param_utils Namespace Reference

Functions
def	get_name_from_params
def	get_disallowed_ligands
def	rename_param_file
def	rename_pdb_file

Function Documentation

def param_utils.get_disallowed_ligands

(

database

)

Return a set of 3 letter names which are already assigned to ligands in the database

References get_name_from_params(), and basic::database.open().

def param_utils.get_name_from_params	(		path,
			database
	)

Given the path to a params file, return the IO_STRING value.  if it doesn't exist, return None

References ObjexxFCL.len(), basic::database.open(), and utility.split().

Referenced by get_disallowed_ligands().

def param_utils.rename_param_file	(		param_path,
			new_name,
			new_conformer_path
	)

Rename a param file residue and update the conformer file path

References basic::options::OptionKeys::stepwise.enumerate, and basic::database.open().

def param_utils.rename_pdb_file	(		pdb_path,
			new_name
	)

Renames all the HETATM resnames in the specified pdb to new_name

References basic::options::OptionKeys::stepwise.enumerate, ObjexxFCL.len(), and basic::database.open().