Module: contacts

A module to pick contacts from a contact map in different ways. It is important to note the difference between pickInLargestCluster and fillInLargestCluster.

Members

BioHelpers_FABER.contacts.fillInLargestCluster(x: ndarray, N: int) → list

Picks randomly contacts in the largest clusters of a contact map x. If the largest cluster is not big enough, the largest cluster will filled completely and the second (or third or fourth a.s.o.) largest cluster will contain the remaining contacts randomly.

Parameters:

  • x (np.ndarray) – Contact map

  • N (int) – Number of contacts to pick

Returns:

List of choosen contacts

Return type:

list

BioHelpers_FABER.contacts.pickBestGauss(x: ndarray, N: int, num_it: int, var: float) → list

Picks the random distribution with the best Gauss Score

Parameters:

  • x (np.ndarray) – Contact map

  • N (int) – Number of contacts to pick

  • num_it (int) – Number of iterations, to find the best Gauss map

  • var (float) – Variance of the Gaussian distributions

Returns:

List of choosen contacts

Return type:

list

BioHelpers_FABER.contacts.pickBestGaussFalse(x: ndarray, N: int, lam: float, neigh: int, num_it: int, var: float) → list

Picks the random distribution with the best Gauss Score

Parameters:

  • x (np.ndarray) – Contact map

  • N (int) – Number of contacts to pick

  • lam (float) – Ratio of false positive \(\lambda\)

  • neigh (int) – Number of off-diagonals to delete

  • num_it (int) – Number of iterations, to find the best Gauss map

  • var (float) – Variance of the Gaussian distributions

Returns:

List of choosen contacts

Return type:

list

BioHelpers_FABER.contacts.pickInLargestCluster(x: ndarray, N: int) → list

Picks randomly contacts in the largest clusters of a contact map x. If the largest cluster is not big enough, the second largest cluster will be added to the largest cluster and so on. The contacts will be randomly picked from this set of possible contacts.

Parameters:

  • x (np.ndarray) – Contact map

  • N (int) – Number of contacts to pick

Returns:

List of choosen contacts

Return type:

list

BioHelpers_FABER.contacts.pickMaxDistance(x: ndarray, N: int) → list

Picks a random seed and from that the contact farest apart and so on

Parameters:

  • x (np.ndarray) – Contact map

  • N (int) – Number of contacts to pick

Returns:

List of choosen contacts

Return type:

list

BioHelpers_FABER.contacts.pickRandom(x: ndarray, N: int) → list

Picks N unique random contacts from a given contact matrix

Parameters:

  • x (np.ndarray) – Contact map

  • N (int) – Number of contacts to pick

Returns:

List of randomly picked contacts

Return type:

list

BioHelpers_FABER.contacts.pickRandomFalse(x: ndarray, N: int, lam: float, neigh: int) → list

Picks \(N-\lambda N\) unique random contacts from a given native contact matrix, combined with \(\lambda N\) false positive contacts. \(\lambda N\) will be rounded to the nearest integer.

Parameters:

  • x (np.ndarray) – Contact map

  • N (int) – Number of contacts to pick

  • lam (float) – Ratio of false positive \(\lambda\)

  • neigh (int) – Number of off-diagonals to delete

Returns:

List of randomly picked contacts

Return type:

list