNODOTS' in Python C-extension modules mean?

Asked 2019-Aug-14 at 15:06

When I want to compile Python C-extension modules on Linux, the file name of the compiled modules is for example .cpython-@PYVERNODOTS@m-x86_64-linux-gnu.so. However this only happens, when I compile for Python 3.7, in Python 3.6 the file name is .cpython-36m-x86_64-linux-gnu.so. The problem is, that Python 3.7 is unable to import the module with PYVERNODOTS in the file name, so here are my questions: What does PYVERNODOTS mean? How can I fix the import issue?

EDIT:

I tested this on Ubuntu with Python 3.7.4 from Anaconda. The complete setup script is hosted at https://github.com/biotite-dev/biotite/blob/master/setup.py.

...

ANSWER

Answered 2019-Aug-14 at 15:05

This seems to be an issue with Python 3.7.4. Running the compilation under Python 3.7.3 fixed this problem.

Source https://stackoverflow.com/questions/57473816

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

Vulnerabilities

No vulnerabilities reported

Install biotite

You can install using 'pip install biotite' or download it from GitHub, PyPI.
You can use biotite like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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