pyqmmm.md.residue_lister

Get a list of all residues in a PDB for the supplemental information.

Module Contents

Functions

extract_residue_names(filename)	Extract residue names and their indices from a PDB file.
write_residues_to_file(residues[, output_filename])	Write the extracted residues to a file, one residue per line.
list_residues()	Parses all the residues in the PDB and returns them as a single list.

pyqmmm.md.residue_lister.extract_residue_names(filename)

Extract residue names and their indices from a PDB file.

Parameters:

filename (str) – The name of the PDB file to read.

Returns:

A list of formatted residue names with their indices (e.g., MET1, THR2, GLU3).

Return type:

list

pyqmmm.md.residue_lister.write_residues_to_file(residues, output_filename='residues.dat')

Write the extracted residues to a file, one residue per line.

Parameters:

• residues (list) – A list of formatted residue names with their indices (e.g., MET1, THR2, GLU3).

• output_filename (str, optional) – The name of the output file, by default “residues.dat”.

pyqmmm.md.residue_lister.list_residues()

Parses all the residues in the PDB and returns them as a single list.