API Documentation

Targets

targets.py Functions and classes for handling the target data.

class plbenchmark.targets.Target(name: str)[source]

Class to store the data of one target.

add_ligand_data()[source]

Adds data from ligands to plbenchmark.targets.target. Molecule images and the minimum and maximum affinity are added.

Returns: None

find_links()[source]

Processes primary data to have links in the html string of the target data

Returns: None

get_dataframe(columns=None)[source]

Access the target data as a pandas.DataFrame

Parameters: cols – list of columns which should be returned in the pandas.DataFrame
Returns: pandas.DataFrame

get_edge_set()[source]

Get plbenchmark:edges:edgeSet associated with the target

Returns: plbenchmark:edges:edgeSet object

get_edge_set_dataframe(columns=None)[source]

Get plbenchmark:edges:edgeSet associated with the target as a pandas.DataFrame

Parameters: columns – list of columns which should be returned in the pandas.DataFrame
Returns: plbenchmark:edges:edgeSet object

get_edge_set_html(columns=None)[source]

Get plbenchmark:edges:edgeSet associated with the target in a html string

Parameters: columns – list of edge which should be returned
Returns: html string

get_graph()[source]

Get a graph representation of the ligand perturbations associated with the target in a matplotlib.figure

Returns: matplotlib.figure

get_ligand_set()[source]

Get ligandSet associated with the target

Returns: plbenchmark.ligands.ligandSet object

get_ligand_set_dataframe(columns=None)[source]

Get ligandSet associated with the target in a pandas.DataFrame

Parameters: columns – list of columns which should be returned in the pandas.DataFrame
Returns: pandas.DataFrame

get_ligand_set_html(columns=None)[source]

Get ligandSet associated with the target in a html string

Parameters: columns – list of columns which should be returned
Returns: html string

get_name()[source]

Access the name of the target.

Returns: name as a string

class plbenchmark.targets.TargetSet(*arg, **kw)[source]

Class inherited from dict to store all available targets in plbenchmark.

get_dataframe(columns=None)[source]

Convert targetSet class to pandas.DataFrame

Parameters: columns – list of columns which should be returned in the pandas.DataFrame
Returns: pandas.DataFrame

get_html(columns=None)[source]

Access the plbenchmark:targets:targetSet as a HTML string

Parameters: cols – list of columns which should be returned in the pandas.DataFrame
Returns: HTML string

get_names()[source]

Get a list of available target names

Returns: list of strings

get_target(name)[source]

Accesses one target of the targetSet

Parameters: name – string name of the target
Returns: plbenchmark.targets.target class

plbenchmark.targets.get_target_data_path(target)[source]

Gets the file path of the target data

Parameters: target – string with target name
Returns: list of directories (have to be joined with ‘/’ to get the file path relative to the plbenchmark repository)

plbenchmark.targets.get_target_dir(target)[source]

Gets the directory name of the target

Parameters: target – string with target name
Returns: string with directory name

plbenchmark.targets.set_data_dir(path='/home/docs/checkouts/readthedocs.org/user_builds/plbenchmarks/checkouts/main/plbenchmark/sample_data')[source]

Gets the directory name of the target

Parameters: path – string with path to data directory

Ligands

ligands.py Functions and classes for handling the ligand data.

class plbenchmark.ligands.Ligand(d: dict, target: Optional[str] = None)[source]

Store and convert the data of one ligand in a pandas.Series.

add_mol_to_frame()[source]

Adds a image file of the ligand to the pandas.Dataframe

Returns: None

derive_observables(derived_type='dg', destination='DerivedMeasurement', out_unit=None)[source]

Derive observables from (stored) primary data, which is then stored in the pandas.DataFrame

Parameters

derived_type – type of derived observable, can be any of ‘dg’ ‘ki’, ‘ic50’ or ‘pic50’
destination – string with column name for ‘pandas.DataFrame’ where the derived observable should be stored.
out_unit – unit of type pint unit of derived coordinate

Returns

None

find_links()[source]

Processes primary data to have links in the html string of the ligand data

Returns: None

get_coordinate_file_path()[source]

Get file path relative to the plbenchmark repository of the SDF coordinate file of the docked ligand

Returns: file path as string

get_dataframe(columns=None)[source]

Access the ligand data as a pandas.Dataframe

Parameters: columns – list of columns which should be returned in the pandas.Dataframe
Returns: pandas.Dataframe

get_html(columns=None)[source]

Access the ligand as a HTML string

Parameters: columns – list of columns which should be returned in the pandas.Dataframe
Returns: HTML string

get_image()[source]

Creates a molecule image.

