MDMC.readers.configurations package
Submodules
MDMC.readers.configurations.ase module
MDMC wrapper for the ASE reader.
- class MDMC.readers.configurations.ase.ASEReader(file_name: str)[source]
Bases:
ConfigurationReader
Reader that wraps around the ASE reader.
- extension = 'N/A'
MDMC.readers.configurations.cif module
Reads a .cif file into an MDMC molecule, optionally ignoring symmetry data. Adapted from https://wiki.fysik.dtu.dk/ase/_modules/ase/io/cif.html#read_cif.
- class MDMC.readers.configurations.cif.CIFReader(file_name: str)[source]
Bases:
ConfigurationReader
Reads a .cif file into a list of MDMC Atoms.
- extension = 'cif'
MDMC.readers.configurations.conf_reader module
Module for observable reader abstract class
MDMC.readers.configurations.conf_reader_factory module
Factory class for generating readers for configurations
- class MDMC.readers.configurations.conf_reader_factory.ConfigurationReaderFactory[source]
Bases:
ReaderFactory
Provides a factory for creating readers. Any module within the readers submodule can be created with a string of the class name, as long as it is a subclass of
ConfigurationReader
.- static base_class() type[ConfigurationReader] [source]
This should be implemented to return the base class of objects returned by the
ReaderFactory
- classmethod create_reader_from_ext(extension: str, file_name: str) ConfigurationReader [source]
- Parameters:
- Returns:
An initialized configuration reader which has the extension specified by
extension
- Return type:
- Raises:
NotImplementedError – If
extension
does not match theextension
property of any subclass ofConfigurationReader
MDMC.readers.configurations.packmol_pdb module
A reader for reading in the PDB configuration of whole packmol systems
- class MDMC.readers.configurations.packmol_pdb.PackmolPDBReader(file_name: str)[source]
Bases:
ConfigurationReader
A class to read in packmol PDB output files
- extension = 'NONE'
MDMC.readers.configurations.pdb module
Module for reading pdb files
- class MDMC.readers.configurations.pdb.ProteinDataBankReader(file_name: str)[source]
Bases:
ConfigurationReader
A class for reading pdb configuration files
Examples
To use a pdb reader to read a file called ‘paracetamol.pdb’ and create a set of ``Molecule``s from it:
file = 'water.pdb' pdb_reader = pdb(file) with pdb_reader: pdb_reader.parse() water = pdb_reader.molecules[0]
- property bonds: list[Bond]
Returns the bonds within the molecule, as specified by “CONECT” statements in the pdb file
- create_bond(atom1: Atom, atom2: Atom) None [source]
Checks the bond lengths of the atoms in the molecule and creates a bond if it is below a certain threshold
This is needed because PDB files are able to include H-bonds (which MDMC does not support) alongside other types of bonds, which are undistinguishable from each other in a pdb file. Therefore, cutting off the bond length at a reasonable distance prevents an extremely long bond being introduced into a molecule structure
- extension = 'pdb'
- parse(**settings: dict) None [source]
Parses the file data so that it is in a format expected by the class calling the data reader
For readers which are not specific to one data type, the calling class must be determined so that the file data can be parsed into the appropriate data type.
- Parameters:
**settings (dict) – dictionary of settings for reader
Module contents
A subpackage for reading files containing atomic configurations
- MDMC.readers.configurations.read(file: str, docstring: bool = False, **settings: dict) list[Atom] | None [source]
Reads a configuration file and returns a list of atoms corresponding to the atoms in the file
Note
The docstring of the required reader (as determined from the file) can be accessed by passing help=True. This may be necessary to determine the reader specific **settings that can be passed. In this case, the file will not be read and None will be returned, rather than a list of Atom objects.
- Parameters:
file (str) – The file name of the configuration file
docstring (bool, optional) – This will show the docstring (help) related to the type of configuration file that has been passed. If this is True, the file will not be read and None will be returned. The default is False.
**settings – Parameters passed to ConfigurationReader.parse
- Returns:
Atom objects corresponding to the configuration in the file. None will be returned if docstring=True.
- Return type:
Examples
To read a CIF file and define the atom_types of the atoms:
atoms = read('example.cif', atom_types=[1, 1, 2, 2, 2, 1, 3])
To get the docstring (help) for reading a CIF file:
read('example.cif', help=True)