schrodinger.application.desmond.new_fep_edge_data module¶
-
class
schrodinger.application.desmond.new_fep_edge_data.
FepLegs
(complex, solvent, vacuum)¶ Bases:
tuple
-
__contains__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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complex
¶ Alias for field number 0
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count
(value, /)¶ Return number of occurrences of value.
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index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
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solvent
¶ Alias for field number 1
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vacuum
¶ Alias for field number 2
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class
schrodinger.application.desmond.new_fep_edge_data.
FepLambdas
(ref, mut)¶ Bases:
tuple
-
__contains__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
-
count
(value, /)¶ Return number of occurrences of value.
-
index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
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mut
¶ Alias for field number 1
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ref
¶ Alias for field number 0
-
-
exception
schrodinger.application.desmond.new_fep_edge_data.
BlameSidError
[source]¶ Bases:
Exception
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
schrodinger.application.desmond.new_fep_edge_data.
compare_mean_stdev_samples
(a, b)[source]¶ This is a utility function for unittesting. Tests if
a
andb
are the same. Both arguments should be results from_mean_stdev_samples
.
-
schrodinger.application.desmond.new_fep_edge_data.
compare_mean_stdev_samples_2
(a, b)[source]¶ This is a utility function for unittesting. Tests if
a
andb
are the same. But arguments should be a pair of results from_mean_stdev_samples
.
-
schrodinger.application.desmond.new_fep_edge_data.
compare_mean_stdev_samples_4
(a, b)[source]¶ This is a utility function for unittesting. Tests if
a
andb
are the same. But arguments should be a pair of results for both lambda states, and each pair contains two results from_mean_stdev_samples
(usually corresponding to the complex and the solvent legs)
-
schrodinger.application.desmond.new_fep_edge_data.
arg_premise
(key_pattern: str)[source]¶ This decorator is to pass the
val
of theana.Premise
object via the corresponding argument to the function. See its usage below.The
ana.Premise
object is created with the givenkey_pattern
, which will be evaluated to the real key for getting the datum from the database.- Parameters
key_pattern – This argument can contain f-string variables, e.g.,
"Keywords[i].ResultLambda{fep_lambda}.Keywords[i].ProtLigInter.LigWatResult"
, where the{fep_lambda}
part is a f-string variable. Currently, only{fep_lambda}
is supported. Note this argument’s value itself is a simple string (not a f-string). It will be converted to a f-string and evaluated on the fly by theon_*
decorators (see the docstrings there for detail), where all supported f-string variables must be defined.
-
schrodinger.application.desmond.new_fep_edge_data.
arg_option
(key_pattern: str, default=None)[source]¶ Similar to
arg_premise
, except that the type isana.Option
instead ofana.Premise
.- Parameters
key_pattern – See the docstring of
arg_premise
.default – The default value of the datum if the key is not in the database.
-
schrodinger.application.desmond.new_fep_edge_data.
arg_aid_offset
(func)[source]¶ This decorator is to pass the value of
aid_offset
, which depends on the specific leg, via the corresponding argument to the function. See its usage below.
-
schrodinger.application.desmond.new_fep_edge_data.
on_complex_lambda_0
(func)[source]¶ Calls
func
with complex leg and FEP lambda state 0.
-
schrodinger.application.desmond.new_fep_edge_data.
on_complex
(func)[source]¶ Calls
func
with complex leg. The FEP lambda state is irrelevant.
-
schrodinger.application.desmond.new_fep_edge_data.
on_complex_lambdas
(func)[source]¶ Calls
func
with complex leg and both FEP lambda states 0 and 1.- Return type
2-tuple
- Returns
The results returned by
func
for FEP lambda states 0 and 1, respectively.
-
schrodinger.application.desmond.new_fep_edge_data.
on_complex_solvent_lambda_0
(func)[source]¶ Calls
func
with both complex and solvent legs and with FEP lambda state 0.- Return type
2-tuple
- Returns
The two elements are for the complex and solvent legs, respectively.
