pyrosetta.toolbox.load_ligand Namespace Reference

Functions
def	load_from_pubchem (cid, sdffilename="")
	methods for obtaining ligand chemical files and producing params .files More...
def	sdf2mdl (sdfile, mdlfilename)
def	molfile2params_quick (mdlfile, name)
def	params_from_pubchem (cid, name)
def	add_cid_to_database (cid, name)
def	pose_from_pubchem (cid, name, temporary=True)
	returns a pose of the molecule More...
def	pose_from_params (filename, params_list)

Variables
	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

add_cid_to_database()

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().

load_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(), print(), and str().

Referenced by pyrosetta.toolbox.load_ligand.params_from_pubchem().

molfile2params_quick()

def pyrosetta.toolbox.load_ligand.molfile2params_quick	(		mdlfile,
			name
	)

Referenced by pyrosetta.toolbox.load_ligand.params_from_pubchem().

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(), pyrosetta.toolbox.load_ligand.sdf2mdl(), and str().

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

pose_from_params()

def pyrosetta.toolbox.load_ligand.pose_from_params	(		filename,
			params_list
	)

References pyrosetta.distributed.io.pose_from_file, and pyrosetta.Vector1().

pose_from_pubchem()

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.

sdf2mdl()

def pyrosetta.toolbox.load_ligand.sdf2mdl	(		sdfile,
			mdlfilename
	)

References pyrosetta.tests.distributed.test_dask.format, and print().

Referenced by pyrosetta.toolbox.load_ligand.params_from_pubchem().

Variable Documentation

database

pyrosetta.toolbox.load_ligand.database = os.path.abspath(os.environ["PYROSETTA_DATABASE"])

Permanent solution, add the .params to the minirosetta_database of PyRosetta.

fa_custom

string pyrosetta.toolbox.load_ligand.fa_custom = "residue_types/custom"

fa_standard

string pyrosetta.toolbox.load_ligand.fa_standard = database + "/chemical/residue_type_sets/fa_standard/"

Referenced by mtransferase.apply(), HECTMover.build_AtomID_vec(), convert_to_native_test(), UBQ_E2Mover.init_on_new_input(), UBQ_GTPase_disulfide_Mover.init_on_new_input(), HECTAllMover.init_on_new_input(), HECTUBQMover.init_on_new_input(), main(), rna_fullatom_multiscore_test(), rna_fullatom_score_test(), and HECTMover.ubq_constraints().