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GlideError
Exception class for fatal errors raised by the Glide driver.
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Glide
High-level class for running the whole "glide_driver"
process, including log file boilerplate, argument parsing, setting
up the necessary driver object, and running it.
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CombinedDriver
A driver for running combined jobs, consisting of a gridgen job and
a distributed docking job.
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DockingDriver
Driver for distributing a docking job.
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GlideJob
Base class for DockingJob and GridgenJob.
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DockingJobFilenameMixin
A mixin offering read-only properties for "derived files"
that may be useful both for DockingJob and DockingSubjob objects.
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DockingJob
This represents the main docking job.
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GridgenJob
Objects of this class represent a gridgen job and additionally have
the machinery for running the job.
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DockingSubjob
Objects of this class represent docking subjobs for which the
ligand input file is provided by the caller.
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SplitDockingSubjob
Objects of this class represent docking subjobs using a split
ligand input file.
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SubjobState
This class provides read access to the contents of the state file
for a subjob, <jobname>_state.json.
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DriverState
This is a convenience wrapper to access values from the 'state' table of
GlideDB as properties of the DriverState object.
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GlideDB
This class encapsulates access to a database used for holding state
while a distributed docking job is running.
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SubjobGenerator
A SubjobGenerator is an iterable that yields DockingSubjob objects
given a DockingJob object and a GlideDB.
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JobRunner
This class provides an abstract interface for running a number of
DockingSubjob's.
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JobDJRunner
JobRunner subclass for running subjobs using JobDJ.
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JobarrayRunner
JobRunner subclass for running subjobs using SGE job arrays.
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LigWriter
Objects of this class can be used as context managers and as
file-like objects (with a .write() method) to write ligands while
abstracting away job-dependent aspects such as compression and file
headers.
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PoseWriter
This is a subclass of LigWriter that also knows how to write the
receptor structure at the beginning of a pv file.
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PlainTextWriter
This class can be used to write plain old files emulating the
interface of the StructureReader class (writing is done by calling
the .append() method).
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get_driver(input_filename,
options)
Return a driver object of the appropriate class given an input file
and command-line options. |
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| add_glide_options(parser) |
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format_cpu_time(time,
msg)
Return a human-readable CPU time message prefaced by 'msg'. |
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humantime(sec)
Given a time in seconds return a string describing the time in days,
hours, minutes, and seconds as necessary to make it
"human-readable". |
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show_progress(st_num,
last=False,
dot_freq=1000,
dots_per_line=50)
Write progress dot every dot_freq structures and a count at the end
of each line. |
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| auto_nstructs(nligs,
t_lig=30.0,
t_launch=10.0) |
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multi_count_structures(filenames)
Count the structures in multiple files of any format supported by
structure.py plus Phase subset. |
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| write_empty_file(filename) |
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| add_output_file(filename) |
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remove_output_file(filename,
leave_empty_file)
Remove a file that we would also like to be removed from the launch
directory. |
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resolve_paths(keywords)
Return a copy of a keywords dictionary in which all the values of
file-related keywords have been resolved to their runtime paths. |
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| get_structure_reader(filename,
reader_format) |
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| compress_structure(st,
as_sd=False) |
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| add_to_zip_if_exists(zipfh,
fname) |
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| unzip_to_dir(gridfile,
dirname) |
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write_readme(dirname)
Write a README file to a directory explaining the temporary nature of
said directory. |
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| check_cutoff(pose,
propname,
cutoff) |
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