schrodinger.application.glide.ligand_designer module¶

This module provides the APIs behind the Ligand Designer panel and workflow. It combines binding site Phase hypothesis generation with R-group enumeration and Glide grid generation and docking. The docking uses a Glide HTTP server for speed.

class schrodinger.application.glide.ligand_designer.State¶

Bases: enum.Enum

An enumeration.

NEW = 1¶

READY = 4¶

RUNNING_GRIDGEN = 2¶

STARTING_SERVER = 3¶

STOPPED = 5¶

class schrodinger.application.glide.ligand_designer.Pose(structure, source_lig, task_id)¶

Bases: tuple

__contains__¶: Return key in self.

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__len__¶: Return len(self).

count(value) → integer -- return number of occurrences of value¶

index(value[, start[, stop]]) → integer -- return first index of value.¶: Raises ValueError if the value is not present.

source_lig¶: Alias for field number 1

structure¶: Alias for field number 0

task_id¶: Alias for field number 2

schrodinger.application.glide.ligand_designer.get_rgroup_atoms_close_to_point(st, xyz, distance)¶

Returns True if any atoms from st are found within the threshold distance of a point, which is defined by its xyz coordinates. Only R-group atoms that don’t have special LD_CORE_ATOM_PROP set are considered.

Parameters:	st (structure.Structure) – structure object xyz (list[float]) – xyz coordinates of point distance (float) – Distance threshold
Returns:	True if atoms within distance are found and False otherwise
Return type:	bool

exception schrodinger.application.glide.ligand_designer.ServerTimedOutError¶

Bases: RuntimeError

Exception raised if the Glide server times out

__init__¶: Initialize self. See help(type(self)) for accurate signature.

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.glide.ligand_designer.Site¶

Bases: object

Base class for a generic “hypothesis site”. A site is defined by a point in space (.xyz property) and has a method to check whether a pose satisfies the desired interaction.

Subclasses must override the .xyz property.

xyz¶

Returns:	Cartesian coordinates of this site
Return type:	iterable(float, float, float)

isSatisfied(pose)¶

Check if a pose satisfies the interaction with the given site.

Return type:	bool

__init__¶: Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.glide.ligand_designer.PhaseSite(site)¶

Bases: schrodinger.application.glide.ligand_designer.Site

A site from a Phase hypothesis.

__init__(site)¶

Parameters:	site (schrodinger.infra.phase.PhpSite) – Phase site

xyz¶

Returns:	Cartesian coordinates of this site
Return type:	iterable(float, float, float)

isSatisfied(pose)¶

Check if the ligand pose has any Phase sites that are close enough and have the right type to satisfy the interaction with this PhaseSite.

Return type:	bool

class schrodinger.application.glide.ligand_designer.WatermapSite(atom, wmap_eid)¶

Bases: schrodinger.application.glide.ligand_designer.Site

A WaterMap site.

__init__(atom, wmap_eid)¶

Parameters:	atom (schrodinger.structure._StructureAtom) – WaterMap site atom wmap_eid (str or NoneType) – WaterMap entry ID, used to identify the structure to which this site belongs

atom¶

xyz¶

Returns:	Cartesian coordinates of this site
Return type:	iterable(float, float, float)

dg¶

Returns:	the WaterMap dG value, if available
Return type:	float or None

enthalpy¶

Returns:	the WaterMap enthalpy value, if available
Return type:	float or None

entropy¶

Returns:	the WaterMap entropy value, if available
Return type:	float or None

name¶

Returns:	the name of this WaterMap site
Return type:	str

wmap_eid¶

Returns:	the WaterMap entry ID
Return type:	str or NoneType

isSatisfied(pose)¶: True if any ligand atoms are within WMAP_DISPLACEMENT_CUTOFF of the WaterMap site.

class schrodinger.application.glide.ligand_designer.SphereSite(sphere_data)¶

Bases: schrodinger.application.glide.ligand_designer.Site

A site for a growth space sphere.

