bio_apis 0.2.4

DNA and RNA sequence types and functions
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93

//! Load amber Mol2, lib, and FRCMOD data for a given small organic molecule.
//! These are from the AMBER_GEOSTD collection, CAO Amber 2025, and hosted
//! on our own system.
//!
//! Note: Identifiers in this module can be Amber GeoStd/PDBe (Should be same), or PubChem.

use std::collections::HashMap;

use serde::Deserialize;

use crate::{ReqError, make_agent};

const BASE_URL: &str = "https://www.athanorlab.com";

#[derive(Clone, Debug, Deserialize)]
pub struct GeostdItem {
    pub ident_pdbe: String,
    pub pubchem_cid: Option<u32>,
    pub frcmod_avail: bool,
    pub lib_avail: bool,
}

/// Contains the text content of these files.
#[derive(Clone, Debug, Deserialize)]
pub struct GeostdData {
    pub mol2: String,
    pub frcmod: Option<String>,
    pub lib: Option<String>,
    pub pubchem_cid: Option<u32>,
}

#[derive(Clone, Debug, Deserialize)]
struct GeostdItemResponse {
    pub result: Vec<GeostdItem>,
}

/// Get a list of all molecules available from Amber Geostd, and if they include FRCMOD and lib data.
pub fn get_all_mols() -> Result<Vec<GeostdItem>, ReqError> {
    let agent = make_agent();

    let url = format!("{BASE_URL}/get-all-mols");
    let resp = agent.get(url).call()?.body_mut().read_to_string()?;

    let parsed: GeostdItemResponse = serde_json::from_str(&resp)?;
    Ok(parsed.result)
}

/// Search for molecules by keyword, and find if they include FRCMOD and lib data.
pub fn find_mols(search_text: &str) -> Result<Vec<GeostdItem>, ReqError> {
    let agent = make_agent();

    let mut params = HashMap::new();
    params.insert("search_text", search_text);
    let payload_json = serde_json::to_string(&params)?;

    let url = format!("{BASE_URL}/find-mols");

    let resp = agent
        .post(url)
        .header("Content-Type", "application/json")
        .send(&payload_json)?
        .body_mut()
        .read_to_string()?;

    let parsed: GeostdItemResponse = serde_json::from_str(&resp)?;
    Ok(parsed.result)
}

/// Download a Mol2 file's text, and if available, FRCMOD and Lib, as well as metadata
pub fn load_mol_files(ident: &str) -> Result<GeostdData, ReqError> {
    let agent = make_agent();

    let mut params = HashMap::new();
    params.insert("ident", ident);
    let payload_json = serde_json::to_string(&params)?;

    let url = format!("{BASE_URL}/load-mol-files");

    let resp = agent
        .post(url)
        .header("Content-Type", "application/json")
        .send(&payload_json)?
        .body_mut()
        .read_to_string()?;

    Ok(serde_json::from_str(&resp)?)
}

/// Download a Mol2 file from our Amber Geostd database, returning an Mol2 string.
pub fn load_mol2(ident: &str) -> Result<String, ReqError> {
    let data = load_mol_files(ident)?;
    Ok(data.mol2)
}