13 releases (8 breaking)
0.9.0 | Mar 3, 2021 |
---|---|
0.7.0 | Jan 24, 2021 |
0.6.3 | Oct 2, 2020 |
0.6.1 | Jul 8, 2020 |
#630 in Development tools
60 downloads per month
Used in 4 crates
170KB
5K
SLoC
Purr
Primitives for reading and writing the SMILES language in Rust.
Usage
Add this to your Cargo.toml
:
[dependencies]
purr = "0.9"
Examples
Parse acetamide into an adjacency representation:
use purr::graph::{ Builder, Atom, Bond };
use purr::feature::{ AtomKind, BondKind, Aliphatic };
use purr::read::{ read, Error };
fn main() -> Result<(), Error> {
let mut builder = Builder::new();
read("CC(=O)N", &mut builder, None)?;
assert_eq!(builder.build(), Ok(vec![
Atom {
kind: AtomKind::Aliphatic(Aliphatic::C),
bonds: vec![
Bond::new(BondKind::Elided, 1)
]
},
Atom {
kind: AtomKind::Aliphatic(Aliphatic::C),
bonds: vec![
Bond::new(BondKind::Elided, 0),
Bond::new(BondKind::Double, 2),
Bond::new(BondKind::Elided, 3)
]
},
Atom {
kind: AtomKind::Aliphatic(Aliphatic::O),
bonds: vec![
Bond::new(BondKind::Double, 1)
]
},
Atom {
kind: AtomKind::Aliphatic(Aliphatic::N),
bonds: vec![
Bond::new(BondKind::Elided, 1)
]
}
]));
Ok(())
}
The order of atoms and their substituents reflects their implied order within the corresponding SMILES string. This is important when atomic configuration (e.g., @
, @@
) is present at an atom.
An optional Trace
type maps adjacency features to a cursor position in the original string. This is useful for conveying semantic errors such as hypervalence.
use purr::graph::Builder;
use purr::read::{ read, Error, Trace };
fn main() -> Result<(), Error> {
let mut builder = Builder::new();
let mut trace = Trace::new();
// 012345678901234
read("C(C)C(C)(C)(C)C", &mut builder, Some(&mut trace))?;
// Texas carbon @ atom(2) with cursor range 4..5
assert_eq!(trace.atom(2), Some(4..5));
Ok(())
}
Syntax errors are mapped to the cursor at which they occur.
use purr::graph::Builder;
use purr::read::{ read, Error };
fn main() {
let mut builder = Builder::new();
assert_eq!(read("OCCXC", &mut builder, None), Err(Error::Character(3)));
}
An adjacency can be written using write
.
use purr::graph::{ Builder, Atom, Bond };
use purr::feature::{ AtomKind, BondKind, Aliphatic };
use purr::read::{ read, Error };
use purr::write::Writer;
use purr::walk::walk;
fn main() -> Result<(), Error> {
let mut builder = Builder::new();
read("c1c([37Cl])cccc1", &mut builder, None)?;
let atoms = builder.build().expect("atoms");
let mut writer = Writer::new();
walk(atoms, &mut writer).expect("walk");
assert_eq!(writer.write(), "c(ccccc1[37Cl])1");
Ok(())
}
The output string doesn't match the input string, although both represent the same molecule (Cl-37 chlorobenzene). write
traces atoms
in depth-first order, but the adjacency representation (atoms
) lacks information about how the original SMILES tree was cut.
Versions
Purr is not yet stable. Patch versions never introduce breaking changes, but minor/major versions probably will.
License
Purr is distributed under the terms of the MIT License. See LICENSE-MIT and COPYRIGHT for details.