__init__(sphere_data)¶

Parameters:	sphere_data (namedtuple(float, float, float, float)) – The sphere’s x, y, z coordinates and radius

xyz¶

Returns:	Cartesian coordinates of this site
Return type:	iterable(float, float, float)

isSatisfied(pose)¶: True if any ligand atoms are within the sphere

class schrodinger.application.glide.ligand_designer.ReactionThread(mol, frozen_atoms, depth=2, max_routes=20, libpath=None, **kwargs)¶

Bases: PyQt5.QtCore.QThread

Thread to run reaction enumeration. All enumeration takes place in RDKit, which is thread-safe.

Variables:	MAX_PRODUCTS – Maximum number of products to enumerate. stop_requested – The calling code can set this to True to stop enumeration. productReady – Signal emitted with a new product.

MAX_PRODUCTS = 10000¶

productReady¶

__init__(mol, frozen_atoms, depth=2, max_routes=20, libpath=None, **kwargs)¶

All arguments will be passed to multiroute.generate_mols.

Parameters:	frozen_atoms (set of int) – frozen atom indices (1-based) depth (int or NoneType) – analysis depth (if None, increasing depths will be attempted until enough routes are found) max_routes (int) – maximum number of routes to sample libpath (list of str) – list of directories to prepend to the standard reagent library search path

setFilterObj(filter_obj)¶: Filter the products by the given filter object.

run()¶: Run reaction enumeration and emit a signal with each product.

HighPriority = 4¶

HighestPriority = 5¶

IdlePriority = 0¶

InheritPriority = 7¶

LowPriority = 2¶

LowestPriority = 1¶

NormalPriority = 3¶

class Priority¶

Bases: int

__init__ = <method-wrapper '__init__' of sip.enumtype object at 0x39caec8>¶

TimeCriticalPriority = 6¶

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

connectNotify(self, QMetaMethod)¶

currentThread() → QThread¶

currentThreadId() → sip.voidptr¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventDispatcher(self) → QAbstractEventDispatcher¶

eventFilter(self, QObject, QEvent) → bool¶

exec(self) → int¶

exec_(self) → int¶

exit(self, returnCode: int = 0)¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

finished¶: finished(self) [signal]

idealThreadCount() → int¶

inherits(self, str) → bool¶

installEventFilter(self, QObject)¶

isFinished(self) → bool¶

isInterruptionRequested(self) → bool¶

isRunning(self) → bool¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

loopLevel(self) → int¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

msleep(int)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

parent(self) → QObject¶

priority(self) → QThread.Priority¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

quit(self)¶

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

requestInterruption(self)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setEventDispatcher(self, QAbstractEventDispatcher)¶

setObjectName(self, str)¶

setParent(self, QObject)¶

setPriority(self, QThread.Priority)¶

setProperty(self, str, Any) → bool¶

setStackSize(self, int)¶

setTerminationEnabled(enabled: bool = True)¶

signalsBlocked(self) → bool¶

sleep(int)¶

stackSize(self) → int¶

start(self, priority: QThread.Priority = QThread.InheritPriority)¶

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

started¶: started(self) [signal]

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

terminate(self)¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = -1) → str¶

usleep(int)¶

wait(self, msecs: int = ULONG_MAX) → bool¶

yieldCurrentThread()¶

class schrodinger.application.glide.ligand_designer.FilterWrapper(filter_obj, descriptors=None)¶

Bases: object

A wrapper for schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter to filter an iterable of Structure while computing RDKit descriptors, modifying the structure in-place.

Variables:	structures_checked – How many structures were passed to `filterStructures`

__init__(filter_obj, descriptors=None)¶

Parameters:	filter_obj (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter) – Filter object to wrap descriptors (iterable of str) – names of descriptors to add to each structure, in addition to those that are required by the filters.

filterStructures(structures)¶

Generator which filters an iterable of structures, yielding those that pass, after adding descriptor properties to them. The input structures are modified.

Parameters:	structures (iterable of schrodinger.structure.Structure) – structures to filter
Return type:	generator of schrodinger.structure.Structure

class schrodinger.application.glide.ligand_designer.LigandDesignerTask(*args, **kwargs)¶

Bases: schrodinger.tasks.tasks.AbstractTask

A LigandDesignerTask stores a ligand, a receptor, and optionally a WaterMap, and provides methods for finding hypotheses and finding which bonds may be enumerated upon for a given hypothesis.

