schrodinger.application.phase.packages.phase_utils module¶

Module with common functionality for all Phase backends.

exception schrodinger.application.phase.packages.phase_utils.MissingInputFileError¶

Bases: Exception

Used when an input file for a job is missing.

class schrodinger.application.phase.packages.phase_utils.RequireValue(option_strings, dest, nargs=None, const=None, **kwargs)¶

Bases: argparse.Action

For arguments of the form -flag <value>, this class stores <value> at the appropriate destination, while prohibiting <value> from being an empty or pure whitespace string. This class may be used as follows for a string-valued argument:

parser.add_argument(‘-out’, action=RequireValue, help=’Output File.’)

It may also be used for positional arguments, numeric arguments, and arguments with choices. However, in the case of numeric arguments, an empty/whitespace value will be rejected before reaching this class since such a value is not numeric. If choices are supplied, an empty/whitespace value will reach this class and be rejected only if that value is one of the allowed choices, in which case this class isn’t appropriate.

__init__(option_strings, dest, nargs=None, const=None, **kwargs)¶

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")

__init__(lower_limit, upper_limit, lower_inclusive=True, upper_inclusive=True)¶

Constructor taking lower and upper limits and whether those limits are inclusive. Use None for a limit that doesn’t exist.

Parameters

lower_limit (Any numeric type or None) – Lower limit of legal range
upper_limit (Any numeric type or None) – Upper limit of legal range
lower_inclusive (bool) – True if lower limit is inclusive
upper_inclusive (bool) – True if upper limit is inclusive

__contains__(value)¶: The “in” operator for the provided value.

exception schrodinger.application.phase.packages.phase_utils.ValidationError¶

Bases: Exception

Used to simplify error passing in argument validation code.

schrodinger.application.phase.packages.phase_utils.calculate_njobs() → int¶: Derives the number of subjobs from the original host list. Behaves like jobcontrol.calculate_njobs(), except that it returns 1, instead of the maximum possible number of processors, when submitting a job to a cluster queue without specifying the number of CPUs, e.g., -HOST boltcpu_short.

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_default_feature_definitions()¶

Reads and returns the default Phase feature definitions.

Returns: Default Phase feature definitions.
Return type: list(phase.PhpFeatureDefinition)

schrodinger.application.phase.packages.phase_utils.get_file_names_from_list_file(list_file, prefer_cwd=False)¶

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
prefer_cwd (bool) – Use file in CWD if it exists, even if the file also exists in the location specified in list_file

Returns

Names of files in the .list file

Return type

list(str)

schrodinger.application.phase.packages.phase_utils.get_glide_sort_path() → str¶: Returns the path to the glide_sort utility.

schrodinger.application.phase.packages.phase_utils.get_host_args(default_host_args='localhost:1')¶: Returns the host specification (e.g., ‘terminator:2’) found in the environment or in the backend job. Returns default_host_args if there was no host specification supplied on the original command line. May be used regardless of whether the job has been launched.

schrodinger.application.phase.packages.phase_utils.get_jobname(args, filename)¶

Returns the job name from subjob if defined, otherwise via jobcontrol.

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.get_subset_name(subset)¶

Strips the subset file extension from subset if found and returns the result.

Parameters

subset – Subset or subset file name
subset – str

Returns

Proper subset name

Return type

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.make_display_command(command)¶

Converts a command provided as a list of strings to a space-delimited string, with quotes around arguments that contain embedded spaces.

Parameters: command (list[str]) – Command to display
Returns: Space-delimited command
Return type: str

schrodinger.application.phase.packages.phase_utils.must_register_input_file(infile, nocopy=False)¶

Determines whether infile needs to be registered as a job control input file. Returns False if nocopy is True or if infile is an absolute file path that doesn’t exist locally. In the latter case, it’s assumed that infile will exist on the remote host, or that the remote backend will handle the error. Returns True if none of the previous conditions applies.

Parameters

infile (str) – Input file to test
nocopy (bool) – If True, function returns False unconditionally

Returns

Whether infile should be registered as an input file

Return type

bool

schrodinger.application.phase.packages.phase_utils.partition_values(num_values, num_bins)¶

Partitions num_values as equally as possible over num_bins and returns the population of each bin. For example, if num_values is 1007 and num_bins is 5, this function would return [201, 202, 201, 202, 201].

Parameters

num_values (int) – The number of values to be partitioned
num_bins (int) – The number of bins over which to divide num_values

Returns

The population of each bin

Return type

list[int]

Raises

ValueError if an illegal combination num_values and num_bins is provided

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.set_jsb_input_file(jsb, infile_path, want_exit=False)¶

Wrapper for JobSpecificationArgsBuilder.setInputFile which may be used to avoid the traceback that occurs when an input file is missing. Instead, the RuntimeError raised in that specific case is trapped and a MissingInputFileError is raised, or sys.exit is called with the error message. Any other exceptions are passed through unmodified.

Parameters

jsb (launchapi.JobSpecificationArgsBuilder) – JobSpecification builder
infile_path (str) – Input file path

Want_exit

Whether to call sys.exit with the error message

Raises

MissingInputFileError if the input file is missing and want_exit is False

schrodinger.application.phase.packages.phase_utils.split_string(s, delimiter=',')¶

Uses the csv module to split a delimited string that may contain occurrences of the delimiter protected by quotes.

Parameters

s (str) – The delimited string to split
delimiter (str) – The delimiter on which to split

Returns

Tokens resulting from the split

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