molframe 0.6.4

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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156

//! Round-trip fidelity of real deposited files across cif, bcif and pdb:
//! text and binary mmCIF must be lossless, PDB must agree within its column
//! precision, and every PDB loss must be reported rather than silent.

use molframe::formats::pdb::{PdbIdentifierNamespace, PdbOptions};
use molframe::{ReadOptions, Structure, StructureDifferenceOptions};
use std::path::PathBuf;

const PDB_TOLERANCE: f32 = 0.0005;

fn bench(name: &str) -> PathBuf {
    PathBuf::from(env!("CARGO_MANIFEST_DIR"))
        .join("../molframe-bench/data")
        .join(name)
}

fn read(bytes: Vec<u8>, name: &str) -> Structure {
    match molframe::read_bytes(bytes, Some(name), &ReadOptions::new()) {
        Ok((structure, _)) => structure,
        Err(failure) => panic!("{name}: {failure:?}"),
    }
}

fn load(name: &str) -> Structure {
    let bytes = std::fs::read(bench(name)).unwrap();
    read(bytes, name)
}

fn auth_options() -> PdbOptions {
    PdbOptions::new().namespace(PdbIdentifierNamespace::Auth)
}

fn difference(
    left: &Structure,
    right: &Structure,
    tolerance: f32,
) -> molframe::StructureDifference {
    molframe::structure_difference(
        left,
        right,
        StructureDifferenceOptions {
            coordinate_tolerance: tolerance,
        },
    )
    .unwrap()
}

fn identical(left: &Structure, right: &Structure, tolerance: f32) -> bool {
    difference(left, right, tolerance).is_empty()
}

#[test]
fn text_mmcif_rewrites_without_any_difference() {
    for name in ["1crn.cif", "1ubq.cif", "4hhb.cif"] {
        let source = load(name);
        let text = molframe::write_mmcif(&source).unwrap();
        let again = read(text.into_bytes(), "again.cif");
        assert!(identical(&source, &again, 0.0), "{name}");
    }
}

#[test]
fn binary_mmcif_matches_text_mmcif_exactly() {
    for name in ["1crn.cif", "1ubq.cif", "4hhb.cif", "1aon.bcif"] {
        let source = load(name);
        let text = molframe::write_mmcif(&source).unwrap();
        let binary = read(molframe::write_bcif(&source).unwrap(), "again.bcif");
        assert!(identical(&source, &binary, 0.0), "{name}");
        assert_eq!(molframe::write_mmcif(&binary).unwrap(), text, "{name}");
    }
}

#[test]
fn pdb_projection_of_mmcif_agrees_within_column_precision() {
    for name in ["1crn.cif", "1ubq.cif", "4hhb.cif"] {
        let source = load(name);
        let pdb = molframe::write_pdb(&source, &auth_options()).unwrap();
        let again = read(pdb.into_bytes(), "again.pdb");
        let diff = difference(&source, &again, PDB_TOLERANCE);
        assert_eq!(atom_fields(&source), atom_fields(&again), "{name}");
        assert_eq!(diff.changed_positions, 0, "{name}");
    }
}

#[test]
fn pdb_rewrites_to_identical_coordinate_records() {
    for name in ["1crn.pdb", "1ubq.pdb", "4hhb.pdb", "2m7c.pdb"] {
        let source = load(name);
        let first = molframe::write_pdb(&source, &auth_options()).unwrap();
        let again = read(first.clone().into_bytes(), "again.pdb");
        let second = molframe::write_pdb(&again, &auth_options()).unwrap();
        assert_eq!(
            coordinate_lines(&first),
            coordinate_lines(&second),
            "{name}"
        );
    }
}

#[test]
fn pdb_to_mmcif_keeps_the_chain_count() {
    for name in ["1ubq.pdb", "4hhb.pdb", "1crn.pdb"] {
        let source = load(name);
        let text = molframe::write_mmcif(&source).unwrap();
        let again = read(text.into_bytes(), "again.cif");
        assert_eq!(
            source.engine().data().chains().count(),
            again.engine().data().chains().count(),
            "{name}"
        );
    }
}

#[test]
fn entity_bearing_mmcif_reports_its_pdb_loss() {
    let source = load("4hhb.cif");
    let (_, findings) = molframe::write_pdb_with_findings(&source, &auth_options()).unwrap();
    assert!(
        findings
            .iter()
            .any(|f| f.code().to_string().contains("W4101"))
    );
}

fn coordinate_lines(pdb: &str) -> Vec<&str> {
    pdb.lines()
        .filter(|l| {
            ["ATOM", "HETAT", "TER", "ANISO"]
                .iter()
                .any(|p| l.starts_with(p))
        })
        .collect()
}

/// Per-atom fields a PDB atom record carries; label chain ids are excluded
/// because PDB writes one namespace and reports the other as lost.
fn atom_fields(structure: &Structure) -> Vec<String> {
    (0..structure.atom_count())
        .map(|i| {
            let atom = structure
                .engine()
                .atom(molframe::AtomIndex::new(i))
                .unwrap();
            format!(
                "{:?}|{:?}|{:?}|{:?}|{:?}|{:?}|{:?}",
                atom.auth_name(),
                atom.component_name(),
                atom.element(),
                atom.alt_label(),
                atom.b_factor(),
                atom.occupancy(),
                atom.formal_charge()
            )
        })
        .collect()
}