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psatm

Create pseudoatoms at the centroid of the catalytic atoms of a residue

https://github.com/ugsubmarine/psatm

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.5%) to scientific vocabulary

Keywords

centroid protein protein-structure pseudoatom
Last synced: 10 months ago · JSON representation ·

Repository

Create pseudoatoms at the centroid of the catalytic atoms of a residue

Basic Info
  • Host: GitHub
  • Owner: ugSUBMARINE
  • License: mit
  • Language: Rust
  • Default Branch: master
  • Homepage:
  • Size: 725 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
centroid protein protein-structure pseudoatom
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

psatm

TEST Software License

Based on a given PDB file, this tool creates a new PDB file that includes pseudoatoms for each residue. These pseudoatoms represent the centroids of each residue's catalytic atoms.

If any atoms are missing, the centroid will be calculated based on the available atoms. If there are no catalytic atoms for a specific residue, a warning will be issued.

alt text

Installation

Install rust and cargo

Run cargo build --release to create a binary of the program.

Usage

psatm INFILE OUTFILE

psatm example/gb1.pdb example/gb1_out.pdb

Examples

Can be found here.

The respective outputs are the files with the postfix _out.

File gb1_missing.pdb has the side chain atoms of residue 42 removed to show the output when atoms are missing.

Owner

  • Name: ugSUBMARINE
  • Login: ugSUBMARINE
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Wirnsberger"
  given-names: "Gregor"
  orcid: "https://orcid.org/0000-0001-8331-8636"
title: "psatm"
version: 0.1
date-released: 2025-02-17
url: "https://github.com/ugSUBMARINE/psatm"

GitHub Events

Total
  • Release event: 1
  • Push event: 2
  • Create event: 1
Last Year
  • Release event: 1
  • Push event: 2
  • Create event: 1

Dependencies

.github/workflows/rust.yml actions
  • actions/checkout v3 composite
Cargo.lock cargo
Cargo.toml cargo