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)

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

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 a pose satisfies the interaction with the given site.

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:
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
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.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(keywords=None, tmpdir=None, *args, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

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
  • DOCK_WAIT – Time in seconds to wait for runBlocking to finish docking
  • input (_LigandDesignerInput) – Task input
  • output (list[Pose]) – List of poses resulting from enumeration job
  • enumeration_errors (list[Exception]) – List of errors resulting from enumeration job
  • filter_obj (filter_core.Filter) – object responsible for storing filter settings for the enumerated poses
  • backendReady – Signal emitted when backend becomes ready
  • serverTimedOut – Signal emitted when server is not ready after GRIDGEN_RETRIES
  • enumerationFinished – Signal emitted when an enumeration job finishes. Emitted with the number of enumerated ligands, ligands matching the filter, poses docked, and poses satisfied.
input
Variables:
  • ligand_st (schrodinger.Structure.structure) – ligand structure
  • 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
  • r_groups (iterable of schrodinger.structure.Structure) – R-group library
output

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

enumeration_errors

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

backendReady
serverTimedOut
jobStarted
posesDocked
enumerationFinished
GRIDGEN_RETRIES = 600
DOCK_WAIT = 60
__init__(keywords=None, tmpdir=None, *args, **kwargs)
Parameters:
filter_obj
backend
hypo
getHypoCt()

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

Return type:schrodinger.Structure
getCurrentInteractions(start=None)
Parameters:start (int or NoneType) – Starting index to renumber sites or None to not renumber
Returns:receptor sites from PhpComplex
Return type:list[phase.PhpSite]
getPotentialInteractions(start=None)
Parameters:start (int or NoneType) – Starting index to renumber sites or None to not renumber
Returns:receptor sites from PhpDeNovoPharm
Return type:list[phase.PhpSite]
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)

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
Returns:list of (staying_atom_index, leaving_atom_index) tuples
Return type:list of (int, int)
run()

If inputs are valid, run the job. This method should be used when running from a GUI.

Raises:RuntimeError – if the job cannot run
runBlocking()

If inputs are valid, run the job and block until finished. This method should be used when running from a script.

Raises:RuntimeError – if the job cannot run
DataClass

alias of builtins.object

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
enumeration_errorsChanged
enumeration_errorsReplaced
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 fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

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.

inherits(self, str) → bool
initAbstract()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

Override this method to define logic specfically for initializing concrete instances of this param. This will generally only run for compound params, as atomic params are not typically instantiated outside of class declaration.

inputChanged
inputReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

outputChanged
outputReplaced
owner()

Returns the owner of this param. Works for both concrete and abstract params. Returns None if the param has no owner. Follows the same rules as ownerChain.

ownerChain()

Returns the owner chain for this param. This works for concrete params and abstract params. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, bar, atom.coord, x] where Foo is a class and all other items are abstract params.

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)
reset(*args)

Resets this compound param to its default value. If no arguments are passed in, the entire param is reset. Any number of abstract params may be optionally passed in to perform a partial reset to default value of specified sub-params. For example, given a compound param with two xyz coordinates as endpoints:

class Line(CompoundParam):
start = Coord(x=1, y=2, z=3) end = Coord(x=4, y=5, z=6)

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

Set the value of this compound param instance. This mutates the compound param to be equal to value; it does not make the compound param /identical/ to value.

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
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()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
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
startEnumeration(site, atom, rgroups, filter_wrapper=None)

Start asynchronous enumeration. If there was a problem with the server, the method will return (not raise!) an exception.

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
  • filter_wrapper (FilterWrapper) – optional filter to apply to the enumeration output
Return type:

Exception or NoneType
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
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:
Returns:

hex digest
Return type:

str