molframe-query 0.6.4

Typed and textual structural selection plans for molframe
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
94
95
96

use super::*;
use crate::{Groups, Query};
use molframe_core::contract::AnalysisPolicy;
use molframe_core::io::{InputBuffer, ReadOptions};
use molframe_core::structure::Structure;

const SOURCE: &str = "data_plan\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 GLY A 1 0 0 0\n\
ATOM 2 O O  GLY A 1 1 0 0\n";

#[test]
fn binding_resolves_globs_to_symbols_and_matches_direct_evaluation() {
    let structure = structure();
    let policy =
        AnalysisPolicy::default().with_identifiers(molframe_core::contract::Namespace::Label);
    let query = match Query::compile("name C*") {
        Ok(query) => query,
        Err(findings) => panic!("compile failed: {findings:?}"),
    };
    let plan = query.plan(&structure, &policy);
    assert!(matches!(plan.expr, PhysicalExpr::ResolvedMembership { .. }));
    let result = match plan.evaluate(&structure, &policy, &Groups::new(), None) {
        Ok(result) => result,
        Err(findings) => panic!("physical evaluation failed: {findings:?}"),
    };
    assert_eq!(result.selection.iter().collect::<Vec<_>>(), vec![0]);
}

#[test]
fn constant_branches_are_folded_before_execution() {
    let structure = structure();
    let policy = AnalysisPolicy::default();
    let query = match Query::compile("all and none") {
        Ok(query) => query,
        Err(findings) => panic!("compile failed: {findings:?}"),
    };
    assert!(matches!(
        query.plan(&structure, &policy).expr,
        PhysicalExpr::None
    ));
}

const GLYCAN: &str = "data_glycan\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.auth_seq_id\n_atom_site.auth_comp_id\n\
_atom_site.auth_asym_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\n\
ATOM 1 N N ASN A 1 10 ASN A 0 0 0\n\
HETATM 2 C C1 NAG B . 601 NAG A 5 0 0\n\
HETATM 3 C C1 MAN B . 604 MAN A 10 0 0\n\
HETATM 4 C C2 MAN B . 604 MAN A 11 0 0\n\
HETATM 5 C C1 MAN B . 605 MAN A 12 0 0\n";

#[test]
fn branched_glycan_residues_are_selected_by_component_name() {
    let input = InputBuffer::from_bytes(GLYCAN.as_bytes().to_vec());
    let structure = match molframe_cif::read(&input, &ReadOptions::new()) {
        Ok((structure, _)) => structure,
        Err(findings) => panic!("fixture failed: {findings:?}"),
    };
    let policy = AnalysisPolicy::default();
    for (text, expected) in [
        ("resname MAN", 3),
        ("label_resname MAN", 3),
        ("auth_resname MAN", 3),
        ("resname MAN and hetero", 3),
        ("resname NAG", 1),
        ("resname man", 0),
    ] {
        let query = match Query::compile(text) {
            Ok(query) => query,
            Err(findings) => panic!("compile failed: {findings:?}"),
        };
        let result = match query.plan(&structure, &policy).evaluate(
            &structure,
            &policy,
            &Groups::new(),
            None,
        ) {
            Ok(result) => result,
            Err(findings) => panic!("evaluation failed: {findings:?}"),
        };
        assert_eq!(result.selection.iter().count(), expected, "{text}");
    }
}

fn structure() -> Structure {
    let input = InputBuffer::from_bytes(SOURCE.as_bytes().to_vec());
    match molframe_cif::read(&input, &ReadOptions::new()) {
        Ok((structure, _)) => structure,
        Err(findings) => panic!("fixture failed: {findings:?}"),
    }
}