Functions

Topology

Loading network

network.load_net(name_file, format='text', verbose=True)

Parameters:

• name_file (str) – Name of input file with network
• format (str) – Format of input file: ‘text’ or ‘native’

Verbose :

Prints out general information of the network loaded.

Returns:

None

Prints out:

general information if verbose=True.

Loading labels

network.load_labels(name_file, format='text')

Parameters:

• name_file (str) – Name of input file with network
• format (str) – Format of input file: ‘text’ or ‘water’

Returns:

None

Prints out:

None

Adding node

network.add_node(label=None, weight=0, iout=False)

Parameters:

• label (str or int.) – Label of new node.
• weight (float) – Weight of new node.
• iout (bool) – Returning index of new node in network.

Returns:

Index of new node if iout=True.

Prints out:

None

Adding link

network.add_link(node_origin, node_final, weight=0, index_origin=False, index_final=False, iout=False)

Parameters:

• node_origin (int or str.) – source of the link.
• node_final (int or str.) – destination of the link.
• weight (float) – weight of link.
• index_origin (bool) – True if node_origin takes the integer value of the index in the network.
• index_final (bool) – True if node_final takes the integer value of the index in the network.
• iout (bool) – Returning the indexes of nodes linked.

Returns:

Index of linked nodes if iout=True.

Prints out:

None

Info

network.info(update=True, verbose=True)

Parameters:

• update (bool) – Computing and updating general variables as network.weight, network.num_nodes, network.k ...
• verbose (bool) – Prints out general information.

Returns:

None

Prints out:

General information of the network if verbose.

Merging network

network.merge_net(net=None, traj=None, verbose=True)

Parameters:

• net (network class.) – network to be merged or included.
• traj – None.
• verbose (bool) – Prints out general information.

Prints out:

General information of the network if verbose.

Extracting network

network.extract_net(nodes=None, verbose=True)

Parameters:

• nodes (list[int]) – List of nodes with which a new network is built.
• verbose (bool) – Prints out general information.

Returns:

network class.

Prints out:

General information of the new network if verbose.

Writting network

network.write_net(name_file=None, format='text', pymol=False, with_index=True, with_cluster=False)

Parameters:

• name_file (str) – Name of new file.
• format (str) – Format of output file: ‘text’ or ‘native’.
• pymol (bool) – True if the file will be read by pymol.
• with_index (bool) – The network will be written with node indexes if True.
• with_cluster (bool) – The hnodes will be written with a cluster indentification.

Writting labels

network.write_labels(name_file=None, format='text')

Parameters:

• name_file (str) – Name of new file
• format (str) – Format of output file: ‘text’

Clustering

MCL

Gradient Clusters