schrodinger.structutils.markush_enumerate module

Support for “R-group” enumeration as in ENUM-108.

class schrodinger.structutils.markush_enumerate.PlaceHolder(group_id, atom, bonds)

Bases: tuple

__add__

Return self+value.

__class__

alias of builtins.type

__contains__

Return key in self.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__

Return self[key].

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__

Implement iter(self).

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.structutils.markush_enumerate'
__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, group_id, atom, bonds)

Create new instance of PlaceHolder(group_id, atom, bonds)

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return a nicely formatted representation string

__rmul__

Return self*value.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

atom

Alias for field number 1

bonds

Alias for field number 2

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

Alias for field number 0

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

schrodinger.structutils.markush_enumerate.get_placeholders(st, groups=None)

Gathers placeholders metadata.

Parameters:
  • st (schrodinger.structure.Structure) – Structure.
  • groups – Dictionary that maps placeholder atom indices onto their group IDs. If None, regard atoms that carry the “GROUP_ID_PROP” property as “placeholders”.
Returns:

List of the placeholders records.
Return type:

list(PlaceHolder)
Raises:

ValueError if something about st looks not right.
schrodinger.structutils.markush_enumerate.get_attachment_points(st)

Returns ordered list of attachment points in st. The order is either based upon atom labels (“ATTACHMENT_PROP”, if available) or decided by the bond order and the peer atom atomic number.

Returns:List of atoms.
Return type:list(int)
class schrodinger.structutils.markush_enumerate.Scaffold(st, groups=None)

Bases: object

Holds reference to the “scaffold” structure. Knows how to join R-groups to the core.

__init__(st, groups=None)
Parameters:groups (dict(int, int) or None) – Dictionary that maps atom indices onto “group IDs”. If None, use “GROUP_ID_PROP” to identify the “placeholder” atoms.
fragmentIDs

Returns set of fragment IDs.

populate(fragments)

Replaces placeholders with fragments.

Parameters:fragments (dict(int, schrodinger.structure.Structure)) – Indexable that maps fragment IDs onto structures.
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.markush_enumerate', '__doc__': '\n Holds reference to the "scaffold" structure. Knows how to join\n R-groups to the core.\n ', '__init__': <function Scaffold.__init__>, 'fragmentIDs': <property object>, 'populate': <function Scaffold.populate>, '__dict__': <attribute '__dict__' of 'Scaffold' objects>, '__weakref__': <attribute '__weakref__' of 'Scaffold' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.structutils.markush_enumerate'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.structutils.markush_enumerate.validate_fragment(st)
Parameters:st (schrodinger.structure.Structure) – Structure.
Raises:ValueError if there is no attachment points.
schrodinger.structutils.markush_enumerate.validate_scaffold(st)
Parameters:st (schrodinger.structure.Structure) – Structure.
Raises:ValueError if there is no placeholders.
schrodinger.structutils.markush_enumerate.convert_fragment_from_v3000(st)

Converts fragment metadata from MDL V3000 conventions to the ones expected by this module.

Parameters:st (schrodinger.structure.Structure) – Structure.
Raises:ValueError if something goes wrong.
schrodinger.structutils.markush_enumerate.convert_scaffold_from_v3000(st)

Converts scaffold metadata from MDL V3000 conventions to the ones expected by this module.

Parameters:st (schrodinger.structure.Structure) – Structure.
class schrodinger.structutils.markush_enumerate.FragmentReader(filename, logger=None)

Bases: object

Reads structures from file, skips “invalid” (in context of ENUM-108) fragments.

__init__(filename, logger=None)

Initialize self. See help(type(self)) for accurate signature.

__iter__()
__next__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.markush_enumerate', '__doc__': '\n Reads structures from file, skips "invalid"\n (in context of ENUM-108) fragments.\n ', '__init__': <function FragmentReader.__init__>, '__iter__': <function FragmentReader.__iter__>, '__next__': <function FragmentReader.__next__>, '__dict__': <attribute '__dict__' of 'FragmentReader' objects>, '__weakref__': <attribute '__weakref__' of 'FragmentReader' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.structutils.markush_enumerate'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.structutils.markush_enumerate.read_scaffold(filename)

Reads scaffold from file.

Parameters:filename (str) – File name.
Returns:Scaffold instance.
Return type:Scaffold
Raises:ValueError on errors.
class schrodinger.structutils.markush_enumerate.FragmentsIterator(sources, random=None)

Bases: object

Iterator over Cartesian product of fragment collections.

__init__(sources, random=None)
Parameters:
  • sources (list of list) – List of [iterable over fragments, id1, id2, …] lists (see r_group_enumerate.parse_rgroups).
  • random (None or int) – If None, enumerate sequentially. If integer, enumerate randomly using random as a seed.
__iter__()
__next__()
Returns:Dictionary that maps fragment IDs onto structures.
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.markush_enumerate', '__doc__': '\n Iterator over Cartesian product of fragment collections.\n ', '__init__': <function FragmentsIterator.__init__>, '__iter__': <function FragmentsIterator.__iter__>, '__next__': <function FragmentsIterator.__next__>, '__dict__': <attribute '__dict__' of 'FragmentsIterator' objects>, '__weakref__': <attribute '__weakref__' of 'FragmentsIterator' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.structutils.markush_enumerate'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.structutils.markush_enumerate.VirtualLibrary(scaffold, sources, random=None, logger=None)

Bases: object

Implements common intended use case logic.

__init__(scaffold, sources, random=None, logger=None)
Parameters:
  • scaffold (Scaffold) – Scaffold.
  • sources (list of list) – List of [iterable over fragments, id1, id2, …] lists (see r_group_enumerate.parse_rgroups). Or list of [filename, id1, id2, …] lists.
  • random (None or int) – If None, enumerate sequentially. If integer, enumerate randomly using random as a seed.
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.markush_enumerate', '__doc__': '\n Implements common intended use case logic.\n ', '__init__': <function VirtualLibrary.__init__>, '__iter__': <function VirtualLibrary.__iter__>, '__next__': <function VirtualLibrary.__next__>, '__dict__': <attribute '__dict__' of 'VirtualLibrary' objects>, '__weakref__': <attribute '__weakref__' of 'VirtualLibrary' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.structutils.markush_enumerate'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__iter__()
__next__()