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pyrosetta.toolbox.rcsb Namespace Reference

Functions

def download_from_web
 
def load_from_rcsb
 
def pose_from_rcsb
 
def load_fasta_from_rcsb
 

Variables

 urllib_urlretrieve = urllib.request.urlretrieve
 

Function Documentation

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().

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().

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().

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

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