schrodinger.ui.sequencealignment.prime module

Prime homology modeling functions.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.ui.sequencealignment.prime.prime_get_default_settings()[source]

Returns a dictionary with default Prime settings.

schrodinger.ui.sequencealignment.prime.prime_build_consensus_model(sequence_group, progress_dialog=None, job_settings='', viewer=None)[source]

Builds a Prime consensus homology model.

schrodinger.ui.sequencealignment.prime.prime_run(settings=None, mode=1, group_list=[], valid_template_list=[], progress_dialog=None, viewer=None, job_settings='')[source]

This function is used to create homology models. It generates input files for Prime, runs the Prime job, and incorporates built models into Maestro. This function is called when the user clicks on “Build Model” button in Build Homology Model panel.

There are several possible homology modeling scenarios that need to be handled by this function:

  1. modeling using a single query and a single template,

2) modeling using a single query and multiple templates with selected template regions: all templates are used to build a single composite model,

3) modeling using a single query and multiple templates in order to build a homo-multimer: each template is used to create an individual model, but query sequence is identical for each of the models,

4) modeling using multiple queries and multiple templates: each query / template pair is treated independently in order to build a hetero-multimer.

In addition, there are possible mixed scenarios, e.g. building a hetero-multimer consisting of homo-multimers.

Note

We are using “query” and “sequence group” as synonyms. A sequence group can include a single query sequence and several template sequences. The “reference” and “query sequence” are also used as synonyms.

Parameters

sequence_group (SequenceGroup) – A default (current) sequence group.

Return type

boolean

Returns

True on successful job completion, False if the job could not be completed.