Crate bio_files

Crate bio_files 

Source
Expand description

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

Re-exports§

pub use pdbqt::Pdbqt;
pub use ab1::*;
pub use map::*;
pub use mmcif::*;
pub use mol2::*;
pub use sdf::*;

Modules§

ab1
For reading AB1 trace files. (Applied Biosystem’s sequencing) BioPython docs
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.
md_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.
mmcif
Load atoms and related data (e.g. secondary structure) from mmCIF files. These are the coordinate files that come from the RCSB PDB.
mol2
For opening Mol2 files. These are common molecular descriptions for ligands. We implement the Tripos Mol2 spec variant, as it’s used by Amber Geostd, and has a published spec.
pdbqt
For reading and writing PDBQT (Autodock) files. Unofficial, incomplete spec
prmtop
sdf
For opening Structure Data Format (SDF) files. These are common molecular descriptions for ligands. It’s a simpler format than PDB.

Structs§

AtomGeneric
This represents an atom, and can be used for various purposes. It is used in various format-specific molecules in this library. You may wish to augment the data here with a custom application-specific format.
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
ResidueGeneric

Enums§

BondType
These are the Mol2 standard types, unless otherwise noted.
ExperimentalMethod
The method used to find a given molecular structure. This data is present in mmCIF files as the _exptl.method field.
ResidueEnd
ResidueType
SecondaryStructure

Functions§

create_bonds
Infer bonds from atom distances. Uses spacial partitioning for efficiency. We Check pairs only within nearby bins.