pdbrust 0.7.0

A comprehensive Rust library for parsing and analyzing Protein Data Bank (PDB) files
Documentation 
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use pdbrust::parse_pdb_file;
use proptest::prelude::*;
use std::io::Write;
use tempfile::NamedTempFile;

fn create_test_pdb(content: &str) -> NamedTempFile {
    let mut file = NamedTempFile::new().unwrap();
    file.write_all(content.as_bytes()).unwrap();
    file
}

fn generate_atom_record(serial: i32, x: f64, y: f64, z: f64) -> String {
    format!(
        "ATOM  {:>5} {:>4}{}{:>3} {}{:>4}{}   {:>8.3}{:>8.3}{:>8.3}{:>6.2}{:>6.2}      {:>4}{:>2}{:>2}",
        serial, "N", " ", "ALA", "A", serial, " ", x, y, z, 1.00, 13.79, "", "N", ""
    )
}

proptest! {
    #[test]
    fn test_valid_atom_records(
        serial in 1..1000i32,
        // PDB format uses 8.3 notation: max 8 chars with 3 decimal places
        // Valid range is approximately -999.999 to 9999.999
        x in -999.0..999.0f64,
        y in -999.0..999.0f64,
        z in -999.0..999.0f64,
    ) {
        let content = generate_atom_record(serial, x, y, z);
        let file = create_test_pdb(&content);
        let result = parse_pdb_file(file.path());
        assert!(result.is_ok());
        let structure = result.unwrap();
        assert_eq!(structure.atoms.len(), 1);
        let atom = &structure.atoms[0];
        assert_eq!(atom.serial, serial);
        // PDB format has 3 decimal places precision
        assert!((atom.x - x).abs() < 1e-3);
        assert!((atom.y - y).abs() < 1e-3);
        assert!((atom.z - z).abs() < 1e-3);
        assert_eq!(atom.name, "N");
        assert_eq!(atom.residue_name, "ALA");
        assert_eq!(atom.chain_id, "A");
        assert_eq!(atom.residue_seq, serial);
        assert_eq!(atom.alt_loc, None);
        assert_eq!(atom.ins_code, None);
        assert_eq!(atom.occupancy, 1.00);
        assert_eq!(atom.temp_factor, 13.79);
        assert_eq!(atom.element, "N");
    }

    #[test]
    fn test_valid_conect_records(
        atom1 in 1..1000i32,
        atom2 in 1..1000i32,
        atom3 in 1..1000i32,
        atom4 in 1..1000i32,
    ) {
        let content = format!(
            "CONECT{:>5}{:>5}{:>5}{:>5}",
            atom1, atom2, atom3, atom4
        );
        let file = create_test_pdb(&content);
        let result = parse_pdb_file(file.path());
        assert!(result.is_ok());
        let structure = result.unwrap();
        assert_eq!(structure.connects.len(), 1);
        let conect = &structure.connects[0];
        assert_eq!(conect.atom1, atom1);
        assert_eq!(conect.atom2, atom2);
        assert_eq!(conect.atom3, Some(atom3));
        assert_eq!(conect.atom4, Some(atom4));
    }

    #[test]
    fn test_multiple_atoms(
        // PDB format uses 8.3 notation for coordinates
        atoms in prop::collection::vec(
            (1..1000i32, -999.0..999.0f64, -999.0..999.0f64, -999.0..999.0f64),
            1..10
        ),
    ) {
        let mut content = String::new();
        for (serial, x, y, z) in &atoms {
            content.push_str(&generate_atom_record(*serial, *x, *y, *z));
            content.push('\n');
        }
        let file = create_test_pdb(&content);
        let result = parse_pdb_file(file.path());
        assert!(result.is_ok());
        let structure = result.unwrap();
        assert_eq!(structure.atoms.len(), atoms.len());
        for (i, (serial, x, y, z)) in atoms.iter().enumerate() {
            let atom = &structure.atoms[i];
            assert_eq!(atom.serial, *serial);
            // PDB format has 3 decimal places precision
            assert!((atom.x - x).abs() < 1e-3);
            assert!((atom.y - y).abs() < 1e-3);
            assert!((atom.z - z).abs() < 1e-3);
            assert_eq!(atom.name, "N");
            assert_eq!(atom.residue_name, "ALA");
            assert_eq!(atom.chain_id, "A");
            assert_eq!(atom.residue_seq, *serial);
            assert_eq!(atom.alt_loc, None);
            assert_eq!(atom.ins_code, None);
            assert_eq!(atom.occupancy, 1.00);
            assert_eq!(atom.temp_factor, 13.79);
            assert_eq!(atom.element, "N");
        }
    }

