batch_molfile_to_params Namespace Reference

Functions
def	make_params

Variables
string	mol_to_params = "~/rosetta/rosetta_source/src/python/apps/public/molfile_to_params.py"
list	char_set
string	usage = "%prog -d path/to/rosetta/database --script_path=/path/to/molfile_to_params.py molfile_list.txt"
tuple	parser = OptionParser(usage)
list	molfile_list_path = args[0]
tuple	ligand_names = itertools.product(char_set,repeat=3)
tuple	disallowed_ligands = get_disallowed_ligands(options.database+"/")
tuple	exclude_list = open(options.excluded,'r')
tuple	line = line.rstrip()
tuple	molfile_list = open(molfile_list_path,'r')
tuple	molfile = molfile.strip()
tuple	ligand_name = ligand_names.next()
tuple	mol_base_name = molfile.split("/")
tuple	params_status = make_params(molfile,ligand_name,mol_base_name)

Function Documentation

def batch_molfile_to_params.make_params	(		mol_path,
			ligand_name,
			base_name
	)

Make the params file, append the conformers, and move the output into the proper directory

References basic::database.open().

Variable Documentation

list batch_molfile_to_params.char_set

Initial value:

= ['0','1','2','3','4','5',
            '6','7','8','9','A','B',
            'C','D','E','F','G','H',
            'I','J','K','L','M','N',
            'O','P','Q','R','S','T',
            'U','V','W','X','Y','Z']

tuple batch_molfile_to_params.disallowed_ligands = get_disallowed_ligands(options.database+"/")

tuple batch_molfile_to_params.exclude_list = open(options.excluded,'r')

string batch_molfile_to_params.ligand_name = ligand_names.next()

Referenced by main().

tuple batch_molfile_to_params.ligand_names = itertools.product(char_set,repeat=3)

tuple batch_molfile_to_params.line = line.rstrip()

tuple batch_molfile_to_params.mol_base_name = molfile.split("/")

batch_molfile_to_params.mol_to_params = "~/rosetta/rosetta_source/src/python/apps/public/molfile_to_params.py"

tuple batch_molfile_to_params.molfile = molfile.strip()

tuple batch_molfile_to_params.molfile_list = open(molfile_list_path,'r')

list batch_molfile_to_params.molfile_list_path = args[0]

tuple batch_molfile_to_params.params_status = make_params(molfile,ligand_name,mol_base_name)

tuple batch_molfile_to_params.parser = OptionParser(usage)

string batch_molfile_to_params.usage = "%prog -d path/to/rosetta/database --script_path=/path/to/molfile_to_params.py molfile_list.txt"

Referenced by basic.get_usage_from_procfilesystem(), and main().