molframe-cif 0.1.1

PDBx/mmCIF reading and writing 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
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

//! Reconcile entry and entity metadata collected after coordinates started.

use super::entry::{AsymEntity, read_asym_entities, read_cell, read_entities, read_entry};
use crate::document::DataBlock;
use molframe_core::diagnostic::{Code, Diagnostic, Diagnostics};
use molframe_core::index::EntityIndex;
use molframe_core::io::ReadOptions;
use molframe_core::optional::OptionalSymbol;
use molframe_core::structure::StructureData;
use molframe_core::symbol::SymbolId;
use molframe_core::topology::{ChainRecord, ChainTable, EntityKind, EntityTable, PolymerKind};
use std::ops::Range;

pub(super) fn refresh(
    block: &DataBlock,
    options: &ReadOptions,
    data: &mut StructureData,
    findings: &mut Diagnostics,
) {
    if !options.only_atomic_coords {
        data.entry = molframe_core::structure::EntryMetadata::default();
        data.cell = None;
        read_entry(block, data, findings);
        read_cell(block, data);
    }
    refresh_entities(block, data, findings);
}

#[derive(Clone)]
struct ChainSnapshot {
    label: SymbolId,
    auth: OptionalSymbol,
    entity_id: Option<SymbolId>,
    residues: Range<u32>,
}

fn refresh_entities(block: &DataBlock, data: &mut StructureData, findings: &mut Diagnostics) {
    let chains = chain_snapshots(data);
    data.topology.entities = EntityTable::default();
    read_entities(block, data, findings);
    let mappings = read_asym_entities(block, data, findings);
    retain_provisional_entities(&chains, data, findings);

    let mut rebuilt = ChainTable::default();
    for chain in chains {
        let Some(entity) = resolve_entity(&chain, &mappings, data, findings) else {
            continue;
        };
        let polymer_kind = match data.topology.entities.kind(entity) {
            Some(EntityKind::Polymer) => PolymerKind::Other,
            _ => PolymerKind::None,
        };
        if rebuilt
            .push(
                ChainRecord {
                    label_asym_id: chain.label,
                    auth_asym_id: chain.auth,
                    entity,
                    polymer_kind,
                },
                chain.residues,
            )
            .is_err()
        {
            findings.push(Diagnostic::new(Code::E3001));
        }
    }
    data.topology.chains = rebuilt;
}

fn chain_snapshots(data: &StructureData) -> Vec<ChainSnapshot> {
    let mut snapshots = Vec::with_capacity(data.topology.chains.len());
    for chain in data.topology.chains.iter() {
        let (Some(label), Some(residues), Some(entity)) = (
            data.topology.chains.label_asym_id(chain),
            data.topology.chains.residues(chain),
            data.topology.chains.entity(chain),
        ) else {
            continue;
        };
        snapshots.push(ChainSnapshot {
            label,
            auth: OptionalSymbol::from(data.topology.chains.auth_asym_id(chain)),
            entity_id: data.topology.entities.id(entity),
            residues,
        });
    }
    snapshots
}

fn retain_provisional_entities(
    chains: &[ChainSnapshot],
    data: &mut StructureData,
    findings: &mut Diagnostics,
) {
    for id in chains.iter().filter_map(|chain| chain.entity_id) {
        if data.topology.entities.find_by_id(id).is_some() {
            continue;
        }
        if data
            .topology
            .entities
            .push(id, EntityKind::Unknown, OptionalSymbol::NONE, &[])
            .is_err()
        {
            findings.push(Diagnostic::new(Code::E3001));
        }
    }
}

fn resolve_entity(
    chain: &ChainSnapshot,
    mappings: &[AsymEntity],
    data: &mut StructureData,
    findings: &mut Diagnostics,
) -> Option<EntityIndex> {
    if let Some(id) = chain.entity_id
        && let Some(entity) = data.topology.entities.find_by_id(id)
    {
        return Some(entity);
    }
    if let Some(mapping) = mappings
        .iter()
        .find(|mapping| mapping.asym_id == chain.label)
    {
        return Some(mapping.entity);
    }
    if let Some(entity) = data
        .topology
        .entities
        .iter()
        .find(|entity| data.topology.entities.id(*entity).is_none())
    {
        return Some(entity);
    }
    match data
        .topology
        .entities
        .push_without_id(EntityKind::Unknown, OptionalSymbol::NONE, &[])
    {
        Ok(entity) => Some(entity),
        Err(error) => {
            findings.push(Diagnostic::new(Code::E3001).with_context("cause", error.to_string()));
            None
        }
    }
}