pyrosetta.toolbox.rcsb Namespace Reference

Functions
def	download_from_web (url)
def	load_from_rcsb (pdb_code, pdb_filename=None)
def	pose_from_rcsb (pdb_code, ATOM=True, CRYS=False)
def	load_fasta_from_rcsb (pdb_code, fasta_outfile=None)

Variables
	urllib_urlretrieve = urllib.request.urlretrieve

Function Documentation

download_from_web()

def pyrosetta.toolbox.rcsb.download_from_web

(

url

)

Get content from the web and make it available within a
context manager.

References basic::database.open(), and pyrosetta.toolbox.rcsb.urllib_urlretrieve.

Referenced by pyrosetta.toolbox.rcsb.load_fasta_from_rcsb(), and pyrosetta.toolbox.rcsb.load_from_rcsb().

load_fasta_from_rcsb()

def pyrosetta.toolbox.rcsb.load_fasta_from_rcsb	(		pdb_code,
			fasta_outfile = None
	)

Downlaod a FASTA file from RCSB and write it to disk.

Args:
    pdb_code (str): The four-letter accession code of the desired PDB file
    fasta_outfile (str): Optional argument for output filename. Defaults to
    <pdb_code>.fasta.

Examples:
    >>> load_fasta_from_rcsb("1YY8")

References pyrosetta.toolbox.rcsb.download_from_web(), and basic::database.open().

load_from_rcsb()

def pyrosetta.toolbox.rcsb.load_from_rcsb	(		pdb_code,
			pdb_filename = None
	)

Downlaod a PDB file from RCSB and write it to disk.

Args:
    pdb_code (str): The four-letter accession code of the desired PDB file
    pdb_filename (str): Optional argument for output filename.
        Defaults to <pdb_code>.pdb.

Examples:
    >>> load_from_rcsb("1YY8")

References pyrosetta.toolbox.rcsb.download_from_web(), and basic::database.open().

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

pose_from_rcsb()

def pyrosetta.toolbox.rcsb.pose_from_rcsb	(		pdb_code,
			ATOM = True,
			CRYS = False
	)

Downlaod a PDB file from RCSB, write to disk as <pdb_code>.pdb and return
it as a pose. Optionally calls cleanATOM and/or cleanCRYS.

Notes:
    Automatic monomer extraction assumes the PDB contains a homodimer.

Args:
    pdb_code (str): The four-letter accession code of the desired PDB file
    ATOM (bool): Only write ATOM records to disk. Defaults to True.
    CRYS (bool): Attempt to extract a monomer from the target PDB.
        Defaults to False.

Examples:
    >>> pose = pose_from_rcsb("1YY8")

References pyrosetta.toolbox.cleaning.cleanATOM(), pyrosetta.toolbox.cleaning.cleanCRYS(), pyrosetta.toolbox.rcsb.load_from_rcsb(), and pyrosetta.distributed.io.pose_from_file().

Variable Documentation

urllib_urlretrieve

pyrosetta.toolbox.rcsb.urllib_urlretrieve = urllib.request.urlretrieve

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