schrodinger.glide module

This module provides Python wrappers to the Glide backend C++ library, as well as some helper functions to make use of the library more Pythonic.

schrodinger.glide.LoggerContext(levels: Optional[Dict[str, int]] = None, capture: Optional[bool] = None, main_level: Optional[int] = None, default_main_level: Optional[int] = None) → ContextManager

Context manager to set default logging levels and capturing for a given scope. Returns the new LoggerConfig, which can be used for further configuration or to fetch the captured messages.

Parameters:

• levels – dict of {name: level} to set the logging level for specific loggers. If a name has a “+” suffix, the setting will be recursive (apply to the logger’s children).

• capture – If True, enable capture; if False, disable capture; if None, keep the current capture setting.

• main_level – change the main logging level, with applies to functions that are not covered by any of the keys in levels.

• default_main_level – change the default for the main level, but only if the global default level is not already set, for example by the SCHRODINGER_GLIDE_LOG environment variable or by an enclosing LoggerContext.

Yield:

LoggerConfig

schrodinger.glide.DockingLicense(config=None)

Context manager to check out a docking license, and checking it in on exit. :raise schrodinger.infra.licensing.LicenseCheckoutError: can’t check out

schrodinger.glide.GridgenLicense()

Context manager to check in a docking license, and checking it in on exit. :raise schrodinger.infra.licensing.LicenseCheckoutError: can’t check out

exception schrodinger.glide.InputError

Bases: ValueError

An input file or configuration setting is invalid and the job cannot proceed.

class schrodinger.glide.HBondType

Bases: Enum

NEUTRAL_NEUTRAL = 0

NEUTRAL_CHARGED = 1

CHARGED_CHARGED = 2

class schrodinger.glide.OutOfBoxTreatment

Bases: Enum

strict = 0

restrain = 1

class schrodinger.glide.RotType

Bases: Enum

CORE = 0

PERIPHERAL = 1

class schrodinger.glide.SkipReason

Bases: Enum

ATOMIC_NUMBER = 0

ATOM_OVERLAP = 1

BAD_ATOM = 2

CONFGEN = 3

EMPTY_MCS = 4

FORCE_FIELD = 5

LIGAND_DATA = 6

LIGAND_SIZE = 7

MINIMIZATION = 8

NO_ATOMS = 9

NO_GOOD_POSES = 10

NO_MATCH = 11

NO_POSES_STORED = 12

PHASE_DB = 13

PULL = 14

REFINE = 15

ROTBONDS = 16

ROUGH_SCORE = 17

EXCEPTION = 18

class schrodinger.glide.MinimizerStatus

Bases: Enum

OK = 0

OutOfBox = 1

Exception = 2

class schrodinger.glide.Ptype

Bases: Enum

DSC_PHOBHYD = 0

DSC_PHOBHVY = 1

DSC_DONOR = 2

DSC_ACCEP = 3

DSC_POLAR = 4

DSC_METAL = 5

DSC_MAX_BASE = 5

DSC_HALO_DONOR = 12

DSC_HALO_ACCEP = 13

DSC_DEFAULT = 0

class schrodinger.glide.Hybridization

Bases: Enum

FreeAtom = 0

sp1 = 1

sp2 = 2

sp3 = 3

exception schrodinger.glide.SkipLigand(reason, message)

Bases: Exception

Exception class for errors that mean that we cannot proceed with the current ligand, but are otherwise nonfatal. The expectation is that they will be caught and handled by the main ligand loop.

Variables:

• message – specific error message

• reason – general reason for skipping the ligand, as one of the members of the SkipReason enum (e.g., SkipReason.CONFGEN)

__init__(reason, message)

reason: SkipReason

message: str

toJSON()

classmethod fromJSON(json_str: str) → SkipLigand

schrodinger.glide.get_unsupported_features(glide_job)

Check if the job is using any keyword not supported by Skate. (Developer keywords are ignored.)

Returns:

list of unsupported keyword names used by the job

Return type:

List(str)

class schrodinger.glide.Config(glide_job=None)

Bases: object

Glide job configuration; holds the values of all the keywords from the Glide input file (.in), and default values for unspecified keywords.

This class has a generic get() method that works for all types, but only for official keywords. For unofficial keywords, use the type-specific methods inherited from the parent class (getInt, getDouble, getString, getBool, getIntArray, getDoubleArray, getStringArray, getBoolArray), which also take an optional default value as a second argument (use of the second argument is strongly encouraged unless you can be certain that the keyword will be present in the input config).

__init__(glide_job=None)

Parameters:

glide_job (Union[schrodinger.application.glide.glide.GlideJob, dict,str,None]) – SIF input filename, keyword dict, GlideJob object, or None, where None means use default settings for docking.

Raises:

ValueError – job uses unsupported features

get(keyword: str)

Return the value of an official keyword (i.e., one listed in mmim_keywords.yaml).

Parameters:

keyword – keyword name

Return type:

Union[int, float, str, bool, list]

Throw:

KeyError if keyword is unknown. Note that this is unlike dict.get!

getUpdated(additional_keywords: dict)

Return a new Config object with the keywords updated according to the input dictionary. Note that this method does not validate the input keywords for potential keyword conflicts or unsupported features.

Parameters:

additional_keywords (Dict[str, Union[int, float, str, bool, list]]) – dictionary of keyword-value pairs

Return type:

Config

getInt(*args)

getBool(*args)

getDouble(*args)

getString(*args)

getIntArray(*args)

getBoolArray(*args)

getDoubleArray(*args)

getStringArray(*args)

getType(keyword)