molframe 0.6.1

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
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
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133

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 = selected.expect("select failed");
    assert_eq!(selected.selection.iter().collect::<Vec<_>>(), vec![0, 1]);
}

#[test]
fn facade_selection_uses_the_callers_cancellation_for_simple_and_spatial_queries() {
    let structure = structure();
    let policy = AnalysisPolicy {
        identifiers: Namespace::Label,
        ..AnalysisPolicy::default()
    };
    let context = ExecutionContext::default();
    for query in ["name C1", "within 1.1 of name C1"] {
        let expected = structure.select(query, &policy).expect("default query");
        let actual = structure
            .select_with_context(query, &policy, &context)
            .expect("governed query");
        assert_eq!(
            actual
                .atoms()
                .map(molframe_core::structure::AtomRef::index)
                .collect::<Vec<_>>(),
            expected
                .atoms()
                .map(molframe_core::structure::AtomRef::index)
                .collect::<Vec<_>>()
        );
    }
    context.cancellation().cancel();
    for query in ["name C1", "within 1.1 of name C1"] {
        let failure = structure
            .select_with_context(query, &policy, &context)
            .expect_err("cancelled");
        assert!(failure.to_string().contains("E1904"));
    }
}

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"
    );
}

const TWO_CHAINS: &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.auth_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 H 1 0 0 0\nATOM 2 C C2 LIG A H 1 1 0 0\n\
ATOM 3 C C3 LIG B L 1 2 0 0\nATOM 4 C C4 LIG B L 1 50 0 0\n";

#[test]
fn a_conjunction_selects_the_same_atoms_in_either_order() {
    let structure = match read_bytes(
        TWO_CHAINS.as_bytes().to_vec(),
        Some("two.cif"),
        &ReadOptions::new(),
    ) {
        Ok((structure, _)) => structure,
        Err(findings) => panic!("read failed: {findings:?}"),
    };
    let policy = AnalysisPolicy::default();
    let pick = |query: &str| -> Vec<u32> {
        match structure.select_text(query, &policy) {
            Ok(selected) => selected.selection.iter().collect(),
            Err(findings) => panic!("select failed: {findings:?}"),
        }
    };
    let forward = pick("chain H and within 1.5 of chain L");
    assert_eq!(forward, vec![1]);
    assert_eq!(forward, pick("within 1.5 of chain L and chain H"));
    assert_eq!(
        pick("chain H and byres chain L"),
        pick("byres chain L and chain H")
    );
}