molframe 0.5.2

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

//! Optional CIF-domain projections attached by the public facade.

#[cfg(feature = "modelcif")]
use molframe_core::Code;
use molframe_core::io::{ReadOptions, ReadResult};
use molframe_core::{Diagnostic, Structure};

pub(super) fn keep_non_model_extension_category(category: &str) -> bool {
    #[cfg(feature = "crystal")]
    if matches!(
        category,
        "pdbx_struct_oper_list"
            | "pdbx_struct_assembly"
            | "pdbx_struct_assembly_gen"
            | "struct_ncs_oper"
            | "space_group"
            | "symmetry"
            | "space_group_symop"
            | "symmetry_equiv"
    ) {
        return true;
    }
    #[cfg(not(feature = "crystal"))]
    let _ = category;
    false
}

/// Attaches extensions from a document supplied by an explicitly materialising format.
pub(super) fn attach_materialized_cif_metadata(
    document: &molframe_cif::Document,
    structure: Structure,
    findings: Vec<Diagnostic>,
    options: &ReadOptions,
) -> ReadResult {
    #[cfg(feature = "modelcif")]
    let (structure, findings) = {
        let projected = molframe_modelcif::lower(document);
        attach_model(structure, findings, projected)
    };
    let (structure, findings) = attach_non_model(document, structure, findings);
    options.finish(structure, findings)
}

#[cfg(feature = "modelcif")]
pub(super) fn attach_projected_metadata(
    document: &molframe_cif::Document,
    structure: Structure,
    findings: Vec<Diagnostic>,
    projected: Result<
        (molframe_modelcif::ModelCif, Vec<Diagnostic>),
        molframe_modelcif::ModelCifError,
    >,
    options: &ReadOptions,
) -> ReadResult {
    let (structure, findings) = attach_model(structure, findings, projected);
    let (structure, findings) = attach_non_model(document, structure, findings);
    options.finish(structure, findings)
}

#[cfg(feature = "modelcif")]
fn attach_model(
    mut structure: Structure,
    mut findings: Vec<Diagnostic>,
    projected: Result<
        (molframe_modelcif::ModelCif, Vec<Diagnostic>),
        molframe_modelcif::ModelCifError,
    >,
) -> (Structure, Vec<Diagnostic>) {
    match projected {
        Ok((model, model_findings)) => {
            findings.extend(model_findings);
            if !model.is_empty() {
                match model.plddt_annotation(&structure) {
                    Ok(Some(column)) => {
                        let mut data = structure.data().clone();
                        let _ = data.annotations.insert(
                            molframe_core::annotation::PLDDT_ANNOTATION,
                            molframe_core::annotation::AtomAnnotation::Real(column),
                        );
                        structure = Structure::new(data);
                    }
                    Ok(None) => {}
                    Err(error) => findings.push(
                        Diagnostic::new(Code::E1901)
                            .with_message(error.to_string())
                            .in_category("ma_qa_metric_local"),
                    ),
                }
                structure = structure.with_extension(molframe_modelcif::MODEL_CIF_EXTENSION, model);
            }
        }
        Err(error) => findings.push(model_error(&error)),
    }
    (structure, findings)
}

#[cfg(feature = "modelcif")]
pub(super) fn model_error(error: &molframe_modelcif::ModelCifError) -> Diagnostic {
    Diagnostic::new(Code::E1901)
        .with_message(error.to_string())
        .in_category("ma_*")
}

fn attach_non_model(
    document: &molframe_cif::Document,
    structure: Structure,
    findings: Vec<Diagnostic>,
) -> (Structure, Vec<Diagnostic>) {
    #[cfg(feature = "crystal")]
    {
        let mut structure = structure;
        let mut findings = findings;
        match molframe_xtal::lower_assemblies(document) {
            Ok(assemblies) if !assemblies.is_empty() => {
                structure =
                    structure.with_extension(molframe_xtal::ASSEMBLIES_EXTENSION, assemblies);
            }
            Ok(_) => {}
            Err(values) => findings.extend(values),
        }
        match molframe_xtal::lower_ncs(document) {
            Ok(ncs) if !ncs.is_empty() => {
                structure = structure.with_extension(molframe_xtal::NCS_EXTENSION, ncs);
            }
            Ok(_) => {}
            Err(values) => findings.extend(values),
        }
        match molframe_xtal::lower_symmetry(document) {
            Ok(symmetry) if !symmetry.is_empty() => {
                structure = structure.with_extension(molframe_xtal::SYMMETRY_EXTENSION, symmetry);
            }
            Ok(_) => {}
            Err(values) => findings.extend(values),
        }
        (structure, findings)
    }
    #[cfg(not(feature = "crystal"))]
    {
        let _ = document;
        (structure, findings)
    }
}