src.smirnoff_hack Namespace Reference

Functions
def	oe_cached_find_smarts_matches (self, molecule, smarts, aromaticity_model='OEAroModel_MDL')
def	rdk_cached_find_smarts_matches (self, molecule, smarts, aromaticity_model='OEAroModel_MDL')
def	cached_validate (smirks, validate_valence_type=True, toolkit_registry=OpenEyeToolkitWrapper)
def	oe_cached_assign_partial_charges (self, molecule, partial_charge_method=None, use_conformers=None, strict_n_conformers=False)
def	at_cached_assign_partial_charges (self, molecule, partial_charge_method=None, use_conformers=None, strict_n_conformers=False)
def	oe_cached_generate_conformers (self, molecule, n_conformers=1, rms_cutoff=None, clear_existing=True)
def	rdk_cached_generate_conformers (self, molecule, n_conformers=1, rms_cutoff=None, clear_existing=True)

Variables
	oe_original_find_smarts_matches = OpenEyeToolkitWrapper.find_smarts_matches
dictionary	OE_TOOLKIT_CACHE_find_smarts_matches = {}
	rdk_original_find_smarts_matches = RDKitToolkitWrapper.find_smarts_matches
dictionary	RDK_TOOLKIT_CACHE_find_smarts_matches = {}
	original_validate = ChemicalEnvironment.validate
dictionary	TOOLKIT_CACHE_ChemicalEnvironment_validate = {}
	oe_original_assign_partial_charges = OpenEyeToolkitWrapper.assign_partial_charges
dictionary	OE_TOOLKIT_CACHE_assign_partial_charges = {}
	at_original_assign_partial_charges = AmberToolsToolkitWrapper.assign_partial_charges
dictionary	AT_TOOLKIT_CACHE_assign_partial_charges = {}
dictionary	OE_TOOLKIT_CACHE_molecule_conformers = {}
	oe_original_generate_conformers = OpenEyeToolkitWrapper.generate_conformers
dictionary	RDK_TOOLKIT_CACHE_molecule_conformers = {}
	rdk_original_generate_conformers = RDKitToolkitWrapper.generate_conformers

Function Documentation

at_cached_assign_partial_charges()

def src.smirnoff_hack.at_cached_assign_partial_charges	(		self,
			molecule,
			partial_charge_method = None,
			use_conformers = None,
			strict_n_conformers = False
	)

Definition at line 69 of file smirnoff_hack.py.

cached_validate()

def src.smirnoff_hack.cached_validate	(		smirks,
			validate_valence_type = True,
			toolkit_registry = OpenEyeToolkitWrapper
	)

Definition at line 32 of file smirnoff_hack.py.

oe_cached_assign_partial_charges()

def src.smirnoff_hack.oe_cached_assign_partial_charges	(		self,
			molecule,
			partial_charge_method = None,
			use_conformers = None,
			strict_n_conformers = False
	)

Definition at line 55 of file smirnoff_hack.py.

oe_cached_find_smarts_matches()

def src.smirnoff_hack.oe_cached_find_smarts_matches	(		self,
			molecule,
			smarts,
			aromaticity_model = 'OEAroModel_MDL'
	)

Definition at line 8 of file smirnoff_hack.py.

oe_cached_generate_conformers()

def src.smirnoff_hack.oe_cached_generate_conformers	(		self,
			molecule,
			n_conformers = 1,
			rms_cutoff = None,
			clear_existing = True
	)

Definition at line 83 of file smirnoff_hack.py.

rdk_cached_find_smarts_matches()

def src.smirnoff_hack.rdk_cached_find_smarts_matches	(		self,
			molecule,
			smarts,
			aromaticity_model = 'OEAroModel_MDL'
	)

Definition at line 19 of file smirnoff_hack.py.

rdk_cached_generate_conformers()

def src.smirnoff_hack.rdk_cached_generate_conformers	(		self,
			molecule,
			n_conformers = 1,
			rms_cutoff = None,
			clear_existing = True
	)

Definition at line 95 of file smirnoff_hack.py.

Variable Documentation

at_original_assign_partial_charges

src.smirnoff_hack.at_original_assign_partial_charges = AmberToolsToolkitWrapper.assign_partial_charges

Definition at line 67 of file smirnoff_hack.py.

AT_TOOLKIT_CACHE_assign_partial_charges

dictionary src.smirnoff_hack.AT_TOOLKIT_CACHE_assign_partial_charges = {}

Definition at line 68 of file smirnoff_hack.py.

oe_original_assign_partial_charges

src.smirnoff_hack.oe_original_assign_partial_charges = OpenEyeToolkitWrapper.assign_partial_charges

Definition at line 53 of file smirnoff_hack.py.

oe_original_find_smarts_matches

src.smirnoff_hack.oe_original_find_smarts_matches = OpenEyeToolkitWrapper.find_smarts_matches

Definition at line 6 of file smirnoff_hack.py.

oe_original_generate_conformers

src.smirnoff_hack.oe_original_generate_conformers = OpenEyeToolkitWrapper.generate_conformers

Definition at line 82 of file smirnoff_hack.py.

OE_TOOLKIT_CACHE_assign_partial_charges

dictionary src.smirnoff_hack.OE_TOOLKIT_CACHE_assign_partial_charges = {}

Definition at line 54 of file smirnoff_hack.py.

OE_TOOLKIT_CACHE_find_smarts_matches

dictionary src.smirnoff_hack.OE_TOOLKIT_CACHE_find_smarts_matches = {}

Definition at line 7 of file smirnoff_hack.py.

OE_TOOLKIT_CACHE_molecule_conformers

dictionary src.smirnoff_hack.OE_TOOLKIT_CACHE_molecule_conformers = {}

Definition at line 81 of file smirnoff_hack.py.

original_validate

src.smirnoff_hack.original_validate = ChemicalEnvironment.validate

Definition at line 30 of file smirnoff_hack.py.

rdk_original_find_smarts_matches

src.smirnoff_hack.rdk_original_find_smarts_matches = RDKitToolkitWrapper.find_smarts_matches

Definition at line 17 of file smirnoff_hack.py.

rdk_original_generate_conformers

src.smirnoff_hack.rdk_original_generate_conformers = RDKitToolkitWrapper.generate_conformers

Definition at line 94 of file smirnoff_hack.py.

RDK_TOOLKIT_CACHE_find_smarts_matches

dictionary src.smirnoff_hack.RDK_TOOLKIT_CACHE_find_smarts_matches = {}

Definition at line 18 of file smirnoff_hack.py.

RDK_TOOLKIT_CACHE_molecule_conformers

dictionary src.smirnoff_hack.RDK_TOOLKIT_CACHE_molecule_conformers = {}

Definition at line 93 of file smirnoff_hack.py.

TOOLKIT_CACHE_ChemicalEnvironment_validate

dictionary src.smirnoff_hack.TOOLKIT_CACHE_ChemicalEnvironment_validate = {}

Definition at line 31 of file smirnoff_hack.py.