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Functions | Variables
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 
)
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 
)
def pyrosetta.toolbox.load_ligand.params_from_pubchem (   cid,
  name 
)
def pyrosetta.toolbox.load_ligand.pose_from_params (   filename,
  params_list 
)
def pyrosetta.toolbox.load_ligand.pose_from_pubchem (   cid,
  name,
  temporary = True 
)
def pyrosetta.toolbox.load_ligand.sdf2mdl (   sdfile,
  mdlfilename 
)

Variable Documentation

tuple pyrosetta.toolbox.load_ligand.database = os.path.abspath(os.environ["PYROSETTA_DATABASE"])
string pyrosetta.toolbox.load_ligand.fa_custom = "residue_types/custom"
string pyrosetta.toolbox.load_ligand.fa_standard = database+"/chemical/residue_type_sets/fa_standard/"