frequencies

Frequencies.getResidueFrequenciesSum(…)	For a given ensemble of residues, compute their relative frequencies sum.
Frequencies.getResidueFrequenciesLogSum(…)	For a given ensemble of residues, compute their relative frequencies log sum.
Frequencies.getResidueFrequenciesSquareSum(…)	For a given ensemble of residues, compute their relative frequencies square sum.
Frequencies.getResidueFrequenciesAverage(…)	For a given ensemble of residues, compute their relative frequencies sum normalized by the number of residues.
Frequencies.getContactFrequenciesSum(…)	For a given ensemble of contacts, compute their relative frequencies sum.
Frequencies.getContactFrequenciesLogSum(…)	For a given ensemble of contacts, compute their relative frequencies log sum.
Frequencies.getContactFrequenciesSquareSum(…)	For a given ensemble of contacts, compute their relative frequencies square sum.
Frequencies.getContactFrequenciesAverage(…)	For a given ensemble of contacts, compute their relative frequencies sum normalized by the number of contacts.

class Frequencies(poses: List[DockingPP.pose.Pose])

An object that stores frequencies computed for a list of poses

nb_poses_used: int = None

The number of poses used for frequencies computation

count_contact: Dict[Tuple[int, int], int] = None

Dictionary that stores raw counts of contacts in poses.

count_residue: Dict[str, Dict[int, int]] = None

Dictionary that stores raw counts of residues at interface in poses.

available_scores = None

A dictionary that stores available scores for rescoring. These scores are computed for a given list of contacts or a given list of residues at interface from contacts relative frequencies or relative frequencies of residues at interface calculated here. The available scores are stored with their name, their type (if we need frequencies of contacts or residues at interface to compute them), and the function to compute them.

property rel_frequencies_contact

The relative frequencies of contacts in poses.

Returns

Dictionary with tuple (i,j) as key (where i is the index of residue in receptor and j is the index of residue in ligand) and score as value.

Return type

Dict[Tuple[int, int], float]

property rel_frequencies_residue

The relative frequencies of residues at interface in poses.

Returns

Dictionary with molecule role as key (ligand or receptor) and dictionary of frequencies for the molecule as value. Dictionary of frequencies has residue index as key and score as value.

Return type

Dict[str, Dict[int, float]]

getResidueFrequenciesSum(list_residue: Dict[str, Set[int]]) → float

For a given ensemble of residues, compute their relative frequencies sum.

Parameters

list_residue (Dict[str, Set[int]]) – Ensemble of residues to compute frequencies sum. It’s a dictionary with same format as DockingPP.pose.Pose residues_interface attribute (dictionary with molecule type as key and set of residues index as value).

Returns

The sum of residues relative frequencies.

Return type

float

getResidueFrequenciesLogSum(list_residue: Dict[str, Set[int]]) → float

For a given ensemble of residues, compute their relative frequencies log sum.

Parameters

list_residue (Dict[str,Set[int]]) – Ensemble of residues to compute frequencies log sum. It’s a dictionary with same format as DockingPP.pose.Pose residues_interface attribute (dictionary with molecule type as key and set of residues index as value).

Returns

The log sum of residues relative frequencies.

Return type

float

getResidueFrequenciesSquareSum(list_residue: Dict[str, Set[int]]) → float

For a given ensemble of residues, compute their relative frequencies square sum.

Parameters

list_residue (Dict[str, Set[int]]) – Ensemble of residues to compute frequencies square sum. It’s a dictionary with same format as DockingPP.pose.Pose residues_interface attribute (dictionary with molecule type as key and set of residues index as value).

Returns

The square sum of residues relative frequencies.

Return type

float

getResidueFrequenciesAverage(list_residue: Dict[str, Set[int]]) → float

For a given ensemble of residues, compute their relative frequencies sum normalized by the number of residues.

Parameters

list_residue (Dict[str, Set[int]]) – Ensemble of residues to compute frequencies square sum. It’s a dictionary with same format as DockingPP.pose.Pose residues_interface attribute (dictionary with molecule type as key and set of residues index as value).

Returns

The normalized sum of residues relative frequencies.

Return type

float

getContactFrequenciesSum(list_contact: Set[Tuple[int, int]]) → float

For a given ensemble of contacts, compute their relative frequencies sum.

Parameters

list_contact (Set[Tuple[int, int]]) – Set of contacts to compute frequencies sum. It’s a set of tuple(i,j) with i the index of residue in receptor and j the index of residue in ligand.

Returns

The sum of contacts relative frequencies.

Return type

float

getContactFrequenciesLogSum(list_contact: Dict[Tuple[int, int], int]) → float

For a given ensemble of contacts, compute their relative frequencies log sum.

Parameters

list_contact (Set[Tuple[int, int]]) – Set of contacts to compute frequencies sum. It’s a set of tuple(i,j) with i the index of residue in receptor and j the index of residue in ligand.

Returns

The log sum of contacts relative frequencies.

Return type

float

getContactFrequenciesSquareSum(list_contact: Dict[Tuple[int, int], int]) → float

For a given ensemble of contacts, compute their relative frequencies square sum.

Parameters

list_contact (Set[Tuple[int, int]]) – Set of contacts to compute frequencies sum. It’s a set of tuple(i,j) with i the index of residue in receptor and j the index of residue in ligand.

Returns

The square sum of contacts relative frequencies.

Return type

float

getContactFrequenciesAverage(list_contact: Dict[Tuple[int, int], int]) → float

For a given ensemble of contacts, compute their relative frequencies sum normalized by the number of contacts.

Parameters

list_contact (Set[Tuple[int, int]]) – Set of contacts to compute frequencies sum. It’s a set of tuple(i,j) with i the index of residue in receptor and j the index of residue in ligand.

Returns

The normalized sum of contacts relative frequencies.

Return type

float