-
schrodinger.application.desmond.new_fep_edge_data.
on_complex_solvent
(func)[source]¶ Calls
func
with both complex and solvent legs.func
does NOT require a specification of the FEP lambda state. In most cases, the decorated property will return a 2-tuple. The elements correspond to the complex and the solvent legs. In these cases, the lambda states are irrelevant. In some other cases, the property will return four values for the following leg/lambda-state combinations: complex/lambda0, complex/lambda1, solvent/lambda0, and solvent/lambda1; in these case, the values will be rearranged into thelambda0(complex, solvent), lambda1(complex, solvent)
format to be consistent with properties decorated byon_complex_solvent_lambdas
.- Return type
2-tuple
-
schrodinger.application.desmond.new_fep_edge_data.
on_complex_solvent_lambdas
(func)[source]¶ Calls
func
with both complex and solvent legs and with both FEP lambda states 0 and 1.- Return type
Tuple[2-tuple, 2-tuple]
- Returns
The two elements are for FEP lambda states 0 and 1. Each element is a 2-tuple of the results by
func
for the complex and solvent legs, respectively.
-
class
schrodinger.application.desmond.new_fep_edge_data.
ResData
(molnum, chain, name, number, commonname)[source]¶ Bases:
schrodinger.application.desmond.new_fep_edge_data.ResData
A class to store the molecule number, chain, name, and number of a residue
-
static
make
(res: schrodinger.structure._structure._Residue) → schrodinger.application.desmond.new_fep_edge_data.ResData[source]¶
-
property
fullname
¶ Return a string formatted as “<chain>:<resname>_<resnum>”.
-
property
name_num
¶ Return a string formatted as “<resname>_<resnum>”.
-
__contains__
(key, /)¶ Return key in self.
-
__len__
()¶ Return len(self).
-
chain
¶ Alias for field number 1
-
commonname
¶ Alias for field number 4
-
count
(value, /)¶ Return number of occurrences of value.
-
index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
-
molnum
¶ Alias for field number 0
-
name
¶ Alias for field number 2
-
number
¶ Alias for field number 3
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static
-
class
schrodinger.application.desmond.new_fep_edge_data.
TorsionPotential
(raw_data: List[float], a1, a2, a3, a4)[source]¶ Bases:
object
-
__init__
(raw_data: List[float], a1, a2, a3, a4)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
property
energy_profile
¶ Returns energy profile that’s offset to zero.
-
property
max
¶ Returns the maximum value of the energy profile.
-
property
aids
¶
-
-
class
schrodinger.application.desmond.new_fep_edge_data.
FepData
(fep_type: str, complex_model: schrodinger.application.desmond.cms.Cms, complex_analysis_results: schrodinger.application.desmond.ana.ArkDb, solvent_analysis_results: schrodinger.application.desmond.ana.ArkDb, vacuum_analysis_results: Optional[schrodinger.application.desmond.ana.ArkDb] = None)[source]¶ Bases:
object
A data scraper class to extract and reorganize from FEP simulations and raw SID analysis results.
-
__init__
(fep_type: str, complex_model: schrodinger.application.desmond.cms.Cms, complex_analysis_results: schrodinger.application.desmond.ana.ArkDb, solvent_analysis_results: schrodinger.application.desmond.ana.ArkDb, vacuum_analysis_results: Optional[schrodinger.application.desmond.ana.ArkDb] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
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property
fep_type
¶
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property
leg_names
¶
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property
complex_model
¶
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property
receptor
¶
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property
ref
¶
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property
mut
¶
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atom_mapping
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_wateraround_counts
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_fragments
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_torsions
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_torsion_strain
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_intrahbond_counts
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_sasa
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_molecular_sa
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_polar_sa
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_gyration_radius
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_rmsd
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ligand_rmsd_wrt_protein
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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protein_secondary_structure
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_residue_sequence
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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receptor_residue_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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receptor_backbone_rmsd
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_backbone_rmsf
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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residues_around_ligand
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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residues_around_ligand_both_lambda_states
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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similarity_matrix_by_protein_ligand_interactions
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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trajectory_intervals
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
num_trajectory_frames
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
trajectory_timelines
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
dg_sliding_time_function
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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dg_reverse_time_function
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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dg_forward_time_function
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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dg
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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ddg
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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df_per_window
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_charge
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_num_heavy_atoms
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_num_atoms
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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property
receptor_title
¶
-
receptor_num_residues_per_chain
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
receptor_num_residues
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_num_rotatable_bonds
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_num_fragments
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_molecular_formula
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_charge
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
alchemical_solvent
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
num_atoms_alchemical_solvent
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_molecular_mass
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_num_hotatoms
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_asl
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_pdb_resname
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
ligand_smiles
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
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edge_id
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
node_ids
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
jobname
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
num_replicas
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
num_water_molecules
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
num_atoms
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
sim_time
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
sim_temperature
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
sim_ff
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
sim_ensemble
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
sim_charge
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
num_salt_atoms
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
salt_concentration
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-