pyrosetta.toolbox.cleaning Namespace Reference

Functions
def	cleanATOM (pdb_file, out_file=None, ext=".clean.pdb")
def	cleanCRYS (pdb_file, olig=2, out_file=None)

Function Documentation

cleanATOM()

def pyrosetta.toolbox.cleaning.cleanATOM	(		pdb_file,
			out_file = None,
			ext = ".clean.pdb"
	)

Extract all ATOM and TER records in a PDB file and write them to a new file.

Args:
    pdb_file (str): Path of the PDB file from which ATOM and TER records
        will be extracted
    out_file (str): Optional argument to specify a particular output filename.
        Defaults to <pdb_file>.clean.pdb.
    ext (str): File extension to use for output file. Defaults to ".clean.pdb"

References basic::database.open().

Referenced by pyrosetta.toolbox.rcsb.pose_from_rcsb().

cleanCRYS()

def pyrosetta.toolbox.cleaning.cleanCRYS	(		pdb_file,
			olig = 2,
			out_file = None
	)

Extract a monomer from an oligomeric PDB file and write it to a new file.

Notes:
    This is a simple sequence comparison.

Args:
    pdb_file (str): Path of the PDB file from which ATOM and TER records
        will be extracted.
    olig (int): Number of subunits in the input complex.
    out_file (str): Optional argument to specify a particular output filename.
        Defaults to <pdb_file>.mono.pdb.

References enumerate_junctions.int, ObjexxFCL.len(), pyrosetta.distributed.io.pose_from_file, range, round(), set(), and str().

Referenced by pyrosetta.toolbox.rcsb.pose_from_rcsb().