Variables:

GRIDGEN_RETRIES – Number of times to check whether gridgen is finished
input – Task input
output – Poses and statistics from enumeration task
filter_obj (filter_core.Filter) – object responsible for storing filter settings for the enumerated poses
posesDocked – Signal emitted when poses are docked
noPosesDocked – Signal emitted when a ligand produces no valid poses

input¶

Variables:

ligand_st (schrodinger.Structure.structure) – ligand structure
original_ligand_st (schrodinger.Structure.structure) – original ligand before enumerations
receptor_st (schrodinger.Structure.structure) – receptor structure
wmap_sts (list(schrodinger.Structure.structure)) – watermap structures
site (Site) – target site
leaving_atom_index – this atom and others reachable from it in the direction “away” from the core will be replaced by the R-group
staying_atom_index – The atom number of the core atom bonded to the leaving atom
bond_is_breakable – whether the bond between the staying atom and leaving atom is part of a known reaction
use_reaction – whether to use reaction-based enumeration if bond is breakable
r_groups (iterable of schrodinger.structure.Structure) – R-group library

output¶

Variables:	poses (list[Pose]) – List of poses resulting from enumeration job num_ligands – Number of ligands generated by R-group enumeration. ligands_matched – Number of ligands matched by the filter. num_poses – Number of poses returned from Glide.

posesDocked¶

noPosesDocked¶

GRIDGEN_RETRIES = 300¶

initConcrete(keywords=None, tmpdir=None, *args, **kwargs)¶

Parameters:	keywords – See `LigandDesigner` for documentation tmpdir – See `LigandDesigner` for documentation

filter_obj¶

backend¶

getHypo()¶: Compute and cache a ligand pharmacophore hypothesis based on the receptor’s binding site atoms

getHypoCt()¶

Get the Phase ligand hypothesis for the binding site as a Structure.

Return type:	schrodinger.Structure

getBindingSiteAtoms()¶

Returns:	Atom indices of the receptor that are close to the ligand
Return type:	list[int]

getWmapSites()¶: The WaterMap sites, as a dict by name, sorted by delta G.

getSite(site_name)¶: Return a Site by name. It may be a WatermapSite (conventinally named W1, W2, etc.) or a Phase hypothesis site (with names such as D1, D2 for donors; A1, A2 for acceptors; R1, R2 for aromatic rings; etc.).

getBonds(min_angle=90.0, bond_order=None)¶

Return a list of ligand bonds that could be broken to perform an R-group enumeration in an attempt to satisfy the interaction with a given site.

Parameters:	min_angle (float) – minimum angle, in degrees, between the site and the bond to be broken for R-group enumeration, with the leaving atom at the vertex bond_order (int or NoneType) – required bond order, or None to allow any bond order
Returns:	list of (staying_atom_index, leaving_atom_index) tuples
Return type:	list of (int, int)

resetPicks()¶: Reset user picks

dockBatchLigands(ligand_sts)¶

run()¶

Start the real run method by connecting it to the _backendReady signal and getting the backend ready.

Implementation of abstract method of tasks.AbstractTask.

cancel()¶

readyBackend()¶

Gets the backend ready without blocking the GUI

self._backend_checker.wait() blocks Python execution until the backend is ready or it times out. If the backend isn’t ready, causes the task to fail.

Returns:	Whether the backend is ready

AUTO_TASKDIR = <object object>¶

CMDLINE = 1¶

DEFAULT_TASKDIR_SETTING = None¶

DONE = 3¶

DataClass¶: alias of builtins.object

FAILED = 2¶

GUI = 2¶

INTERRUPT_ENABLED = False¶

RUNNING = 1¶

TEMP_TASKDIR = <object object>¶

WAITING = 0¶

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

addFuncToGroup(func, group=None, order=None)¶

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:	func – the function to add group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default. order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPreprocessor(func, order=-2000)¶

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:	func – the function to add order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)¶

blockSignals(self, bool) → bool¶

block_signal_propagation()¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

classmethod configureParam()¶: Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

classmethod defaultValue(*args, **kwargs)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

classmethod fromJson(json_obj)¶

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:	json_obj (dict) – A json-loaded dictionary to create an object from.
Returns:	An instance of this class.