Returns: PIL.Image object

get_molecule()[source]

Get molecule object with coordinates of the docked ligand

Returns: file path as string

get_name()[source]

Access the name of the ligand.

Returns: name: string

class plbenchmark.ligands.LigandSet(target, *arg, **kw)[source]

Class inherited from dict to store all available ligands of one target.

get_dataframe(columns=None)[source]

Access the ligandSet as a pandas.Dataframe

Parameters: columns – list of columns which should be returned in the pandas.Dataframe
Returns: pandas.Dataframe

get_html(columns=None)[source]

Access the plbenchmark:ligands.ligandSet as a HTML string

Parameters: columns – list of columns which should be returned in the pandas.Dataframe
Returns: HTML string

get_ligand(name)[source]

Accesses one ligand of the ligandSet

Parameters: name – string name of the ligand
Returns: plbenchmark.ligands.ligand class

get_list()[source]

Returns list of ligands

Returns: list of ligand names

get_molecules()[source]

Returns a dict with names as keys and values as py:class:openforcefield:topology:Molecule objects

Returns: dict

Edges

edges.py Functions and classes for handling the perturbation edges.

class plbenchmark.edges.Edge(d: dict)[source]

Store and convert the data of one perturbation (“edge”) in a pandas.Series.

Parameters: d – dict with the edge data
Returns: None

add_ligand_data(ligand_set)[source]

Adds data from ligands to edge. Molecule images and the affinity difference are added.

Parameters: ligand_set – plbenchmark:ligands:ligandSet class of the same target
Returns: None

get_dataframe(columns=None)[source]

Access the edge data as a pandas.DataFrame

Parameters: cols – list of columns which should be returned in the pandas.DataFrame
Returns: pandas.DataFrame

get_dict()[source]

Access the edge data as a dict which contains the name of the edge as key and the names of the two ligands as list.

Returns: dict

get_name()[source]

Access the name of the edge.

Returns: name as string

class plbenchmark.edges.EdgeSet(target, *arg, **kw)[source]

Class inherited from dict to store all available edges of one target.

get_dataframe(columns=None)[source]

Access the plbenchmark:edges.edgeSet as a pandas.DataFrame

Parameters: cols – list of columns which should be returned in the pandas.DataFrame
Returns: pandas.DataFrame

get_dict()[source]

Access the plbenchmark:edges.edgeSet as a dict which contains the name of the edges as key and the names of the two ligands in a list as items.

Returns: dict

get_edge(name)[source]

Accesses one edge of the plbenchmark.edges.edgeSet

Parameters: name – string name of the edge
Returns: plbenchmark:edges:edge class

get_html(columns=None)[source]

Access the plbenchmark:edges.edgeSet as a HTML string

Parameters: cols – list of columns which should be returned in the pandas.DataFrame
Returns: HTML string

Utils

utils.py Contains utility functions

plbenchmark.utils.convert_error(error_value, value, original_type, final_type, temperature=300.0, out_unit=None)[source]

Converts an experimental value into another derived quantity with specified unit.

Parameters

error_value – float, error of val, numerical value
value – float, numerical value
original_type – string, code for the original observable. Can be dg, ki, ic50, pic50
final_type – string, code for the desired derived quantity. Can be dg, ki, ic50, pic50
temperature – float, temperature in kelvin
out_unit – unit of type pint, output unit of final_type, needs to fit to the requested final_type

Returns

pint.Quantity with desired unit

plbenchmark.utils.convert_value(value, original_type, final_type, temperature=300.0, out_unit=None)[source]

Converts an experimental value into another derived quantity with specified unit.

Parameters

value – float, numerical value
original_type – string, code for the original observable. Can be dg, ki, ic50, pic50
final_type – string, code for the desired derived quantity. Can be dg, ki, ic50, pic50
temperature – float, temperature in kelvin
out_unit – unit of type pint, output unit of final_type, needs to fit to the requested final_type

Returns

pint.Quantity with desired unit

plbenchmark.utils.find_doi_url(doi)[source]

Finds the links to a digital object identifier (doi).

Parameters: doi – string
Returns: string compiled string including the urls to the publication

plbenchmark.utils.find_pdb_url(pdb)[source]

Finds the links to a pdb or a list of pdb codes.

Parameters: pdb – string or list of strings
Returns: string compiled string including the urls to the pdb entries