Expand description
The generic
label in names in this module are to differentiate from ones used in more specific
applications.
Re-exports§
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§
- Atom
Generic - 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.
- Bond
Generic - Chain
Generic - Residue
Generic
Enums§
- Bond
Type - These are the Mol2 standard types, unless otherwise noted.
- Experimental
Method - The method used to find a given molecular structure. This data is present in mmCIF files
as the
_exptl.method
field. - Residue
End - Residue
Type - Secondary
Structure
Functions§
- create_
bonds - Infer bonds from atom distances. Uses spacial partitioning for efficiency. We Check pairs only within nearby bins.