Commad line facility for SIMBAD scripts
CCP4Version
[source]¶Bases: distutils.version.StrictVersion
The CCP4 version class
Methods
parse (vstring) |
LogColorFormatter
(fmt=None, datefmt=None)[source]¶Bases: logging.Formatter
Formatter for log messages
Methods
converter (…) |
Convert seconds since the Epoch to a time tuple expressing local time. |
format (record) |
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formatException (ei) |
Format and return the specified exception information as a string. |
formatTime (record[, datefmt]) |
Return the creation time of the specified LogRecord as formatted text. |
usesTime () |
Check if the format uses the creation time of the record. |
LogColors
[source]¶Bases: enum.Enum
Color container for log messages
CRITICAL
= 31¶DEBUG
= 34¶DEFAULT
= 0¶ERROR
= 31¶WARNING
= 33¶LogController
(reset=True)[source]¶Bases: object
Controller class for log messaging
Methods
add_console ([level, format, stream]) |
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add_logfile (file[, level, format]) |
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close () |
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get_levelname (level) |
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get_logger () |
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level_valid (level) |
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reset () |
LogLevels
[source]¶Bases: enum.Enum
Log level container
DEBUG
= 10¶ERROR
= 40¶INFO
= 20¶NOTSET
= 0¶WARNING
= 30¶cleanup
(directory, output_dir, csv, results_to_keep)[source]¶Function to clean up working directory results not reported by GUI
get_work_dir
(run_dir, work_dir=None, ccp4_jobid=None, ccp4i2_xml=None)[source]¶Figure out the relative working directory by provided options
make_output_dir
(run_dir, output_dir, csv, mr_program)[source]¶Make a directory containing output files
Parameters: | run_dir : str
output_dir : str
csv : file
mr_program : str
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make_workdir
(run_dir, ccp4_jobid=None, ccp4i2_xml=None, rootname=’SIMBAD_’)[source]¶Make a work directory rooted at work_dir and return its path
Parameters: | run_dir : str
ccp4_jobid : int, optional
ccp4i2_xml : str, optional
rootname : str, optional
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Returns: | work_dir : str
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Raises: | ValueError
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submit_mr_jobs
(mtz, mr_dir, search_results, refine_type, refine_cycles, args)[source]¶Function to submit molecular replacement jobs
Parameters: | mtz : str
mr_dir : str
mr_dir : str
search_results : list
refine_type : str
refine_cycles : int
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Returns: | object
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