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ramachandraw

Ramachandran plotting tool

https://github.com/alxdrcirilo/ramachandraw

Science Score: 54.0%

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    Low similarity (12.4%) to scientific vocabulary

Keywords

bioinformatics protein-structure ramachandran
Last synced: 7 months ago · JSON representation ·

Repository

Ramachandran plotting tool

Basic Info
  • Host: GitHub
  • Owner: alxdrcirilo
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 804 KB
Statistics
  • Stars: 20
  • Watchers: 1
  • Forks: 10
  • Open Issues: 0
  • Releases: 1
Topics
bioinformatics protein-structure ramachandran
Created over 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Ramachandran plotting tool

ramachandraw coverage python version Poetry Ruff license: MIT PyPI PyPI - Downloads

Draws a Ramachandran plot based on the input PDB file (e.g. 1mbn.pdb). Makes use of a Gaussian KDE (kernel density estimation) to plot the density of favoured torsion angles (φ and ψ).

Single mode | Batch mode :-------------------------:|:-------------------------: |

Installation

RamachanDraw is hosted on PyPi.

bash pip install ramachandraw

Usage

RamachanDraw includes useful functions to effortlessly draw a Ramachandran plot.

Fetch the PDB file

To draw a Ramachandran plot, we need a PDB file. RamachanDraw conveniently includes a function to automatically fetch and locally store the PDB file for the given PDB id.

Example

```python from ramachandraw.utils import fetch_pdb

fetchpdb(pdbid, verbose) ```

  • pdb_id (str|list|tuple): PDB id(s) corresponding to the PDB file(s) to be downloaded
  • verbose (bool) (optional): set the verbosity, defaults to False
  • Returns: path(s) to PDB file(s)

Extract φ and ψ torsion angles

RamachanDraw extracts the φ and ψ torsion angles from the PDB file by taking advantage of the Biopython module. Additionally, aminoacid residues that were not drawn on the plot can be extract using the return_ignored argument.

Example

```python from ramachandraw.parser import getphipsi

phipsi(pdbfilepath, prune, hide_warnings) ```

  • pdb_id (str|list|tuple): PDB filepath(s)
  • prune (bool) (optional): prunes aminoacids with missing torsion angle(s), defaults to True
  • hide_warnings (bool) (optional): sets the verbosity of the PDB structure parser, defaults to True
  • Returns: Dictionary with keys as aminoacid residues and values as (φ, ψ) angles.

Ramachandran plot

Makes use of the matplotlib module to draw a highly customizable Ramachandran plot.

Example

```python from ramachandraw.utils import plot

plot(pdb_filepath, cmap="viridis", alpha=0.75, dpi=100, save=True, show=False, filename="plot.png") ```

  • pdb_file (str|list|tuple): PDB id(s) corresponding to the PDB entry to be downloaded
  • cmap (str) (optional): colormap to be used (from matplotlib) for the density of the favoured ("allowed") regions; default is viridis.
  • alpha (float) (optional): sets the opacity of the colormap (value between 0-1); default is 0.75.
  • dpi (int) (optional): resolution (in dots per inch); default is 100.
  • save (bool) (optional):
    • True: saves the plot locally; default is True.
  • show (bool) (optional):
    • True: shows the plot using the Qt5Agg backend; default is False.
  • filename (str) (optional): filename to be used in case the plot is saved (i.e. save=True); default is plot.png.
  • Returns: Ramachandran plot (matplotlib.axes.Axes object) that can be further customized if needed

Example

Herein you will find an example from the PDB id corresponding to the myoglobin entry: 1MBN - in the Protein Data Bank.

Single PDB

```python from ramachandraw.parser import getphipsi from ramachandraw.utils import fetch_pdb, plot

PDB id

pdb_id = "1mbn"

Draw the Ramachandran plot

plot(fetchpdb(pdbid))

Generate a dictionary to store the (phi, psi) torsion angles

torsionangles = getphipsi(fetchpdb(pdb_id)) ```

Batch of PDBs

```python from ramachandraw.parser import getphipsi from ramachandraw.utils import fetch_pdb, plot

PDB id

pdb_ids = ["1mbn", "4hhb"]

Draw the Ramachandran plot

plot(fetchpdb(pdbids))

Generate a list of dictionaries to store the (phi, psi) torsion angles

torsionangles = getphipsi(fetchpdb(pdb_ids)) ```

Contributing

Feedback and constructive criticism is welcome. If necessary, open an issue in the issues tab.

License

MIT

Owner

  • Name: Alexandre Cirilo
  • Login: alxdrcirilo
  • Kind: user
  • Location: The Netherlands

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Ramachandraw
version: 1.0.1
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Alexandre
    family-names: Dias Cirilo
repository-code: 'https://github.com/alxdrcirilo/ramachandraw'
repository-artifact: 'https://pypi.org/project/ramachandraw/'
abstract: Ramachandran plotting tool.
keywords:
  - bioinformatics
  - ramachandran
  - protein structure
license: MIT

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 5
Last Year
  • Issues event: 2
  • Issue comment event: 5

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 24
  • Total Committers: 4
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.417
Top Committers
Name Email Commits
alxdrcirilo a****8@h****m 14
Alexandre Cirilo 3****o@u****m 8
underasail u****l@y****m 1
Noah Liguori-Bills n****s@u****u 1
Committer Domains (Top 20 + Academic)
uconn.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 6
  • Total pull requests: 10
  • Average time to close issues: 11 days
  • Average time to close pull requests: 22 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 1.83
  • Average comments per pull request: 0.0
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 2
  • Pull requests: 3
  • Average time to close issues: 2 days
  • Average time to close pull requests: 5 minutes
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • 2young-2simple-sometimes-naive (1)
  • Wenxi-Zhang (1)
  • abhishekiiitdcb (1)
  • bittner (1)
  • noahlb123 (1)
  • SShaminur (1)
Pull Request Authors
  • alxdrcirilo (10)
  • dependabot[bot] (4)
  • Aquaplant (2)
  • noahlb123 (1)
  • underasail (1)
Top Labels
Issue Labels
documentation (2) invalid (1) enhancement (1)
Pull Request Labels
documentation (10) enhancement (6) dependencies (4) good first issue (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 237 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: ramachandraw

Ramachandran plotting tool

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 237 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 11.4%
Stargazers count: 14.5%
Average: 15.4%
Downloads: 19.6%
Dependent repos count: 21.7%
Maintainers (1)
alxdrcirilo
Last synced: 8 months ago

Dependencies

setup.py pypi
  • biopython >=1.75
  • matplotlib >=3.1.2
  • rich >=9.3