schrodinger.application.desmond.new_fep_edge_data module

class schrodinger.application.desmond.new_fep_edge_data.FepLegs(complex, solvent, vacuum)

Bases: tuple

complex

Alias for field number 0

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

mut

Alias for field number 1

ref

Alias for field number 0

exception schrodinger.application.desmond.new_fep_edge_data.BlameSidError

Bases: Exception

schrodinger.application.desmond.new_fep_edge_data.compare_mean_stdev_samples(a, b)

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)

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)

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)

This decorator is to pass the val of the task.Premise object via the corresponding argument to the function. See its usage below.

The task.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)

Similar to arg_premise, except that the type is task.Option instead of task.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)

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)

Calls func with complex leg and FEP lambda state 0.

schrodinger.application.desmond.new_fep_edge_data.on_complex(func)

Calls func with complex leg. The FEP lambda state is irrelevant.

schrodinger.application.desmond.new_fep_edge_data.on_complex_lambdas(func)

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)

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)

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)

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)

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

property fullname: str

Return a string formatted as “<chain>:<resname>_<resnum>”.

property name_num: str

Return a string formatted as “<resname>_<resnum>”.

class schrodinger.application.desmond.new_fep_edge_data.TorsionPotential(raw_data: List[float], a1, a2, a3, a4)

Bases: object

__init__(raw_data: List[float], a1, a2, a3, a4)

property energy_profile: numpy.ndarray

Returns energy profile that’s offset to zero.

property max: float

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.arkdb.ArkDb, solvent_analysis_results: schrodinger.application.desmond.arkdb.ArkDb, vacuum_analysis_results: Optional[schrodinger.application.desmond.arkdb.ArkDb] = None)

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.arkdb.ArkDb, solvent_analysis_results: schrodinger.application.desmond.arkdb.ArkDb, vacuum_analysis_results: Optional[schrodinger.application.desmond.arkdb.ArkDb] = None)

property fep_type

property leg_names

property complex_model

property receptor

property ref

property mut

property atom_mapping: List[Tuple[int, int]]

Returns the AID (atom ID) pairs of the mapped atoms. Each element is a pair of AIDs, where the first one is of the mutant and the second of the reference. The AIDs are local with respect to the alchemical structures.

property ligand_wateraround_counts

property ligand_fragments

property ligand_torsions: Iterator[Tuple[schrodinger.application.desmond.new_fep_edge_data.TorsionPotential, schrodinger.application.desmond.new_fep_edge_data.TorsionPotential]], Iterator[Tuple[schrodinger.application.desmond.new_fep_edge_data.TorsionPotential, schrodinger.application.desmond.new_fep_edge_data.TorsionPotential]]

Returns two iterators for lambda states 0 and 1, respectively. Each iterator is over a list of 2-tuples of torsion potentials respectively for the complex and solvent legs.

property ligand_torsion_strain

property ligand_intrahbond_counts

property ligand_sasa

property ligand_molecular_sa

property ligand_polar_sa

property ligand_gyration_radius

property ligand_rmsd

property ligand_rmsd_wrt_protein

property protein_secondary_structure

property receptor_residue_sequence: List[schrodinger.application.desmond.new_fep_edge_data.ResData]

Return the residue sequence from N- to C-end. This property assumes that there is only one receptor structure.

property receptor_residue_b_factor

property receptor_backbone_rmsd

property receptor_backbone_rmsf

property residues_around_ligand

property residues_around_ligand_both_lambda_states

Returns a list of residues around the ligand molecule in both lambda states. Eech residue is a string of the form: “<chain>:<resname>_<resnum>”, and the list is sorted by the chain and the resnum.

property similarity_matrix_by_protein_ligand_interactions

property trajectory_intervals

property num_trajectory_frames

property trajectory_timelines: Tuple[numpy.ndarray, numpy.ndarray]

Returns two 1-D numpy arrays containing the trajectory-frames’ times for the complex and the solvent legs, respectively. CAVEAT: This relies on a not-super-safe assumption: The trajectory frames are always recorded with a start at 0 and a uniform interval.

property dg_sliding_time_function

property dg_reverse_time_function

property dg_forward_time_function

property dg

property ddg: schrodinger.application.desmond.measurement.Measurement

Returns the ddG = dG_complex - dG_solvent.

property df_per_window

property receptor_charge

property receptor_num_heavy_atoms

property receptor_num_atoms

property receptor_title: str

property receptor_num_residues_per_chain

property receptor_num_residues

property ligand_num_rotatable_bonds

property ligand_num_fragments

property ligand_molecular_formula

property ligand_charge

property alchemical_solvent

property num_atoms_alchemical_solvent

property ligand_molecular_mass

property ligand_num_hotatoms

property ligand_asl

property ligand_pdb_resname

property ligand_smiles

property edge_id

property node_ids

property jobname

property num_replicas

property num_water_molecules

property num_atoms

property sim_time

property sim_temperature

property sim_ff

property sim_ensemble

property sim_charge

property num_salt_atoms

property salt_concentration