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	generate_nonstandard_residue_set
	Temporary solution, load the ligand for this session. More...
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 toolbox.load_ligand.add_cid_to_database	(		cid,
			name
	)

Definition at line 147 of file load_ligand.py.

References basic.init(), basic::database.open(), and toolbox.load_ligand.params_from_pubchem().

Referenced by toolbox.load_ligand.pose_from_pubchem().

def toolbox.load_ligand.generate_nonstandard_residue_set

(

params_list

)

Temporary solution, load the ligand for this session.

Returns a "custom" ResidueTypeSet with the normal ResidueTypes and any
    new ones added as a Vector1 of .params filenames,
    the input  <params_list>

example(s):
    res_set = generate_nonstandard_residue_set( Vector1( ['ATP.params'] ) )
See Also:
    Pose
    Residue
    ResidueType
    ResidueTypeSet

Definition at line 92 of file load_ligand.py.

Referenced by toolbox.load_ligand.pose_from_params(), and toolbox.load_ligand.pose_from_pubchem().

def toolbox.load_ligand.load_from_pubchem	(		cid,
			sdffilename = ''
	)

methods for obtaining ligand chemical files and producing params .files

Definition at line 30 of file load_ligand.py.

References basic::database.open().

Referenced by toolbox.load_ligand.params_from_pubchem().

def toolbox.load_ligand.molfile2params_quick	(		mdlfile,
			name
	)

Definition at line 82 of file load_ligand.py.

Referenced by toolbox.load_ligand.params_from_pubchem().

def toolbox.load_ligand.params_from_pubchem	(		cid,
			name
	)

Definition at line 123 of file load_ligand.py.

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

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

def toolbox.load_ligand.pose_from_params	(		filename,
			params_list
	)

Definition at line 203 of file load_ligand.py.

References toolbox.load_ligand.generate_nonstandard_residue_set().

def toolbox.load_ligand.pose_from_pubchem	(		cid,
			name,
			temporary = True
	)

returns a pose of the molecule

Definition at line 183 of file load_ligand.py.

References toolbox.load_ligand.add_cid_to_database(), toolbox.load_ligand.generate_nonstandard_residue_set(), and toolbox.load_ligand.params_from_pubchem().

def toolbox.load_ligand.sdf2mdl	(		sdfile,
			mdlfilename
	)

Definition at line 64 of file load_ligand.py.

Referenced by toolbox.load_ligand.params_from_pubchem().

Variable Documentation

tuple toolbox.load_ligand.database = os.path.abspath( os.environ['PYROSETTA_DATABASE'] )

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

Definition at line 143 of file load_ligand.py.

string toolbox.load_ligand.fa_custom = 'residue_types/custom'

Definition at line 145 of file load_ligand.py.

string toolbox.load_ligand.fa_standard = database+'/chemical/residue_type_sets/fa_standard/'

Definition at line 144 of file load_ligand.py.

Referenced by UBQ_GTPase_disulfide_Mover.init_on_new_input(), UBQ_GTPaseMover.init_on_new_input(), and UBQ_E2Mover.init_on_new_input().