molframe 0.5.1

A batteries-included structural bioinformatics engine
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

use super::*;
use crate::{Namespace, ReadOptions, read_bytes};

const SOURCE: &str = "data_q\n\
loop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n\
_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n\
_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\n\
ATOM 1 C C1 LIG A 1 0 0 0\nATOM 2 C C2 LIG A 1 1 0 0\n";

fn structure() -> crate::Structure {
    match read_bytes(
        SOURCE.as_bytes().to_vec(),
        Some("query.cif"),
        &ReadOptions::new(),
    ) {
        Ok((structure, _)) => structure,
        Err(findings) => panic!("read failed: {findings:?}"),
    }
}

#[test]
fn structure_text_selection_connects_query_and_spatial_execution() {
    let policy = AnalysisPolicy {
        identifiers: Namespace::Label,
        ..AnalysisPolicy::default()
    };
    let selected = structure().select_text("within 1.1 of name C1", &policy);
    let selected = match selected {
        Ok(selected) => selected,
        Err(findings) => panic!("select failed: {findings:?}"),
    };
    assert_eq!(selected.selection.iter().collect::<Vec<_>>(), vec![0, 1]);
}

const SHELL: &str = "data_s\n\
loop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n\
_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n\
_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\n\
ATOM 1 C CA ALA A 1 0 0 0\nATOM 2 C CB ALA A 1 1 0 0\n\
HETATM 3 C C1 LIG B 2 0 3 0\nATOM 4 C CA GLY A 3 20 0 0\n";

#[test]
fn context_reading_operands_keep_their_written_order_under_cost_planning() {
    let structure = match read_bytes(
        SHELL.as_bytes().to_vec(),
        Some("shell.cif"),
        &ReadOptions::new(),
    ) {
        Ok((structure, _)) => structure,
        Err(findings) => panic!("read failed: {findings:?}"),
    };
    let policy = AnalysisPolicy {
        identifiers: Namespace::Label,
        ..AnalysisPolicy::default()
    };
    let rows = |text: &str| match structure.select_text(text, &policy) {
        Ok(selected) => selected.selection.iter().collect::<Vec<_>>(),
        Err(findings) => panic!("select failed: {findings:?}"),
    };
    // The membership test is cheaper than the geometric one, so a cost-ordering
    // planner would run it first and hide the ligand from `within`.
    let shell = rows("(within 4 of (resname LIG)) and (not (resname LIG))");
    assert_eq!(shell, vec![0, 1]);
    assert_eq!(
        rows("(not (resname LIG)) and (within 4 of (resname LIG))"),
        Vec::<u32>::new(),
        "the written order is the evaluation order for context-reading operands"
    );
}