:rtype : cls

classmethod fromJsonFilename(filename)¶

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

getAbstractParam(*args, **kwargs)¶

getAddedFuncs(group=None)¶

getFuncGroup(group=None)¶

Retrieve the functions belonging to the specified group.

Parameters:	group (FuncGroupMarker) – the group marker
Returns:	the functions in the specified group, in order
Return type:	list

classmethod getJsonBlacklist()¶

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE: Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)¶

classmethod getParamValue(*args, **kwargs)¶

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:	name (str) – The name of the subparam to get the value for.

classmethod getSubParams()¶: Return a dictionary mapping subparam names to their values.

getTaskDir()¶: Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)¶: Return the appropriate absolute path for an input or output file in the taskdir.

get_version()¶: Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()¶: Context manager that saves any Exception raised inside

inherits(self, str) → bool¶

initAbstract()¶

initializeValue()¶: @overrides: parameters.CompoundParam

inputChanged¶

inputReplaced¶

installEventFilter(self, QObject)¶

classmethod isAbstract()¶: Whether the param is an “abstract” param.

isDefault(*args, **kwargs)¶

isInterruptionRequested()¶

isRunning()¶

isSignalConnected(self, QMetaMethod) → bool¶

isStartable()¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

kill()¶

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)¶

max_progress¶

max_progressChanged¶

max_progressReplaced¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

name¶

nameChanged¶

nameReplaced¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

outputChanged¶

outputReplaced¶

classmethod owner()¶

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()¶

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()¶

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject¶

preprocessors()¶

Returns:	A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)¶

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:	chain (FuncChainDecorator) – which chain to process result_callback – the callback that will get called with the result of each function in the chain
Returns:	a list of the results from the functions

progress¶

progressChanged¶

progressReplaced¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

replicate()¶: Create a new task with the same input and settings (but no output)

requestInterruption()¶

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)¶

classmethod runFromCmdLine()¶

runPostprocessing(callback=None)¶

runPreprocessing(callback=None, calling_context=None)¶

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:

callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

classmethod setParamValue(*args, **kwargs)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

classmethod setReference(param1, param2)¶

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters:	param1 – The first abstract param to keep synced param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)¶

signalsBlocked(self) → bool¶

skip_eq_check()¶

specifyTaskDir(taskdir_spec)¶

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:	taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)¶

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters:	skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

status¶

statusChanged¶

statusReplaced¶

taskDirSetting()¶: Returns the taskdir spec. See specifyTaskDir() for details.

taskDone¶

taskFailed¶

taskStarted¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toDict(*args, **kwargs)¶

toJson(_mark_version=True)¶

Create and returns a data structure made up of jsonable items.

Return type:	An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)¶

tr(self, str, disambiguation: str = None, n: int = -1) → str¶

valueChanged¶

wait(timeout=None)¶

Block until the task is finished executing or timeout seconds have passed.

Parameters:	timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.glide.ligand_designer.NonBlockingBackendChecker(*args, **kwargs)¶

Bases: PyQt5.QtCore.QObject

Class to get a LigandDesigner object to the ready state without blocking the GUI.

Variables:	ready – Whether the backend is ready

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

wait(timeout=600)¶

Block python execution (but not the GUI) until the backend is ready or the timeout is reached.

Parameters:	timeout (int or NoneType) – Timeout in seconds or None to not timeout.
Returns:	Whether the backend is ready

setBackend(backend)¶

Set the backend object to call isReady on

stopChecking()¶: Stop checking whether the backend is ready

setTimedOut()¶

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

inherits(self, str) → bool¶

installEventFilter(self, QObject)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

parent(self) → QObject¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

signalsBlocked(self) → bool¶

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = -1) → str¶

class schrodinger.application.glide.ligand_designer.LigandDesigner(ligand_st, receptor_st, keywords=None, tmpdir=None)¶

Bases: PyQt5.QtCore.QObject

A LigandDesigner is set up with a ligand and a receptor. It provides methods for performing the enumeration job. This is an R-group enumeration on a single bond, followed by core-constrained Glide docking of each generated ligand and a filter to ensure that the poses satisfy the hypothesis.

