Module: cmap

The module cmap is a module for comparison analysis of various predicted contactmaps. One focus is on analysung the contact map topology.

Examples

Members

class BioHelpers_FABER.cmap.Cmap(length: int = 0, variance: float = 4.0)

Class to load restraint files and compare different predicted contacts.

native_contacts

Contact matrix from native PDB, labelling here: all residues from 1 to L (no unmodelled regions)

Type:

np.ndarray

contacts

Loaded Contacts from file, with unmodelled regions!

Type:

dict[str, np.ndarray]

ppvs

PPV for each contact matrix, keys are the same like in contacts

Type:

dict[str, float]

gauss

Gauss measure for each contact matrix, keays are the like in contacts

Type:

dict[str, float]

l

Length of the molecule in Residues contact_definition (float): Distance \(d\). If distance \(d(N_i, N_j)<d\) between the two nitrogen atoms of residues \(i\) and \(j\), then it is treated as a contact. Default \(d=9.5\) Angstrom.

Type:

int

variance

Variance for the Gauss meausre. Default \(\sigma^2 = 4\).

Type:

float

poisitioning

List of the border of unmodelled regions. Labelling from 1.

Type:

list

get_unmodelled_regions() → list[tuple[int]]

All the unmodelled regions in self.positioning[0] and self.positioning[-1]

Returns:

List of tuples

Return type:

list[tuple[int]]

load_contacts_from_restraints(filename: str, contact_name: str = ' ') → None

Loading Contact Map from a SimRNA Restraint file. The contacts are stored internally in a dictionary unter contact_name, PPV and Gauss Score are calculated automatically.

Parameters:

• filename (str) – Filename of the SimRNA Restraint File

• contact_name (str, optional) – Key name of the Contact Map. Defaults to “ “.

load_native_pdb(filename: str, id: str = ' ', reference: str = 'nitrogen', contact_threshold: float = 9.5, start_from_one: bool = True, added_tail: int = 0) → None

Method to load the experimental PDB file for comparison

Parameters:

• filename (str) – Filename of the PDB File.

• id (str, optional) – ID of the PDB. Has no influence on the comparison. Defaults to “ “.

num_to_id(position: int) → int

Maps the residue number (0 to L) from the pdb to the correct Residue ID

Parameters:

position (int) – Residue number

Returns:

Residue ID

Return type:

int

static simrna_restraints_to_contacts(data: list[str]) → list[tuple[int, int]]

Convert a simrna Restraint file into a contact list.

Parameters:

data (list[str]) – List of all lines from a simrna restraint file.

Returns:

list of contacts, format \((i,j)\)

Return type:

list[tuple[int, int]]