schrodinger.application.phase.packages.phase_utils module

Module with common functionality for all Phase backends.

Copyright Schrodinger LLC, All Rights Reserved.

class schrodinger.application.phase.packages.phase_utils.RestrictedRange(lower_limit, upper_limit, lower_inclusive=True, upper_inclusive=True)

Bases: object

Provides generalized range checking suitable for the add_argument function of argparser.ArgumentParser. For example:

parser = argparse.ArgumentParser() parser.add_argument(“-dihed”, type=float, metavar=”<degrees>”,

choices=[RestrictedRange(-180.0, 180.0)], help=”Dihedral angle in degrees.”)
parser.add_argument(“-path”, type=int, metavar=”<length>”,
choices=[RestrictedRange(1, None)], help=”Non-zero path length in bonds.”)

More general usage is as follows:

legal_range = RestrictedRange(-180.0, 180.0) dihed = 120.0 if dihed in legal_range:

print(“Dihedral is legal”)
schrodinger.application.phase.packages.phase_utils.combine_log_files(subjobs, logger)

Concatenates the contents of subjob log files.

Parameters:
  • subjobs (list(str)) – Subjob names
  • logger (Logger) – Logger to which concatenated log files are to be written
schrodinger.application.phase.packages.phase_utils.convert_to_sd(maefile, sdfile)

Converts a Maestro file to a compressed SD file. Fails only if maefile is missing or defective.

Parameters:
  • maefile (str) – Maestro file to be converted
  • sdfile – Output SD file, which is assuemd to be compressed
  • sdfile – str
schrodinger.application.phase.packages.phase_utils.get_file_names_from_list_file(list_file)

Returns the names of the files in the provided list file, taking proper account of whether the current process is running under job control and whether any of the files are Phase databases.

Parameters:list_file – Name of the .list file
Returns:Names of files in the .list file
Return type:list(str)
schrodinger.application.phase.packages.phase_utils.get_jobname(args, filename=None)

Returns a job name derived in the following order of precedence:

  1. args.subjob if defined
  2. SCHRODINGER_JOBNAME if defined
  3. jobcontrol.get_backend().getJob().name if defined
  4. The basename of filename. Must be supplied if other methods fail.
Parameters:
  • args (argparse.Namespace) – Command line arguments
  • filename (str) – Name of file to use as a last resort job name
Returns:

job name
Return type:

str
schrodinger.application.phase.packages.phase_utils.get_internal_zip_path(*argv)

Joins the components of a path within a Zip file using forward slashes, as per the Zip spec.

Parameters:argv (tuple of str) – Components in path
Returns:Components in path joined with forward slashes
Return type:str
schrodinger.application.phase.packages.phase_utils.get_proper_path(file_path, use_runtime=False)

Returns the appropriate path to use for the provided file, taking into account whether the current process is running under job control and whether file_path is a Phase database.

Parameters:
  • file_path (str) – File whose proper path is being sought
  • use_runtime (bool) – Forces use of runtime path even if not running as job
Returns:

The proper path to use for the provided file
Return type:

str
schrodinger.application.phase.packages.phase_utils.get_subjob_names(num_subjobs, prefix)

Returns a list of subjobs names of the form <prefix>_sub_<n>, where <n> runs from 1 to num_subjobs.

Parameters:
  • num_subjobs (int) – Number of subjobs
  • prefix (str) – Prefix for all subjob names
Returns:

Subjob names
Return type:

list(str)
schrodinger.application.phase.packages.phase_utils.is_numeric(value)

Returns True if the provided string value can be cast to a float.

Parameters:value (str) – The string to be tested
Returns:Whether value is numeric
Return type:bool
schrodinger.application.phase.packages.phase_utils.is_phase_database_path(source)

Returns whether the provided source of structures is a Phase database.

Parameters:source (str) – Path to source of structures
Returns:whether the source is a Phase database
Return type:bool
schrodinger.application.phase.packages.phase_utils.is_phase_project_path(file_path, zipped=False)

Returns True if the file_ path corresponds to a Phase project. Set zipped to True to check for a zipped project.

Parameters:
  • file_path – Path to file
  • file_path – str
Returns:

Whether file_path is a Phase project (or zipped project)
Return type:

bool
schrodinger.application.phase.packages.phase_utils.read_lines_in_file(file_name)

Reads and returns the non-empty lines in a file.

Parameters:file_name (str) – The file to read
Returns:The lines in the file, minus any leading/trailing whitespace
Return type:list(str)
schrodinger.application.phase.packages.phase_utils.write_list_to_file(file_name, list_of_strings)

Writes a list of strings to a file with newlines after each string.

Parameters:
  • file_name (str) – Name of file to which the strings should be written
  • list_of_strings – The list of strings to write
schrodinger.application.phase.packages.phase_utils.write_string_to_file(file_name, s)

Writes a string to a file with a trailing newline.

Parameters:
  • file_name (str) – Name of file to which the string should be written
  • s (str) – The string to write