pyrosetta.toolbox.load_ligand Namespace Reference

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"

Function Documentation

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
	)

References pyrosetta.toolbox.load_ligand.load_from_pubchem(), pyrosetta.toolbox.load_ligand.molfile2params_quick(), and pyrosetta.toolbox.load_ligand.sdf2mdl().

Referenced by pyrosetta.toolbox.load_ligand.add_cid_to_database(), and pyrosetta.toolbox.load_ligand.pose_from_pubchem().

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().

Variable Documentation

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().