https://github.com/sciencegenome/pdb-euclidean-proteome
rust pdb proteome
https://github.com/sciencegenome/pdb-euclidean-proteome
bioinformatics evolutionary-algorithms evolutionary-biology evolutionary-computation evolutionary-genome pangenome
Last synced: about 2 months ago
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rust pdb proteome
- Host: GitHub
- URL: https://github.com/sciencegenome/pdb-euclidean-proteome
- Owner: sciencegenome
- License: mit
- Created: 2025-01-28T20:43:59.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2025-01-30T21:00:55.000Z (4 months ago)
- Last Synced: 2025-02-16T01:31:47.465Z (3 months ago)
- Topics: bioinformatics, evolutionary-algorithms, evolutionary-biology, evolutionary-computation, evolutionary-genome, pangenome
- Language: Rust
- Homepage:
- Size: 6.45 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# pdb-euclidean-proteome
- rust evolutionary proteome
- it reports only chains with atoms for the id and sequence and euclidean distance for all irrespective of chain and atoms.
- Euclidean distance chain comparsion for two point coordinate protein.
- Euclidean distance chain coordinate comparsion for all protein atoms of the chain.
- please see the last commit message and if it says compiled binary then it is completed or else still in development version.
```
cargo build
```
```
➜ evolutionary-proteome git:(main) ✗ ./target/debug/pdb-proteome -h
set of evolutionary analysis for proteome
Usage: pdb-proteome
Commands:
pdb-id
pdb-sequence extract the sequence of the pdf file
euclidean-comparative calculate the euclidean distance bettwen two chain coordinates
euclidean-all calculates the euclidean distance for all chain atoms
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
```
```
➜ evolutionary-proteome git:(main) ✗
./target/debug/pdb-proteome euclidean-comparative sample.pdb A 10 10 N CA
The eucledian distance between to given coordinates of the same chain is 1.4656264
➜ evolutionary-proteome git:(main) ✗
./target/debug/pdb-proteome euclidean-comparative sample.pdb A 1 1 N CA
The eucledian distance between to given coordinates of the same chain is 1.4909409
```
```
➜ evolutionary-proteome git:(main) ✗ ./target/debug/pdb-proteome euclidean-all sample.pdb A
The vector containing the eucleadian distance for those chain atoms are:
[1.4909409, 1.5401275, 1.254727, 3.479588, 1.4994173, 1.4884146 ...]
and will write a eucledian file as
32.231 15.281 -13.143 32.184 14.697 -11.772 1.4909409
32.184 14.697 -11.772 33.438 13.89 -11.387 1.5401275
33.438 13.89 -11.387 34.102 13.07 -12.066 1.254727
34.102 13.07 -12.066 30.797 14.065 -11.625 3.479588
30.797 14.065 -11.625 30.976 12.589 -11.819 1.4994173
30.976 12.589 -11.819 29.608 12.016 -11.694 1.4884146
29.608 12.016 -11.694 28.942 12.335 -12.945 1.4526931
28.942 12.335 -12.945 27.67 12.696 -13.05 1.3263968
27.67 12.696 -13.05 26.901 12.777 -11.999 1.3048087
26.901 12.777 -11.999 27.161 12.963 -14.255 2.2785378
```
Gaurav Sablok