use super::super::pdb::{PdbOptions, write};
use molframe_core::io::{InputBuffer, ReadOptions};
use molframe_core::{SecondaryStructure as Ss, Structure};
use std::fmt::Write as _;
#[test]
fn author_numbering_need_not_increase_along_a_secondary_range() {
let structure = identity_fixture(
&[("A", "20", ""), ("A", "10", ""), ("A", "15", "")],
&[Ss::PolyProline, Ss::PolyProline, Ss::Unknown],
);
let output = write(
&structure,
&PdbOptions::new().namespace(super::super::pdb::PdbIdentifierNamespace::Auth),
)
.expect("author projection");
let (roundtrip, _) = crate::read(
&InputBuffer::from_bytes(output.into_bytes()),
&ReadOptions::new(),
)
.expect("read output");
assert_eq!(
roundtrip.secondary_structure(),
structure.secondary_structure()
);
}
#[test]
fn selecting_out_a_residue_splits_secondary_records_without_extending_endpoints() {
struct WithoutMiddle;
impl molframe_core::io::Select for WithoutMiddle {
fn accept_residue(&self, residue: molframe_core::index::ResidueIndex) -> bool {
residue.get() != 1
}
}
let structure = identity_fixture(
&[("A", "10", "A"), ("A", "10", "B"), ("A", "10", "C")],
&[Ss::PolyProline; 3],
);
let output = crate::write_selected(&structure, &PdbOptions::new(), &WithoutMiddle)
.expect("selected writer");
assert_eq!(
output
.lines()
.filter(|line| line.starts_with("HELIX"))
.count(),
2
);
let (roundtrip, _) = crate::read(
&InputBuffer::from_bytes(output.into_bytes()),
&ReadOptions::new(),
)
.expect("read selected output");
assert_eq!(roundtrip.secondary_structure(), &[Ss::PolyProline; 2]);
assert_eq!(
roundtrip
.data()
.residues()
.filter_map(molframe_core::structure::ResidueRef::ins_code)
.collect::<Vec<_>>(),
["A", "C"]
);
}
#[test]
fn a_missing_secondary_component_refuses_before_streaming() {
let source = write(&fixture(), &PdbOptions::new())
.expect("fixture writer")
.replace("GLY", " ");
let (structure, _) = crate::read(
&InputBuffer::from_bytes(source.into_bytes()),
&ReadOptions::new(),
)
.expect("blank component fixture");
let mut output = Vec::new();
assert!(crate::write_to(&structure, &PdbOptions::new(), &mut output).is_err());
assert!(output.is_empty());
}
fn fixture() -> Structure {
let mut source = String::new();
for residue in 1..=7 {
writeln!(source, "ATOM {residue:>5} CA GLY A{residue:>4} {:>8.3} 0.000 0.000 1.00 10.00 C", f64::from(residue) * 3.8).expect("write into String");
}
source.push_str(
"END
",
);
let input = InputBuffer::from_bytes(source.into_bytes());
let (raw, _) = crate::read(&input, &ReadOptions::new()).expect("fixture reads");
let mut data = raw.data().clone();
data.secondary_structure = vec![
Ss::AlphaHelix,
Ss::ThreeTenHelix,
Ss::PiHelix,
Ss::PolyProline,
Ss::OtherHelix,
Ss::Strand,
Ss::Unknown,
]
.into();
Structure::new(data)
}
#[test]
fn generated_helix_classes_and_sheets_round_trip() {
let structure = fixture();
let text = write(&structure, &PdbOptions::new()).expect("write");
let input = InputBuffer::from_bytes(text.into_bytes());
let (roundtrip, _) = crate::read(&input, &ReadOptions::new()).expect("read output");
assert_eq!(
structure.secondary_structure(),
roundtrip.secondary_structure()
);
}
#[test]
fn renamed_chains_are_used_in_secondary_records_too() {
let structure = fixture();
let text = write(&structure, &PdbOptions::new().chain_map("A", "Z")).expect("write");
for record in text.lines().filter(|line| line.starts_with("HELIX")) {
assert_eq!(&record[19..20], "Z");
assert_eq!(&record[31..32], "Z");
}
let input = InputBuffer::from_bytes(text.into_bytes());
let (roundtrip, _) = crate::read(&input, &ReadOptions::new()).expect("read output");
assert_eq!(
structure.secondary_structure(),
roundtrip.secondary_structure()
);
}
fn identity_fixture(rows: &[(&str, &str, &str)], states: &[Ss]) -> Structure {
let mut source = String::new();
for (serial, &(chain, sequence, insertion)) in (1..).zip(rows) {
writeln!(source, "ATOM {serial:>5} CA GLY {chain:1}{sequence:>4}{insertion:1} 0.000 0.000 0.000 1.00 10.00 C").expect("String");
