schrodinger.infra.mmim module

Wrapper classes and functions for dealing with the MMIM library, which is used to read & write Impact and QSite input files.

See MMIMDict documentation for more details.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.infra.mmim.convert_string(key, value)

Given a key (as integer or string) and a value (string), try to convert the value to the proper type for this keyword. Return converted value. Will raise a KeyError if the wrong key value is specified.

NOTE: Used by glide.py

class schrodinger.infra.mmim.MMIMArgList(handle, key, converter=None, getter=None, setter=None, get_len=None, set_len=None)

Bases: schrodinger.infra.mmkv.MMKVArgList

__init__(handle, key, converter=None, getter=None, setter=None, get_len=None, set_len=None)

Create an instance from the MMKV/MMIM handle and key (int or string).

Takes functions to get and set indexed values, and a function to determine the length. If these are not provided, they are looked up based on the key provided.

get_len and set_len methods should be defined for array types only.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.mmim', '__init__': <function MMIMArgList.__init__>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(index)

__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.

__iter__()

__le__

Return self<=value.

__len__()

__lt__

Return self<value.

__module__ = 'schrodinger.infra.mmim'

__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).

__setitem__(index, 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)

append(value)

Append a new value to the current MMKV arglist.

Parameters:value (str, int, bool, or float depending on the MMKV arglist type) – The new value to append.

setSize(size)

Set the size of the MMKV argument list.

class schrodinger.infra.mmim.MMIMDict(handle)

Bases: collections.abc.MutableMapping

A class for setting and getting MMIM keyword values. Given an MMIM handle, create an instance as follows:

mydict = MMIMDict(mmim_handle)

Then set any keywords:

mydict[<keywordname>] = <value>

__init__(handle)

Create an instance from the given MMIM handle.

__getitem__(key)

Return the value stored in the MMIM handle for the given key (integer or string). Note that if no explicit setting has been made for a keyword that the default value will be returned.

__setitem__(key, value)

Set the value for the provided key (integer or string) to <value>. If the key type is an MMIM arglist (array), then the value provided must be an list with elements of the proper type.

__delitem__(key)

keys() → a set-like object providing a view on D's keys

__len__()

__iter__()

__abstractmethods__ = frozenset()

__class__

alias of abc.ABCMeta

__contains__(key)

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.infra.mmim', '__doc__': '\n A class for setting and getting MMIM keyword values.\n Given an MMIM handle, create an instance as follows:\n\n mydict = MMIMDict(mmim_handle)\n\n Then set any keywords:\n\n mydict[<keywordname>] = <value>\n\n ', '_NOT_IMPLEMENTED_MSG': 'mmim cannot report known keys.', '__init__': <function MMIMDict.__init__>, '__getitem__': <function MMIMDict.__getitem__>, '__setitem__': <function MMIMDict.__setitem__>, '__delitem__': <function MMIMDict.__delitem__>, 'keys': <function MMIMDict.keys>, '_get_handlers_for_key': <function MMIMDict._get_handlers_for_key>, '__len__': <function MMIMDict.__len__>, '__iter__': <function MMIMDict.__iter__>, '__dict__': <attribute '__dict__' of 'MMIMDict' objects>, '__weakref__': <attribute '__weakref__' of 'MMIMDict' objects>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})

__dir__() → list

default dir() implementation

__eq__(other)

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__ = None

__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.infra.mmim'

__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).

__reversed__ = None

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()

__str__

Return str(self).

classmethod __subclasshook__(C)

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)

clear() → None. Remove all items from D.

get(k[, d]) → D[k] if k in D, else d. d defaults to None.

items() → a set-like object providing a view on D's items

pop(k[, d]) → v, remove specified key and return the corresponding value.

If key is not found, d is returned if given, otherwise KeyError is raised.

popitem() → (k, v), remove and return some (key, value) pair

as a 2-tuple; but raise KeyError if D is empty.

setdefault(k[, d]) → D.get(k,d), also set D[k]=d if k not in D

update([E, ]**F) → None. Update D from mapping/iterable E and F.

If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v

values() → an object providing a view on D's values