moldescriptor_reader

A module for reading moldescriptor files.

Summary

Classes:

MoldescriptorReader

This is a class to read moldescriptor files.

Reference

class MoldescriptorReader(filename: str)

Bases: BaseReader

This is a class to read moldescriptor files. Moldescriptor files are used by the PQ and QMCFC MD engines to store the mol types of a system. The moldescriptor file is a text file that contains the mol types of a system. The mol types are defined by the elements, atom types and partial charges of the atoms of the mol type. For more information of how a moldescriptor file should look like please see the documentation of the PQ code.

Calling the read method returns a list of mol types. Each mol type is a Residue object.

Parameters:

filename (str) – The filename of the moldescriptor file.

read() → Residues

The read method reads a moldescriptor file and returns a list of mol types. Each mol type is a Residue object.

Returns:

The residues (mol types) read from the moldescriptor file.

Return type:

Residues

Raises:

• MoldescriptorReaderError – If the number of columns in the header of a mol type is not 3.

• MoldescriptorReaderError – If a mol type declares more atoms than atom lines follow before the end of the file.

logger = <CustomLogger PQAnalysis.MoldescriptorReader (INFO)>