molframe-core 0.6.4

Core types, storage and analysis contracts 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

use super::*;

#[test]
fn edges_are_normalised_deduplicated_and_sorted() {
    let mut builder = BondTableBuilder::new();
    builder.push(BondRecord {
        atom_a: AtomIndex::new(2),
        atom_b: AtomIndex::new(0),
        order: BondOrder::Double,
        provenance: BondProvenance::File,
        kind: OptionalSymbol::NONE,
    });
    builder.push(BondRecord {
        atom_a: AtomIndex::new(0),
        atom_b: AtomIndex::new(2),
        order: BondOrder::Single,
        provenance: BondProvenance::InferredDistance,
        kind: OptionalSymbol::NONE,
    });
    builder.push(BondRecord {
        atom_a: AtomIndex::new(1),
        atom_b: AtomIndex::new(0),
        order: BondOrder::Single,
        provenance: BondProvenance::User,
        kind: OptionalSymbol::NONE,
    });
    let table = builder.finish();
    let records: Vec<_> = table.iter().collect();
    assert_eq!(records.len(), 2);
    assert_eq!((records[0].atom_a.get(), records[0].atom_b.get()), (0, 1));
    assert_eq!((records[1].atom_a.get(), records[1].atom_b.get()), (0, 2));
    assert_eq!(records[1].order, BondOrder::Double);
}

#[test]
fn adjacency_is_compact_bidirectional_and_stably_sorted() {
    let mut builder = BondTableBuilder::new();
    for endpoint in [3, 1, 2] {
        builder.push(BondRecord {
            atom_a: AtomIndex::new(0),
            atom_b: AtomIndex::new(endpoint),
            order: BondOrder::Single,
            provenance: BondProvenance::File,
            kind: OptionalSymbol::NONE,
        });
    }
    let table = builder.finish();
    assert_eq!(
        table.adjacency(4).neighbours(AtomIndex::new(0)),
        &[AtomIndex::new(1), AtomIndex::new(2), AtomIndex::new(3)]
    );
    assert_eq!(
        table.adjacency(4).neighbours(AtomIndex::new(2)),
        &[AtomIndex::new(0)]
    );
}

#[test]
fn coordination_requires_its_deposited_class_independently_of_order_and_provenance() {
    let mut dictionary = crate::symbol::Interner::default();
    let mut bond = BondRecord::unclassified(
        AtomIndex::new(0),
        AtomIndex::new(1),
        BondOrder::Single,
        BondProvenance::File,
    );
    assert!(!bond.is_metal_coordination(&dictionary));
    for (kind, coordinated) in [
        ("covale", false),
        ("metalc", true),
        ("METALC", true),
        ("disulf", false),
        ("source-specific", false),
    ] {
        let symbol = dictionary.intern(kind).expect("connection class");
        bond.kind = OptionalSymbol::some(symbol);
        assert_eq!(bond.is_metal_coordination(&dictionary), coordinated);
    }
}