diff --git a/Cargo.lock b/Cargo.lock index fd4de1b..c9d5229 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1,6 +1,6 @@ # This file is automatically @generated by Cargo. # It is not intended for manual editing. -version = 3 +version = 4 [[package]] name = "adler" @@ -17,15 +17,6 @@ dependencies = [ "num-traits", ] -[[package]] -name = "atomic-polyfill" -version = "1.0.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8cf2bce30dfe09ef0bfaef228b9d414faaf7e563035494d7fe092dba54b300f4" -dependencies = [ - "critical-section", -] - [[package]] name = "autocfg" version = "1.1.0" @@ -59,12 +50,6 @@ dependencies = [ "cfg-if", ] -[[package]] -name = "critical-section" -version = "1.1.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7059fff8937831a9ae6f0fe4d658ffabf58f2ca96aa9dec1c889f936f705f216" - [[package]] name = "crossbeam-deque" version = "0.8.5" @@ -122,15 +107,6 @@ dependencies = [ "miniz_oxide", ] -[[package]] -name = "hash32" -version = "0.2.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b0c35f58762feb77d74ebe43bdbc3210f09be9fe6742234d573bacc26ed92b67" -dependencies = [ - "byteorder", -] - [[package]] name = "hash32" version = "0.3.1" @@ -142,22 +118,9 @@ dependencies = [ [[package]] name = "hashbrown" -version = "0.14.3" +version = "0.15.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604" - -[[package]] -name = "heapless" -version = "0.7.17" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cdc6457c0eb62c71aac4bc17216026d8410337c4126773b9c5daba343f17964f" -dependencies = [ - "atomic-polyfill", - "hash32 0.2.1", - "rustc_version", - "spin", - "stable_deref_trait", -] +checksum = "bf151400ff0baff5465007dd2f3e717f3fe502074ca563069ce3a6629d07b289" [[package]] name = "heapless" @@ -165,7 +128,7 @@ version = "0.8.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0bfb9eb618601c89945a70e254898da93b13be0388091d42117462b265bb3fad" dependencies = [ - "hash32 0.3.1", + "hash32", "stable_deref_trait", ] @@ -177,9 +140,9 @@ checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8" [[package]] name = "indexmap" -version = "2.2.1" +version = "2.7.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "433de089bd45971eecf4668ee0ee8f4cec17db4f8bd8f7bc3197a6ce37aa7d9b" +checksum = "62f822373a4fe84d4bb149bf54e584a7f4abec90e072ed49cda0edea5b95471f" dependencies = [ "equivalent", "hashbrown", @@ -197,16 +160,6 @@ version = "0.2.8" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058" -[[package]] -name = "lock_api" -version = "0.4.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45" -dependencies = [ - "autocfg", - "scopeguard", -] - [[package]] name = "matrixmultiply" version = "0.3.8" @@ -301,15 +254,15 @@ checksum = "de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c" [[package]] name = "pdbtbx" -version = "0.11.0" +version = "0.12.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d8aeda12d25a2e102a6e3f1efd8fe2afd054cbafa7d54414d5015e8e0f4beb4b" +checksum = "932b111b429ecfb94434569372e9538543b1abee9c51908f7a92f18b934f03bf" dependencies = [ "doc-cfg", "flate2", "indexmap", "rayon", - "rstar 0.11.0", + "rstar", "serde", ] @@ -375,24 +328,13 @@ dependencies = [ "crossbeam-utils", ] -[[package]] -name = "rstar" -version = "0.11.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "73111312eb7a2287d229f06c00ff35b51ddee180f017ab6dec1f69d62ac098d6" -dependencies = [ - "heapless 0.7.17", - "num-traits", - "smallvec", -] - [[package]] name = "rstar" version = "0.12.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "133315eb94c7b1e8d0cb097e5a710d850263372fd028fff18969de708afc7008" dependencies = [ - "heapless 0.8.0", + "heapless", "num-traits", "smallvec", ] @@ -405,19 +347,10 @@ dependencies = [ "nalgebra", "pdbtbx", "rayon", - "rstar 0.12.0", + "rstar", "snafu", ] -[[package]] -name = "rustc_version" -version = "0.4.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366" -dependencies = [ - "semver", -] - [[package]] name = "safe_arch" version = "0.7.1" @@ -427,18 +360,6 @@ dependencies = [ "bytemuck", ] -[[package]] -name = "scopeguard" -version = "1.2.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49" - -[[package]] -name = "semver" -version = "1.0.21" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b97ed7a9823b74f99c7742f5336af7be5ecd3eeafcb1507d1fa93347b1d589b0" - [[package]] name = "serde" version = "1.0.196" @@ -499,15 +420,6 @@ dependencies = [ "syn", ] -[[package]] -name = "spin" -version = "0.9.8" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6980e8d7511241f8acf4aebddbb1ff938df5eebe98691418c4468d0b72a96a67" -dependencies = [ - "lock_api", -] - [[package]] name = "stable_deref_trait" version = "1.2.0" diff --git a/Cargo.toml b/Cargo.toml index 810101c..8313180 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -7,12 +7,12 @@ readme = "README.md" repository = "https://github.com/maxall41/RustSASA" license = "MIT" license-file = "LICENSE" -keywords = ["Rust","Bioinformatics","SASA"] +keywords = ["Rust", "Bioinformatics", "SASA"] documentation = "https://docs.rs/rust-sasa/latest/rust_sasa/" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] -pdbtbx = "0.11.0" +pdbtbx = "0.12.0" rstar = "0.12.0" nalgebra = "0.33.0" rayon = "1.10.0" diff --git a/src/lib.rs b/src/lib.rs index dabbfb6..ccc0be2 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -164,7 +164,6 @@ fn is_accessible_rstar( /// use rust_sasa::{Atom, calculate_sasa_internal}; /// let (mut pdb, _errors) = pdbtbx::open( /// "./example.cif", -/// StrictnessLevel::Medium /// ).unwrap(); /// let mut atoms = vec![]; /// for atom in pdb.atoms() { @@ -231,7 +230,6 @@ pub fn calculate_sasa_internal( /// use rust_sasa::{Atom, calculate_sasa, calculate_sasa_internal, SASALevel}; /// let (mut pdb, _errors) = pdbtbx::open( /// "./example.cif", -/// StrictnessLevel::Medium /// ).unwrap(); /// let result = calculate_sasa(&pdb,None,None,SASALevel::Residue); /// ``` diff --git a/src/test.rs b/src/test.rs index 9743366..ba01e4d 100644 --- a/src/test.rs +++ b/src/test.rs @@ -248,7 +248,7 @@ mod tests { #[test] fn internal_test() { - let (mut pdb, _errors) = pdbtbx::open("./example.cif", StrictnessLevel::Medium).unwrap(); + let (mut pdb, _errors) = pdbtbx::open("./example.cif").unwrap(); let mut atoms = vec![]; for atom in pdb.atoms() { atoms.push(Atom { @@ -275,7 +275,7 @@ mod tests { } #[test] fn external_test() { - let (mut pdb, _errors) = pdbtbx::open("./example.cif", StrictnessLevel::Medium).unwrap(); + let (mut pdb, _errors) = pdbtbx::open("./example.cif").unwrap(); let protein_sasa = calculate_sasa(&pdb, None, None, SASALevel::Protein).unwrap(); let chain_sasa = calculate_sasa(&pdb, None, None, SASALevel::Chain).unwrap();