use molframe_core::io::{InputBuffer, ReadOptions};
use molframe_core::{SecondaryStructure as Ss, Structure};
use std::fmt::Write as _;
fn fixture() -> Structure {
let mut source = String::from(
"data_secondary
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.pdbx_PDB_model_num
",
);
for index in 1..=8 {
writeln!(source, "ATOM {index} C CA GLY A {index} {index} 0 0 1")
.expect("write into String");
}
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::Turn,
Ss::Unknown,
]
.into();
Structure::new(data)
}
#[test]
fn canonical_secondary_records_round_trip_all_representable_states() {
let structure = fixture();
let text = crate::write_canonical_with_options(
&structure,
&crate::CifWriteOptions::new().with_block_id("secondary"),
)
.expect("write");
assert!(text.contains("HELX_P C4 10"), "{text}");
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 missing_secondary_sequence_refuses_before_streaming() {
let input = InputBuffer::from_bytes(b"data_missing\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\n_atom_site.pdbx_PDB_model_num\nATOM 1 C CA GLY A . 0 0 0 1\n".to_vec());
let (raw, _) =
crate::read(&input, &ReadOptions::new()).expect("missing label sequence is readable");
let mut data = raw.data().clone();
data.secondary_structure = vec![Ss::PolyProline].into();
let structure = Structure::new(data);
let mut output = Vec::new();
let result = crate::write_canonical_to(
&structure,
&crate::CifWriteOptions::new().with_block_id("secondary"),
&mut output,
);
assert!(result.is_err());
assert!(output.is_empty());
}
fn identity_fixture(rows: &str, states: &[Ss]) -> Structure {
let source = format!(
"data_identity\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.auth_asym_id\n_atom_site.label_seq_id\n_atom_site.auth_seq_id\n_atom_site.pdbx_PDB_ins_code\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\n_atom_site.pdbx_PDB_model_num\n{rows}"
);
let (raw, _) = crate::read(
&InputBuffer::from_bytes(source.into_bytes()),
&ReadOptions::new(),
)
.expect("read identity fixture");
let mut data = raw.data().clone();
data.secondary_structure = states.to_vec().into();
Structure::new(data)
}
#[test]
fn canonical_secondary_preserves_label_namespace_chain_order_and_author_insertions() {
let states = [
Ss::PolyProline,
Ss::PolyProline,
Ss::Unknown,
Ss::OtherHelix,
Ss::Strand,
];
let structure = identity_fixture(
"ATOM 1 C CA GLY A B 5 -2 A 0 0 0 1\nATOM 2 C CA GLY A B 1 -2 B 1 0 0 1\nATOM 3 C CA GLY A B 3 10000 . 2 0 0 1\nATOM 4 C CA GLY B A 5 -2 A 3 0 0 1\nATOM 5 C CA GLY B A 1 -2 B 4 0 0 1\n",
&states,
);
let mut output = Vec::new();
crate::write_canonical_to(
&structure,
&crate::CifWriteOptions::new().with_block_id("identity"),
&mut output,
)
.expect("actual canonical writer");
let (roundtrip, _) = crate::read(&InputBuffer::from_bytes(output), &ReadOptions::new())
.expect("actual readback");
assert_eq!(roundtrip.secondary_structure(), states);
let ids: Vec<_> = roundtrip
.data()
.residues()
.map(|r| (r.label_seq_id(), r.auth_seq_id(), r.ins_code()))
.collect();
let original: Vec<_> = structure
.data()
.residues()
.map(|r| (r.label_seq_id(), r.auth_seq_id(), r.ins_code()))
.collect();
assert_eq!(ids, original);
}
#[test]
fn repeated_label_numbers_under_insertion_codes_are_renumbered_not_refused() {
let states = [Ss::PolyProline, Ss::OtherHelix];
let structure = identity_fixture(
"ATOM 1 C CA GLY A A 1 10 A 0 0 0 1\nATOM 2 C CA GLY A A 1 10 B 1 0 0 1\n",
&states,
);
let mut output = Vec::new();
crate::write_canonical_to(
&structure,
&crate::CifWriteOptions::new().with_block_id("identity"),
&mut output,
)
.expect("distinct label numbers make the identities unambiguous");
let (roundtrip, _) =
crate::read(&InputBuffer::from_bytes(output), &ReadOptions::new()).expect("readback");
assert_eq!(roundtrip.secondary_structure(), states);
let labels: Vec<_> = roundtrip
.data()
.residues()
.map(molframe_core::structure::ResidueRef::label_seq_id)
.collect();
assert_eq!(labels.len(), 2);
assert_ne!(labels[0], labels[1]);
}
#[test]
fn independent_model_secondary_annotations_refuse_before_streaming() {
let first = fixture();
let mut data = first.data().clone();
data.coords = molframe_core::structure::CoordinateStore::Ragged {
models: vec![first],
};
let structure = Structure::new(data);
let mut output = Vec::new();
let result = crate::write_canonical_to(
&structure,
&crate::CifWriteOptions::new().with_block_id("identity"),
&mut output,
);
assert!(result.is_err());
assert!(output.is_empty());
}
#[test]
fn coil_bend_and_isolated_bridge_are_not_projected_as_other_states() {
let structure = identity_fixture(
"ATOM 1 C CA GLY A A 1 1 . 0 0 0 1\nATOM 2 C CA GLY A A 2 2 . 1 0 0 1\nATOM 3 C CA GLY A A 3 3 . 2 0 0 1\n",
&[Ss::Coil, Ss::Bend, Ss::BetaBridge],
);
let output = crate::write_canonical_with_options(
&structure,
&crate::CifWriteOptions::new().with_block_id("identity"),
)
.expect("atom output");
assert!(!output.contains("_struct_conf."));
assert!(!output.contains("_struct_sheet_range."));
}