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 pdbqt::Pdbqt;

pub use ab1::*;

pub use gro::*;

pub use map::*;

pub use mmcif::*;

pub use mol2::*;

pub use sdf::*;

pub use xyz::*;

Modules

ab1

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

amber_typedef

Parses Amber Antechamber DEF files, which are used to load forcefield names.

cif_sf

Loads 2fo-fc mmCIF data. This contains electron density. Does not perform a Fourier transform to convert this data into a density grid; returns that file contents in a struct that can then be converted to densities.

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.

gro

For opening GROMACS .gro files (GRO). These are common molecular descriptions for small molecules and proteins. Positions in GRO are in nm; we convert to Å to match the rest of the codebase.

map

For parsing CCP4/MRC .map files. These contain electron density; they are computed from reflection data, using a fourier transform. We parse them in a direct manner, loading density data on a grid into a flattened array of values.

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.

orca

For interop with the ORCA quantum chemistry software package. For example, This module constructs inputs for ORCA, and can either save them to disk, or run them directly if ORCA is available in the system PATH. It can display and parse the output.

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.

xyz

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.

LipidStandard

Common lipid types, as defined in Amber params. For phospholipics, chains and head groups are separate entries, and can be combined. The repr assumes ingested from lipid21 in a deterministic (e.g. alphabetcial) order.

ResidueEnd

ResidueType

SecondaryStructure

Functions

create_bonds

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