Module to run the AMORE rotation search
AmoreRotationSearch
(amore_exe, mtz, tmp_dir, work_dir, max_to_keep=20)[source]¶Bases: object
A class to perform the amore rotation search
Examples
>>> from simbad.rotsearch.amore_search import AmoreRotationSearch
>>> rotation_search = AmoreRotationSearch('<amore_exe>', '<mtz>', '<work_dir>', '<max_to_keep>')
>>> rotation_search.run(
... '<models_dir>', '<output_dir>', '<nproc>', '<shres>', '<pklim>', '<npic>', '<rotastep>',
... '<min_solvent_content>', '<submit_qtype>', '<submit_queue>', '<monitor>', '<chunk_size>'
... )
>>> rotation_search.summarize()
>>> search_results = rotation_search.search_results
If any results are found, an object is returned containing the pdb_code, and the various associated scores from amore.
Attributes: |
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Methods
run (models_dir[, nproc, shres, pklim, npic, …]) |
Run amore rotation function on a directory of models |
submit_chunk (chunk_scripts, run_dir, nproc, …) |
Submit jobs in small chunks to avoid using too much disk space |
summarize (csv_file) |
Summarize the search results |
get_chunk_size | |
get_total_chunk_cycles |
rotfun_stdin_template
¶run
(models_dir, nproc=2, shres=3.0, pklim=0.5, npic=50, rotastep=1.0, min_solvent_content=20, submit_qtype=None, submit_queue=None, monitor=None, chunk_size=0)[source]¶Run amore rotation function on a directory of models
Parameters: |
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Returns: |
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search_results
¶sortfun_stdin_template
¶submit_chunk
(chunk_scripts, run_dir, nproc, job_name, submit_qtype, submit_queue, monitor)[source]¶Submit jobs in small chunks to avoid using too much disk space
Parameters: |
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summarize
(csv_file)[source]¶Summarize the search results
Parameters: |
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Raises: |
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tabfun_stdin_template
¶