molframe-cif 0.4.0

PDBx/mmCIF reading and writing for molframe
Documentation 
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//! Canonical database sequence-reference output.

use super::value::quoted;
use molframe_core::structure::{SEQUENCE_REFERENCES_EXTENSION, SequenceReferences, Structure};
use std::fmt::{self, Display, Formatter};

pub(super) fn write(out: &mut impl fmt::Write, structure: &Structure) {
    let Some(references) = structure
        .extensions()
        .get::<SequenceReferences>(SEQUENCE_REFERENCES_EXTENSION)
    else {
        return;
    };
    write_sequences(out, references);
    write_alignments(out, references);
}

fn write_sequences(out: &mut impl fmt::Write, references: &SequenceReferences) {
    if references.sequences.is_empty() {
        return;
    }
    let _ = out.write_str(
        "loop_\n\
_struct_ref.id\n\
_struct_ref.entity_id\n\
_struct_ref.db_name\n\
_struct_ref.db_code\n\
_struct_ref.pdbx_db_accession\n\
_struct_ref.pdbx_seq_one_letter_code\n",
    );
    for sequence in &references.sequences {
        let _ = writeln!(
            out,
            "{} {} {} {} {} {}",
            quoted(&sequence.id),
            quoted(&sequence.entity_id),
            optional(sequence.database_name.as_deref()),
            optional(sequence.database_code.as_deref()),
            optional(sequence.accession.as_deref()),
            optional(sequence.one_letter_code.as_deref()),
        );
    }
    let _ = out.write_str("#\n");
}

fn write_alignments(out: &mut impl fmt::Write, references: &SequenceReferences) {
    if references.alignments.is_empty() {
        return;
    }
    let _ = out.write_str(
        "loop_\n\
_struct_ref_seq.align_id\n\
_struct_ref_seq.ref_id\n\
_struct_ref_seq.pdbx_strand_id\n\
_struct_ref_seq.seq_align_beg\n\
_struct_ref_seq.seq_align_end\n\
_struct_ref_seq.db_align_beg\n\
_struct_ref_seq.db_align_end\n",
    );
    for alignment in &references.alignments {
        let chain_ids = alignment.chain_ids.join(",");
        let _ = writeln!(
            out,
            "{} {} {} {} {} {} {}",
            quoted(&alignment.id),
            quoted(&alignment.reference_id),
            optional((!chain_ids.is_empty()).then_some(chain_ids.as_str())),
            alignment.canonical[0],
            alignment.canonical[1],
            alignment.reference[0],
            alignment.reference[1],
        );
    }
    let _ = out.write_str("#\n");
}

fn optional(value: Option<&str>) -> OptionalText<'_> {
    OptionalText(value)
}

struct OptionalText<'a>(Option<&'a str>);

impl Display for OptionalText<'_> {
    fn fmt(&self, formatter: &mut Formatter<'_>) -> fmt::Result {
        match self.0 {
            Some(value) => Display::fmt(&quoted(value), formatter),
            None => formatter.write_str("?"),
        }
    }
}