}
let (raw, _) = crate::read(
&InputBuffer::from_bytes(source.into_bytes()),
&ReadOptions::new(),
)
.expect("read fixture");
let mut data = raw.data().clone();
data.secondary_structure = states.to_vec().into();
Structure::new(data)
}
#[test]
fn secondary_writer_round_trips_insertions_negative_and_both_hybrid36_cases() {
let rows = [
("A", "-2", ""),
("A", "-1", ""),
("A", "10", ""),
("A", "10", "A"),
("A", "10", "B"),
("A", "10", "C"),
("A", "A000", ""),
("A", "A001", ""),
("A", "a000", ""),
("A", "a001", ""),
("B", "10", "A"),
];
let states = [
Ss::OtherHelix,
Ss::OtherHelix,
Ss::Unknown,
Ss::PolyProline,
Ss::PolyProline,
Ss::Unknown,
Ss::Strand,
Ss::Strand,
Ss::ThreeTenHelix,
Ss::ThreeTenHelix,
Ss::PiHelix,
];
let structure = identity_fixture(&rows, &states);
let options = PdbOptions::new().hybrid36(true);
let mut output = Vec::new();
crate::write_to(&structure, &options, &mut output).expect("stream real writer");
let text = str::from_utf8(&output).expect("ASCII");
let pp = text
.lines()
.find(|line| line.starts_with("HELIX") && &line[38..40] == "10")
.expect("PPII record");
assert_eq!(&pp[21..26], " 10A");
assert_eq!(&pp[33..38], " 10B");
let (roundtrip, _) = crate::read(&InputBuffer::from_bytes(output), &ReadOptions::new())
.expect("read actual writer");
assert_eq!(roundtrip.secondary_structure(), states);
let ids: Vec<_> = roundtrip
.data()
.residues()
.map(|residue| (residue.auth_seq_id(), residue.ins_code()))
.collect();
let original: Vec<_> = structure
.data()
.residues()
.map(|residue| (residue.auth_seq_id(), residue.ins_code()))
.collect();
assert_eq!(ids, original);
}
#[test]
fn a_chain_map_collision_refuses_secondary_output_before_streaming() {
let structure = identity_fixture(
&[("A", "1", ""), ("B", "1", "")],
&[Ss::PolyProline, Ss::OtherHelix],
);
let mut output = Vec::new();
let result = crate::write_to(
&structure,
&PdbOptions::new().chain_map("B", "A"),
&mut output,
);
assert!(result.is_err());
assert!(output.is_empty());
}
#[test]
fn secondary_sequence_overflow_refuses_even_with_hybrid36_enabled() {
let raw = fixture();
let mut data = raw.data().clone();
data.topology.residues = molframe_core::topology::ResidueTable::default();
for residue in raw.data().residues() {
let record = molframe_core::topology::ResidueRecord {
label_comp_id: raw
.data()
.topology
.residues
.label_comp_id(residue.index())
.expect("component"),
auth_comp_id: molframe_core::optional::OptionalSymbol::NONE,
label_seq_id: molframe_core::optional::OptionalI32::some(i32::MAX),
auth_seq_id: molframe_core::optional::OptionalI32::NONE,
ins_code: molframe_core::optional::OptionalSymbol::NONE,
het: false,
};
data.topology
.residues
.push(record, residue.index().get()..residue.index().get() + 1)
.expect("residue");
}
let mut output = Vec::new();
assert!(
crate::write_to(
&Structure::new(data),
&PdbOptions::new().hybrid36(true),
&mut output
)
.is_err()
);
assert!(output.is_empty());
}
#[test]
fn unrepresentable_secondary_states_are_not_relabelled_as_helix_or_strand() {
let structure = identity_fixture(
&[
("A", "1", ""),
("A", "2", ""),
("A", "3", ""),
("A", "4", ""),
],
&[Ss::Coil, Ss::Bend, Ss::BetaBridge, Ss::Turn],
);
let text = write(&structure, &PdbOptions::new()).expect("write atoms");
assert!(
!text
.lines()
.any(|line| line.starts_with("HELIX") || line.starts_with("SHEET"))
);
}
#[test]
fn states_a_reader_derived_are_not_written_as_deposited_records() {
let mut data = identity_fixture(
&[("A", "1", ""), ("A", "2", ""), ("A", "3", "")],
&[Ss::AlphaHelix; 3],
)
.data()
.clone();
data.secondary_source = std::sync::Arc::new(vec![molframe_core::SecondarySource::Dssp; 3]);
let text = write(&Structure::new(data), &PdbOptions::new()).expect("write atoms");
assert!(
!text.lines().any(|line| line.starts_with("HELIX")),
"a DSSP assignment is not a deposited HELIX record"
);
}