arls_impl Namespace Reference

Classes
class	PreformattedDescFormatter
class	DockingCase
class	DockingFile

Functions
def	chain_from_iterables (iterables)
def	find_file (regex, paths, required=True)
def	find_programs (options)
def	read_input_list (infile)
def	get_procs_per_case (docking_cases, options)
def	write_setup_script (outfile, options, progs, docking_cases)
def	write_common_flags (outfile, options, docking_cases)
def	write_rpkmin_flags (outfile, options, docking_cases)
def	write_dock_flags (outfile, options, docking_cases)
def	write_minnat_flags (outfile, options, docking_cases)
def	write_rpkmin_script (outfile, options, progs, docking_cases)
def	write_tarball_pre_script (outfile, options, progs, docking_cases)
def	write_dock_condor_script (outfile, options, progs, docking_cases)
def	write_dock_bash_script (outfile, options, progs, docking_cases)
def	write_concat_script (outfile, options, progs, docking_cases)
def	write_analysis_script (outfile, options, progs, docking_cases)
def	write_if_not_exists (filename, options, function, *func_args, **func_kwargs)
def	main (argv)

Function Documentation

chain_from_iterables()

def arls_impl.chain_from_iterables

(

iterables

)

Referenced by write_common_flags(), and write_setup_script().

find_file()

def arls_impl.find_file	(		regex,
			paths,
			required = True
	)

References ObjexxFCL.len().

Referenced by find_programs().

find_programs()

def arls_impl.find_programs

(

options

)

References find_file(), and binder.split().

Referenced by main().

get_procs_per_case()

def arls_impl.get_procs_per_case	(		docking_cases,
			options
	)

References enumerate_junctions.int, ObjexxFCL.len(), and max().

Referenced by write_dock_bash_script(), write_dock_condor_script(), and write_dock_flags().

main()

def arls_impl.main

(

argv

)

Automatic RosettaLigand Setup (ARLS)

Given a list of protein-ligand pairings, generates all the required input
files for RosettaLigand docking, along with suggested flags and submit scripts.
The scripts are numbered 1 - N and should be run in order.
See the Doxygen documentation for important information on using RosettaLigand.

The script takes one argument, a list of protein-ligand pairs to dock.
Each line of the list should consist of the protein name, zero or more cofactor
names, and the ligand name (whitespace separated).
In the current directory should be files with the same name and an appropriate
extension: .pdb for proteins, and one of (.mol, .sdf, .mol2) for ligands and
cofactors. For example, the line "1abc cofactor mylig" could use files named
"1abc.pdb", "cofactor.mol", and "mylig.mol2". No unnecessary work will be done
even if a protein/cofactor/ligand appears in multiple lines.

The protein file should only contain standard amino acid residues.
The cofactor and ligand files should contain a single conformation
   of a single compound (unless using --skip-omega).
The MiniRosetta database should be in ~/rosetta/rosetta_database;
    otherwise use --database.
OpenEye's Omega should be in ~/openeye or on your PATH;
    otherwise use --openeye or --skip-omega.
The OpenEye QUACPAC toolkit should be on your PYTHONPATH
    for charges to be assigned (else use --skip-charges).
You can specify which clustering software to set up the docking runs for with
    --cluster. Specifying BASH will result in a standard shell script-type submission.
    for those without clustering software (It is recommended to also set --njobs.) You
    also can use the BASH output file with MOAB/TORQUE/PBS style clustering software.

References find_programs(), ObjexxFCL.len(), basic::database.open(), read_input_list(), set(), str(), test_terpenes.upper, and write_if_not_exists().

read_input_list()

def arls_impl.read_input_list

(

infile

)

References ObjexxFCL.len().

Referenced by main().

write_analysis_script()

def arls_impl.write_analysis_script	(		outfile,
			options,
			progs,
			docking_cases
	)

write_common_flags()

def arls_impl.write_common_flags	(		outfile,
			options,
			docking_cases
	)

References chain_from_iterables(), join(), and set().

write_concat_script()

def arls_impl.write_concat_script	(		outfile,
			options,
			progs,
			docking_cases
	)

write_dock_bash_script()

def arls_impl.write_dock_bash_script	(		outfile,
			options,
			progs,
			docking_cases
	)

References get_procs_per_case().

write_dock_condor_script()

def arls_impl.write_dock_condor_script	(		outfile,
			options,
			progs,
			docking_cases
	)

References get_procs_per_case().

write_dock_flags()

def arls_impl.write_dock_flags	(		outfile,
			options,
			docking_cases
	)

References get_procs_per_case().

write_if_not_exists()

def arls_impl.write_if_not_exists	(		filename,
			options,
			function,
		*	func_args,
		**	func_kwargs
	)

References plot.function, and basic::database.open().

Referenced by main().

write_minnat_flags()

def arls_impl.write_minnat_flags	(		outfile,
			options,
			docking_cases
	)

write_rpkmin_flags()

def arls_impl.write_rpkmin_flags	(		outfile,
			options,
			docking_cases
	)

write_rpkmin_script()

def arls_impl.write_rpkmin_script	(		outfile,
			options,
			progs,
			docking_cases
	)

References join(), and set().

write_setup_script()

def arls_impl.write_setup_script	(		outfile,
			options,
			progs,
			docking_cases
	)

References chain_from_iterables(), basic::options::OptionKeys::stepwise.enumerate, join(), and set().

write_tarball_pre_script()

def arls_impl.write_tarball_pre_script	(		outfile,
			options,
			progs,
			docking_cases
	)