add_bonds Namespace Reference

Variables
	parser = argparse.ArgumentParser(description="Add bond info to a PDB")
	help
	args = parser.parse_args()
	main = loos.createSystem(args.main_model_file)
	with_bonds = loos.createSystem(args.model_file_with_bonds)
	m = main[i]
	w = with_bonds[i]
	new = loos.PDB.fromAtomicGroup(main)

Detailed Description

Given a model file that has connectivity and a file that has good metadata
write a new pdb file that has the metadata and connectivity information.

Example usage case would be combining a Tinker XYZ file and equivalent PDB file
to produce a PDB file with bond information.

THIS PROGRAM ASSUMES THE CONTENTS OF THE TWO MODELS ARE IDENTICAL: the same
atoms in the same order.