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.

__len__()

Return len(self).

complex

Alias for field number 0

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.

solvent

Alias for field number 1

vacuum

Alias for field number 2

class schrodinger.application.desmond.new_fep_edge_data.FepLambdas(ref, mut)

Bases: tuple

__contains__(key, /)

Return key in self.

__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.

mut

Alias for field number 1

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 and b 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 and b 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 and b 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 the ana.Premise object via the corresponding argument to the function. See its usage below.

The ana.Premise object is created with the given key_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 the on_* 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 is ana.Option instead of ana.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 the lambda0(complex, solvent), lambda1(complex, solvent) format to be consistent with properties decorated by on_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

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.

property fep_type
property leg_names
property complex_model
property receptor
property ref
property mut
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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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