Module to interact with pyrvapi
RvapiMetadata
[source]¶Bases: object
Storage container for metadata required by JsCoFe
Attributes
n_results |
Methods
add (e) |
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to_json () |
n_results
¶SimbadOutput
(rvapi_document, webserver_uri, display_gui, logfile, work_dir, ccp4i2_xml=None, tab_prefix=”)[source]¶Bases: object
Class to display the output of SIMBAD
Examples
>>> from simbad.util import pyrvapi_results
>>> gui = pyrvapi_results.SimbadOutput(<'rvapi_file'>, <'webserver_uri'>, <'display__gui'>,
... <'logfile'>, <'work_dir'>)
>>> gui.display_results(<'show_summary'>)
Attributes
webserver_uri | (str) The uri if run on a webserver |
display_gui | (bool) Option to prevent results being displayed |
logfile | (str) Path to the log file |
work_dir | (str) Path to the work directory [default: None] |
summary | (bool) Option to display summary tab [default: False] |
Methods
adjust_paths_of_files (files) |
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create_contaminant_results_tab (…) |
Function to create the contaminant results tab |
create_graphs (df, graph_sec, graph_widget) |
Function to create/display graphs following MR |
create_lattice_results_tab (lattice_results, …) |
Function to create the lattice results tab |
create_log_tab (logfile) |
Function to create log tab |
create_morda_db_results_tab (…) |
Function to create the MoRDa Database results tab |
create_table (df, table_id) |
Function to create/display tables |
display_results (summarize, results_to_display) |
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display_summary_tab () |
Function to create the MoRDa Database results tab |
fix_path (path) |
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init_from_ccp4i2_xml (ccp4i2_xml, …) |
This code is largely stolen from Andrew Lebedev |
output_log_files (sec, mr_log, ref_log) |
Function to display the log files for the result |
output_result_files (sec, diff_map, ref_map, …) |
Function to display the result files for the result |
rel_path_for_jscofe (path) |
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save_document () |
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store_entry_in_rvapi_meta (rank, source, …) |
create_contaminant_results_tab
(contaminant_results, contaminant_mr_results, results_to_display)[source]¶Function to create the contaminant results tab
Parameters: | contaminant_results : str
contaminant_mr_results : str
results_to_display : int
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Returns: | object
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create_graphs
(df, graph_sec, graph_widget)[source]¶Function to create/display graphs following MR
Returns: | object
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create_lattice_results_tab
(lattice_results, lattice_mr_results, results_to_display)[source]¶Function to create the lattice results tab
Parameters: | lattice_results : str
lattice_mr_results : str
results_to_display : int
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Returns: | object
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create_log_tab
(logfile)[source]¶Function to create log tab
Parameters: | logfile : str
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Returns: | str
object
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create_morda_db_results_tab
(morda_db_results, morda_db_mr_results, results_to_display)[source]¶Function to create the MoRDa Database results tab
Parameters: | morda_db_results : str
morda_db_mr_results : str
results_to_display : int
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Returns: | object
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create_table
(df, table_id)[source]¶Function to create/display tables
Parameters: | df : :Pandas dataframe:
table_id : str
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Returns: | object
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display_summary_tab
()[source]¶Function to create the MoRDa Database results tab
Returns: | object
|
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init_from_ccp4i2_xml
(ccp4i2_xml, pyrvapi_dir, share_jsrview, wintitle)[source]¶This code is largely stolen from Andrew Lebedev
output_log_files
(sec, mr_log, ref_log)[source]¶Function to display the log files for the result
Parameters: | sec : str
mr_log : str
ref_log : str
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Returns: | object
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output_result_files
(sec, diff_map, ref_map, ref_mtz, ref_pdb)[source]¶Function to display the result files for the result
Parameters: | sec : str
diff_map : str
ref_map : str
ref_mtz : str
ref_pdb : str
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Returns: | object
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