bio-forge 0.4.0

A pure Rust library and CLI for the automated repair, preparation, and topology construction of biological macromolecules.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100

# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
#
# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
# with all versions of Cargo and also rewrite `path` dependencies
# to registry (e.g., crates.io) dependencies.
#
# If you are reading this file be aware that the original Cargo.toml
# will likely look very different (and much more reasonable).
# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
name = "bio-forge"
version = "0.4.0"
authors = ["Tony Kan <tianchengkan@gmail.com>"]
build = false
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "A pure Rust library and CLI for the automated repair, preparation, and topology construction of biological macromolecules."
readme = "README.md"
keywords = [
    "bioinformatics",
    "chemoinformatics",
    "proteins",
    "nucleic-acids",
    "pdb",
]
categories = [
    "science",
    "science::bioinformatics",
    "command-line-utilities",
]
license = "MIT"
repository = "https://github.com/TKanX/bio-forge"

[features]
cli = [
    "dep:anyhow",
    "dep:clap",
    "dep:prettytable-rs",
    "dep:indicatif",
]
default = [
    "cli",
    "parallel",
]
parallel = ["dep:rayon"]

[lib]
name = "bio_forge"
path = "src/lib.rs"

[[bin]]
name = "bioforge"
path = "src/bin/bioforge.rs"
required-features = ["cli"]

[dependencies.anyhow]
version = "1.0.100"
optional = true

[dependencies.clap]
version = "4.5.53"
features = ["derive"]
optional = true

[dependencies.indicatif]
version = "0.18.3"
optional = true

[dependencies.nalgebra]
version = "0.34.1"

[dependencies.prettytable-rs]
version = "0.10.0"
optional = true

[dependencies.rand]
version = "0.9.2"

[dependencies.rayon]
version = "1.11.0"
optional = true

[dependencies.serde]
version = "1.0.228"
features = ["derive"]

[dependencies.smol_str]
version = "0.3.4"

[dependencies.thiserror]
version = "2.0.17"

[dependencies.toml]
version = "0.9.8"