emap

class pyemap.emap(file_path, pdb_id, eta_moieties, chain_list, sequences)[source]

Manages the data generated at all stages of PyeMap analysis.

file_path

Crystal structure file being analyzed by PyeMap.

Type:

str

eta_moieties

Non-protein eta moieties automatically identified at the parsing step.

Type:

dict of str: Bio.PDB.Residue.Residue

chain_list

List of chains identified at the parsing step.

Type:

list of str

sequences

Amino acid sequence for each chain in FASTA format

Type:

dict of str, str

residues

Residues included in the graph after the process step.

Type:

dict of str: Bio.PDB.Residue.Residue

user_residues

Custom residues specified by the user.

Type:

dict of str: Bio.PDB.Residue.Residue

init_graph

Graph generated after the process step.

Type:

networkx.Graph

branches

Branches found by PyeMap analysis

Type:

dict of int: Branch

paths

Paths found by PyeMap sorted by lowest to highest score.

Type:

dict of str: ShortestPath

paths_graph

Graph generated after the shortest paths step.

Type:

networkx.Graph

__init__(file_path, pdb_id, eta_moieties, chain_list, sequences)[source]

Initializes emap object.

Parameters:

  • file_path (str) – Name of file

  • eta_moieties (list of Bio.PDB.Residue.Residue) – Customized residue objects generated for automatically detected eta moieties

  • chain_list (list of str) – Chains identified by the parser

  • sequences (dict of str:str) – Key is chain id, value is sequence in fasta format

get_surface_exposed_residues()[source]

Returns list of surface exposed residues.

Returns:

surface_exposed – List of surface exposed residues identified by pyemap

Return type:

list of str

init_graph_to_Image()[source]

Returns PIL image of initial graph

Returns:

img

Return type:

PIL.Image.Image

init_graph_to_file(dest='')[source]

Saves image of graph generated by process step to file.

Parameters:

dest (str) – Destination for writing to file.

paths_graph_to_Image()[source]

Returns PIL image of pathways graph

Returns:

img

Return type:

PIL.Image.Image

paths_graph_to_file(dest='')[source]

Saves image of graph generated by pathways step to file.

Parameters:

dest (str) – Destination for writing to file.

report(dest='')[source]

Returns report of most probable pathways. Writes to file if destination is specified.

Parameters:

dest (str, optional) – Destination for writing to file

Returns:

output – Formatted report of pathways found

Return type:

str

Raises:

RuntimeError – Nothing to report

residue_to_Image(resname, scale=1.0)[source]

Returns PIL image of chemical structure. :param resname: Name of residue :type resname: str :param scale: Output scaling factor, default dimensions are (100,100) :type scale: float, optional

Returns:

img

Return type:

PIL.Image.Image

residue_to_file(resname, dest='', size=(100, 100))[source]

Saves image of residue to file in .svg format.

Parameters:

  • resname (str) – Name of residue (node label) to be saved to file.

  • dest (str, optional) – destination to save the image

  • size ((float,float), optional) – dimensions of image saved to file

visualize_pathway_in_nglview(ptid, view)[source]

Visualize pathway in nglview widget

Parameters: