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Classes | Functions
arls_impl Namespace Reference

Classes

class  DockingCase
 
class  DockingFile
 
class  PreformattedDescFormatter
 

Functions

def chain_from_iterables
 
def find_file
 
def find_programs
 
def read_input_list
 
def get_procs_per_case
 
def write_setup_script
 
def write_common_flags
 
def write_rpkmin_flags
 
def write_dock_flags
 
def write_minnat_flags
 
def write_rpkmin_script
 
def write_tarball_pre_script
 
def write_dock_condor_script
 
def write_dock_bash_script
 
def write_concat_script
 
def write_analysis_script
 
def write_if_not_exists
 
def main
 

Function Documentation

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

References ObjexxFCL.len().

Referenced by find_programs().

def arls_impl.find_programs (   options)

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

Referenced by main().

def arls_impl.get_procs_per_case (   docking_cases,
  options 
)
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(), utility.upper(), and write_if_not_exists().

def arls_impl.read_input_list (   infile)

References ObjexxFCL.len().

Referenced by main().

def arls_impl.write_analysis_script (   outfile,
  options,
  progs,
  docking_cases 
)
def arls_impl.write_common_flags (   outfile,
  options,
  docking_cases 
)
def arls_impl.write_concat_script (   outfile,
  options,
  progs,
  docking_cases 
)
def arls_impl.write_dock_bash_script (   outfile,
  options,
  progs,
  docking_cases 
)

References get_procs_per_case().

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

References get_procs_per_case().

def arls_impl.write_dock_flags (   outfile,
  options,
  docking_cases 
)

References get_procs_per_case().

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

References basic::database.open().

Referenced by main().

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

References fmt.join().

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