    #[test]
    fn test_hetatm_records(
        serial in 1..1000i32,
        // PDB format uses 8.3 notation for coordinates
        x in -999.0..999.0f64,
        y in -999.0..999.0f64,
        z in -999.0..999.0f64,
    ) {
        let content = format!(
            "HETATM{:>5} {:>4}{}{:>3} {}{:>4}{}   {:>8.3}{:>8.3}{:>8.3}{:>6.2}{:>6.2}      {:>4}{:>2}{:>2}",
            serial,
            "O",
            " ",
            "HOH",
            "W",
            serial,
            " ",
            x,
            y,
            z,
            1.00,
            13.79,
            "",
            "O",
            ""
        );
        let file = create_test_pdb(&content);
        let result = parse_pdb_file(file.path());
        assert!(result.is_ok());
        let structure = result.unwrap();
        assert_eq!(structure.atoms.len(), 1);
        let atom = &structure.atoms[0];
        assert_eq!(atom.serial, serial);
        // PDB format has 3 decimal places precision
        assert!((atom.x - x).abs() < 1e-3);
        assert!((atom.y - y).abs() < 1e-3);
        assert!((atom.z - z).abs() < 1e-3);
        assert_eq!(atom.name, "O");
        assert_eq!(atom.residue_name, "HOH");
        assert_eq!(atom.chain_id, "W");
        assert_eq!(atom.residue_seq, serial);
        assert_eq!(atom.alt_loc, None);
        assert_eq!(atom.ins_code, None);
        assert_eq!(atom.occupancy, 1.00);
        assert_eq!(atom.temp_factor, 13.79);
        assert_eq!(atom.element, "O");
    }

    #[test]
    #[ignore = "Multi-model atom association needs parser fix - see issue"]
    fn test_multi_model_structure(
        num_models in 1..5usize,
        atoms_per_model in 1..10usize,
    ) {
        let mut content = String::new();
        for model in 1..=num_models {
            content.push_str(&format!("MODEL {:>4}\n", model));
            for atom in 1..=atoms_per_model {
                content.push_str(&generate_atom_record(
                    atom as i32,
                    0.0,
                    0.0,
                    0.0,
                ));
                content.push('\n');
            }
            content.push_str("ENDMDL\n");
        }
        content.push_str("END\n");

        let file = create_test_pdb(&content);
        let result = parse_pdb_file(file.path());
        assert!(result.is_ok());
        let structure = result.unwrap();
        assert_eq!(structure.models.len(), num_models);
        assert_eq!(structure.atoms.len(), num_models * atoms_per_model);

        for (i, model) in structure.models.iter().enumerate() {
            assert_eq!(model.serial, (i + 1) as i32);
            assert_eq!(model.atoms.len(), atoms_per_model);
        }
    }

    #[test]
    fn test_atom_with_alt_loc(
        serial in 1..1000i32,
        alt_loc in prop::sample::select(&['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z']),
        // PDB format uses 8.3 notation for coordinates
        x in -999.0..999.0f64,
        y in -999.0..999.0f64,
        z in -999.0..999.0f64,
    ) {
        let content = format!(
            "ATOM  {:>5} {:>4}{}{:>3} {}{:>4}{}   {:>8.3}{:>8.3}{:>8.3}{:>6.2}{:>6.2}      {:>4}{:>2}{:>2}",
            serial,
            "N",
            alt_loc,
            "ALA",
            "A",
            serial,
            " ",
            x,
            y,
            z,
            1.00,
            13.79,
            "",
            "N",
            ""
        );
        let file = create_test_pdb(&content);
        let result = parse_pdb_file(file.path());
        assert!(result.is_ok());
        let structure = result.unwrap();
        assert_eq!(structure.atoms.len(), 1);
        let atom = &structure.atoms[0];
        assert_eq!(atom.alt_loc, Some(alt_loc));
    }

    #[test]
    fn test_atom_with_ins_code(
        serial in 1..1000i32,
        ins_code in prop::sample::select(&['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z']),
        // PDB format uses 8.3 notation: max 8 chars with 3 decimal places
        // Valid range is approximately -999.999 to 9999.999
        x in -999.0..999.0f64,
        y in -999.0..999.0f64,
        z in -999.0..999.0f64,
    ) {
        let content = format!(
            "ATOM  {:>5} {:>4}{}{:>3} {}{:>4}{}   {:>8.3}{:>8.3}{:>8.3}{:>6.2}{:>6.2}      {:>4}{:>2}{:>2}",
            serial,
            "N",
            " ",
            "ALA",
            "A",
            serial,
            ins_code,
            x,
            y,
            z,
            1.00,
            13.79,
            "",
            "N",
            ""
        );
        let file = create_test_pdb(&content);
        let result = parse_pdb_file(file.path());
        assert!(result.is_ok());
        let structure = result.unwrap();
        assert_eq!(structure.atoms.len(), 1);
        let atom = &structure.atoms[0];
        assert_eq!(atom.ins_code, Some(ins_code));
    }
}