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Rosetta
2020.11
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Functions | |
def | load_from_pubchem |
methods for obtaining ligand chemical files and producing params .files More... | |
def | sdf2mdl |
def | molfile2params_quick |
def | params_from_pubchem |
def | add_cid_to_database |
def | pose_from_pubchem |
returns a pose of the molecule More... | |
def | pose_from_params |
Variables | |
tuple | database = os.path.abspath(os.environ["PYROSETTA_DATABASE"]) |
Permanent solution, add the .params to the minirosetta_database of PyRosetta. More... | |
string | fa_standard = database+"/chemical/residue_type_sets/fa_standard/" |
string | fa_custom = "residue_types/custom" |
def pyrosetta.toolbox.load_ligand.add_cid_to_database | ( | cid, | |
name | |||
) |
References pyrosetta.init(), basic::database.open(), and pyrosetta.toolbox.load_ligand.params_from_pubchem().
Referenced by pyrosetta.toolbox.load_ligand.pose_from_pubchem().
def pyrosetta.toolbox.load_ligand.load_from_pubchem | ( | cid, | |
sdffilename = "" |
|||
) |
methods for obtaining ligand chemical files and producing params .files
References basic::database.open(), and fmt.print().
Referenced by pyrosetta.toolbox.load_ligand.params_from_pubchem().
def pyrosetta.toolbox.load_ligand.molfile2params_quick | ( | mdlfile, | |
name | |||
) |
Referenced by pyrosetta.toolbox.load_ligand.params_from_pubchem().
def pyrosetta.toolbox.load_ligand.params_from_pubchem | ( | cid, | |
name | |||
) |
def pyrosetta.toolbox.load_ligand.pose_from_params | ( | filename, | |
params_list | |||
) |
References pyrosetta.distributed.io.pose_from_file, and pyrosetta.Vector1().
def pyrosetta.toolbox.load_ligand.pose_from_pubchem | ( | cid, | |
name, | |||
temporary = True |
|||
) |
returns a pose of the molecule
References pyrosetta.toolbox.load_ligand.add_cid_to_database(), pyrosetta.toolbox.load_ligand.params_from_pubchem(), and pyrosetta.distributed.io.pose_from_file.
def pyrosetta.toolbox.load_ligand.sdf2mdl | ( | sdfile, | |
mdlfilename | |||
) |
References pyrosetta.tests.distributed.test_dask.format, and fmt.print().
Referenced by pyrosetta.toolbox.load_ligand.params_from_pubchem().
tuple pyrosetta.toolbox.load_ligand.database = os.path.abspath(os.environ["PYROSETTA_DATABASE"]) |
Permanent solution, add the .params to the minirosetta_database of PyRosetta.
Referenced by add_rosetta_options_0(), fill_required_options(), utility::sql_database::DatabaseSessionManager.get_session_mysql(), utility::sql_database::DatabaseSessionManager.get_session_postgres(), main(), make_fragments(), basic::options.process(), and validate_dunbrack_binaries().
string pyrosetta.toolbox.load_ligand.fa_custom = "residue_types/custom" |
string pyrosetta.toolbox.load_ligand.fa_standard = database+"/chemical/residue_type_sets/fa_standard/" |
Referenced by UBQ_GTPase_disulfide_Mover.init_on_new_input(), and UBQ_E2Mover.init_on_new_input().