jade.antibody.decoy_data package¶
jade.antibody.decoy_data.DecoyData module¶
-
class
jade.antibody.decoy_data.DecoyData.
DecoyData
(name, has_real_values=True, reverse_top=False)[source]¶ Bases:
object
-
add_data
(strategy, con)[source]¶ Baseclass method - needs to be overridden in subclass :param strategy: Strategy to which we are adding data. :param con: Sqlite3 Connection object
-
get_concatonated_map
(by_score_tuple=False)[source]¶ Returns a defaultDic: Default:
decoy: DecoyDataTriple- by_score_tuple (for sorting on score and having possible redundancy)
- [score, decoy]: DecoyDataTriple
-
get_data_for_decoy
(strategy, decoy)[source]¶ Get the held data for the decoy :param strategy: Strategy Name :param decoy: Decoy name (with dir and suffix) :rtype: DecoyDataTriple
-
get_ordered_decoy_list
(strategy, top_n=None)[source]¶ Get an ordered array of decoy names by energy for a particular strategy :rtype: list of str
-
get_ordered_decoy_list_all
(top_n=None)[source]¶ Get an ordered array of decoy names by energy over all the strategies :rtype: list of str
-
get_pandas_dataframe
(top_n=None, drop_dir_prfix=False)[source]¶ Gets all data as a pandas dataframe. Uses the set name as the score. You can then order, or select specific ones using the data frame. :return: pandas.DataFrame
-
get_strategy_data
(strategy, by_score_tuple=False)[source]¶ For a particular strategy: Return a dictionary of decoy:DataTriple or if by_score_tuple:
[score, decoy] = DataTriple
-
get_top_all_data
(top_n, by_score_tuple=False)[source]¶ Over all the strategies: Return a dictionary of decoy:DataTriple or if by_score_tuple:
[score, decoy] = DataTriple
-
jade.antibody.decoy_data.DecoyDataTypes module¶
-
class
jade.antibody.decoy_data.DecoyDataTypes.
CombinedStrDecoyData
(filters, filt_name)[source]¶ Bases:
jade.antibody.decoy_data.DecoyData.DecoyData
DecoyData class that has value as a string of the 3 main scores. Value held in DecoyDataTriple is a string: dG::total::dSASA for reference.
-
class
jade.antibody.decoy_data.DecoyDataTypes.
IntHbondDecoyData
[source]¶ Bases:
jade.antibody.decoy_data.DecoyData.DecoyData
New way for int hbonds - added directly from IAM.
-
class
jade.antibody.decoy_data.DecoyDataTypes.
InterfaceHBondDecoyDataLoader
[source]¶ Bases:
jade.antibody.decoy_data.DecoyData.DecoyData
DecoyData class that holds the number of LH_A or L_H interface Hbonds, and energies. Very Slow to get this information.
- SO - Subsequent Hbond classes accept this on construction and then parse its information
-
class
jade.antibody.decoy_data.DecoyDataTypes.
InterfaceHbondCountDecoyData
[source]¶
-
class
jade.antibody.decoy_data.DecoyDataTypes.
InterfaceHbondEnergyDecoyData
[source]¶
-
class
jade.antibody.decoy_data.DecoyDataTypes.
dGTotalScoreSubset
[source]¶ Bases:
jade.antibody.decoy_data.DecoyData.DecoyData
dG of the top x percent of total score (for each strategy)