Crate bio_files

The generic label in names in this module are to differentiate from ones used in more specific applications.

Re-exports

pub use ab1::*;

pub use map::*;

pub use mol2::*;

pub use sdf::*;

Modules

ab1

For reading AB1 trace files. (Applied Biosystem’s sequencing) BioPython docs

amber_params

Contains parameters used in Amber Forcefields. For details on these formats, see the Amber Reference Manual, section 15: Reading and modifying Amber parameter files.

dat

For parsing Amber force field dat files, like gaff2.dat (small molecules/ligands). These include parameters used in molecular dynamics. See also: frcmod, which patches these parameters for specific molecules.

frcmod

For operating on frcmod files, which describe Amber force fields for small molecules.

map

For parsing CCP4/MRC .map files. These contain electron density; they are computed from reflection data, using a fourier transform.

mol2

For opening Mol2 files. These are common molecular descriptions for ligands. This unofficial resource descripts the format.

sdf

For opening Structure Data Format (SDF) files. These are common molecular descriptions for ligands. It’s a simpler format than PDB.

Structs

AtomGeneric

BackboneSS

See note elsewhere regarding serial numbers vs indices: In your downstream applications, you may wish to convert sns to indices, for faster operations.

BondGeneric

ChainGeneric

MmCif

ResidueGeneric

Enums

ExperimentalMethod

The method used to find a given molecular structure. This data is present in mmCIF files as the _exptl.method field.

ResidueType

SecondaryStructure