A LigandDesigner keeps its state and intermediate files in a scratch directory. A unique subdirectory is created for each ligand-receptor complex; if another object is created for the same complex, it will share the same directory. This allows the reuse of existing grid files, for example. However, only one LigandDesigner at a time can be performing an enumeration because the underlying Glide server process is single-threaded.

The LigandDesigner implements a non-blocking workflow, so the caller needs to take action to drive it. This is done by calling the isReady() method until true. Example:

ld = LigandDesigner(lig, recep) while not ld.isReady():

time.sleep(1)

# now we are ready!

The idea is that the caller is free to do other stuff while waiting; for example, interacting with the user.

__init__(ligand_st, receptor_st, keywords=None, tmpdir=None)¶

Parameters:	ligand_st (schrodinger.Structure.structure) – ligand structure receptor_st (schrodinger.Structure.structure) – receptor structure keywords (dict) – docking keywords to use to override the defaults tmpdir (path-like object) – directory under which the job files will be written. Default is $SCHRODINGER_TMPDIR.

default_docking_keywords¶

state¶

start()¶: Start the ligand designer workflow.

stop()¶: Stop the ligand designer workflow.

isReady()¶

Return True if the LigandDesigner is ready to enumerate. This method has the side effect of taking steps to advance towards the READY state.

Returns:	server is ready?
Return type:	bool

startDockLigands(ligands)¶

Start asynchronous docking. If there was a problem with the server, the method will raise an exception.

Parameters:	ligands (collections.Iterable(structure.Structure)) – Ligand structures to dock
Raises:	RuntimeError – If called when `self.state` is not READY socket.error – If the server encounters an error

addDockingStructures(structures)¶

setDoneAddingStructures()¶

cancelEnumeration()¶

getRgroupEnumerator(site, atom, rgroups)¶

Get structures produced by R-group enumeration

Parameters:	site (Site) – target site atom (int) – leaving atom index (this atom and others reachable from it in the direction “away” from the core will be replaced by the R-group). rgroups (iterable of schrodinger.structure.Structure) – R-group library
Returns:	Structures produced by R-group enumeration
Return type:	collections.Iterable(structure.Structure)

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

inherits(self, str) → bool¶

installEventFilter(self, QObject)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

parent(self) → QObject¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

signalsBlocked(self) → bool¶

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = -1) → str¶

class schrodinger.application.glide.ligand_designer.GridgenJob(receptor_st, ligand_st, jobdir)¶

Bases: object

__init__(receptor_st, ligand_st, jobdir)¶

Parameters:	ligand_st (schrodinger.Structure.structure) – ligand structure receptor_st (schrodinger.Structure.structure) – receptor structure jobdir (path-like object) – job directory

writeInputs()¶: Write the input files.

launch()¶: Launch the gridgen job.

isDone()¶: Return true if the gridgen job is done. This is based in the existence of the grid file and, if available, the job record.

schrodinger.application.glide.ligand_designer.read_json_file(filename)¶

Read a JSON file. If there are issues reading it (doesn’t exist, syntax errors…) quietly return an empty dict.

Return type:	object

schrodinger.application.glide.ligand_designer.md5sum(input_str)¶

MD5 hex digest of a string.

Return type:	str

schrodinger.application.glide.ligand_designer.get_structure_digest(st, length=8)¶

Return an abbreviated MD5 hex digest given a Structure, after stripping out the structure-level properties.

Parameters:	st (schrodinger.structure.Structure) – input structure (not modified) length (int) – digest length in hex digits
Returns:	hex digest
Return type:	str

schrodinger.application.glide.ligand_designer.get_binding_site_atoms(receptor_st, ligand_st)¶

schrodinger.application.glide.ligand_designer.add_rdkit_descriptors(st, property_names)¶

Add RDKit descriptors to the maestro structure

Parameters:	property_names (list[str]) – Maestro properties corresponding to RDKit descriptors

schrodinger.application.glide.ligand_designer.filter_r_groups(st, staying_atom_idx, leaving_atom_idx, r_groups)¶

Given a structure and a bond to break, return only R-groups that are anticipated to be chemically compatible.

Returns:	R groups compatible with the given bond
Return type:	collections.Iterable[schrodinger.structure.Structure]

schrodinger.application.glide.ligand_designer.get_small_libpath()¶

Return the small reagent library search path.

Return type:	list[str]

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