Various miscellaneous functions
amoptd_fix_path
(optd, newroot, i2mock=False)[source]¶Update all the paths in an AMPLE results dictionary to be rooted at newroot
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construct_references
(optd)[source]¶Construct the reference list
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extract_and_validate_models
(amoptd, sequence=None, single=True, allsame=True)[source]¶Extract models given to AMPLE from arguments in the amoptd and validate that they are suitable
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extract_models_from_archive
(archive, models_dir, suffixes=None, filenames=None)[source]¶Extract models from file archive into directory models_dir
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extract_tar
(archive, directory=None, filenames=None, suffixes=None)[source]¶Extract one or more files from a tar file into a specified directory
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filename_append
(filename=None, astr=None, directory=None, separator=’_’)[source]¶Append astr to filename, before the suffix, and return the new filename.
find_exe
(executable, dirs=None)[source]¶Find the executable exename.
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ideal_helices
(optd)[source]¶Get some ideal helices
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is_exe
(fpath)[source]¶Check if an executable exists
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is_file
(fpath)[source]¶Check if a file exists
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make_workdir
(run_dir, ccp4i2=False)[source]¶Make a work directory rooted at run_dir and return its path
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read_amoptd
(amoptd_fname)[source]¶Read a PICKLE-formatted AMPLE options file
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run_command
(cmd, logfile=None, directory=None, dolog=True, stdin=None, check=False, **kwargs)[source]¶Execute a command and return the exit code.
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Notes
We take care of outputting stuff to the logs and opening/closing logfiles
saveAmoptd
(*args)[source]¶Save AMPLE options to a PICKLE-formatted file
Warning
This function was deprecated and will be removed in future releases. Please use save_amoptd()
instead.
See also
save_amoptd
(amoptd)[source]¶Save AMPLE options to a PICKLE-formatted file
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split_models
(dfile, directory)[source]¶Split a single PDB with multiple models in individual PDB files
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split_quark
(models_dir)[source]¶Given a models_dir containing a single QUARK PDB, split the PDB into constituent models and then delete the original QUARK PDB
tmpFileName
()[source]¶Return a filename for a temporary file
Warning
This function was deprecated and will be removed in future releases. Please use tmp_file_name()
instead.
See also
tmp_file_name
(delete=True, directory=None, suffix=”)[source]¶Return a filename for a temporary file
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