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Rosetta
2019.07
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Functions | |
def | packer_task |
def | generate_resfile_from_pose |
PERIPHERAL METHODS. More... | |
def | generate_resfile_from_pdb |
Variables | |
tuple | parser = optparse.OptionParser() |
INTERPRETING RESULTS. More... | |
string | default = '../test/data/test_in.pdb' |
string | help = 'the PDB file containing the loop to remodel' |
pdb_filename = options.pdb_filename | |
tuple | pose = Pose() |
tuple | PDB_out = bool(options.PDB_out) |
def demo.D050_Packer_task.generate_resfile_from_pdb | ( | pdbfilename, | |
resfilename, | |||
pack = True , |
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design = False , |
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input_sc = True , |
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freeze = [] , |
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specific = {} |
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) |
Writes a resfile for the PDB file <pdbfilename> named <resfilename> <pack> = True allows packing by default <design> = True allows design using all amino acids by default <input_sc> = True allows usage of the original side chain conformation <freeze> is an optional list of (pose) residue numbers to exclude (preserve the side chain conformations of these residues) <specific> is an optional dictionary with (pose) residue numbers as keys and resfile keywords as corresponding values (for setting individual residue options, it may be easier to add these numbers to freeze and edit the resfile manually) example: generate_resfile_from_pdb('1YY8.pdb','1YY8.resfile') See also: generate_resfile_from_pose Pose PackRotamersMover TaskFactory
References demo.D050_Packer_task.generate_resfile_from_pose(), and pyrosetta.distributed.io.pose_from_file.
Referenced by demo.D050_Packer_task.generate_resfile_from_pose().
def demo.D050_Packer_task.generate_resfile_from_pose | ( | pose, | |
resfilename, | |||
pack = True , |
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design = False , |
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input_sc = True , |
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freeze = [] , |
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specific = {} |
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) |
PERIPHERAL METHODS.
Writes a resfile for <pose> named <resfilename> <pack> = True allows packing by default <design> = True allows design using all amino acids by default <input_sc> = True allows usage of the original side chain conformation <freeze> is an optional list of (pose) residue numbers to exclude (preserve the side chain conformations of these residues) <specific> is an optional dictionary with (pose) residue numbers as keys and resfile keywords as corresponding values (for setting individual residue options, it may be easier to add these numbers to freeze and edit the resfile manually) example: generate_resfile_from_pose(pose,'1YY8.resfile') See also: Pose PackRotamersMover TaskFactory
References basic::options::OptionKeys::run.chain, demo.D050_Packer_task.generate_resfile_from_pdb(), basic::database.open(), and ObjexxFCL.rjust().
Referenced by demo.D050_Packer_task.generate_resfile_from_pdb(), and demo.D050_Packer_task.packer_task().
def demo.D050_Packer_task.packer_task | ( | pose, | |
PDB_out = False |
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Demonstrates the syntax necessary for basic usage of the PackerTask object performs demonstrative sidechain packing and selected design using <pose> and writes structures to PDB files if <PDB_out> is True
References demo.D050_Packer_task.generate_resfile_from_pose(), name, fmt.print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, basic::options::OptionKeys::relax::range.range, basic::options::OptionKeys::DisulfideInsertion.scorefxn, and pyrosetta.standard_packer_task().
Referenced by main().
string demo.D050_Packer_task.default = '../test/data/test_in.pdb' |
string demo.D050_Packer_task.help = 'the PDB file containing the loop to remodel' |
tuple demo.D050_Packer_task.parser = optparse.OptionParser() |
INTERPRETING RESULTS.
COMMANDLINE COMPATIBILITY
demo.D050_Packer_task.pdb_filename = options.pdb_filename |
tuple demo.D050_Packer_task.PDB_out = bool(options.PDB_out) |
tuple demo.D050_Packer_task.pose = Pose() |