iQdZddlmZmZddlmZddlZddlZddl m Z ddl Z ej dZ Gdd eZGd d e Zdd ZdS)a8 Base guesser classes --- :mod:`MDAnalysis.guesser.base` ================================================================ Derive context-specific guesser classes from the base class in this module. Classes ------- .. autoclass:: GuesserBase :members: :inherited-members: .. autofunction:: get_guesser ) _GUESSERS_TOPOLOGY_ATTRS) _ConnectionN)DictzMDAnalysis.guesser.baseceZdZdZdZdS) _GuesserMetaaInternal: guesser classes registration When classes which inherit from GuesserBase are *defined* this metaclass makes it known to MDAnalysis. 'context' attribute are read: - `context` defines the context of the guesser class for example: forcefield specific context as MartiniGuesser and file specific context as PDBGuesser. Eg:: class FooGuesser(GuesserBase): format = 'foo' .. versionadded:: 2.8.0 ctt||||t|d<dS)Ncontext)type__init__rupper)clsnamebases classdicts a/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/guesser/base.pyr z_GuesserMeta.__init__Cs; dD%33325 )I&,,..///N)__name__ __module__ __qualname____doc__r rrr r 1s-"66666rr cHeZdZUdZdZiZeed<d dZdZ dZ dZ d d Z dS) GuesserBaseaABase class for context-specific guessers to inherit from Parameters ---------- universe : Universe, optional Supply a Universe to the Guesser. This then becomes the source of atom attributes to be used in guessing processes. (this is relevant to how the universe's guess_TopologyAttrs API works. See :meth:`~MDAnalysis.core.universe.Universe.guess_TopologyAttrs`). **kwargs : dict, optional To pass additional data to the guesser that can be used with different methods. .. versionadded:: 2.8.0 base_guesser_methodsNc "||_||_dSN) _universe_kwargs)selfuniversekwargss rr zGuesserBase.__init___s! rc :|j|dSr)r!update)r"r$s r update_kwargszGuesserBase.update_kwargscs F#####rcVtj|j}|jdddi|}|S)zReturn a copy of this Guesserr#Nr)copydeepcopyr! __class__)r"r$news rr)zGuesserBase.copyfs4t|,,dn55d5f55 rc@||jvrdSdS)zcheck if the passed atrribute can be guessed by the guesser class Parameters ---------- guess: str Attribute to be guessed then added to the Universe Returns ------- bool TF)lowerr)r" attr_to_guesss r is_guessablezGuesserBase.is_guessablels(    D$9 9 94urFc t|}n #t$rt|dwxYw|j} |j|}n4#t$r't t |jd|wxYwt|tr |St|j j |r||sztj t|j j |d}||}d|vr||||<|St d|d|ddStj |S) amap the attribute to be guessed with the apporpiate guessing method Parameters ---------- attr_to_guess: str an atrribute to be guessed then to be added to the universe force_guess: bool To indicate wether to only partialy guess the empty values of the attribute or to overwrite all existing values by guessed one Returns ------- NDArray of guessed values z2 is not a recognized MDAnalysis topology attributez cannot guess this attribute: NT)indices_to_guesszThere is no empty z2 values. Guesser did not guess any new values for z attribute)rKeyErrorattrnamer ValueErrorr r issubclassrhasattrr atomsnparraygetattrare_values_missingloggerinfo)r"r/ force_guesstop_attrguesser_method attr_values empty_valuess r guess_attrzGuesserBase.guess_attr}s  &}5HH    %%%   !)  !2=ANN   ::&..+..   h , , $!>## # 4>' 7 7 .  .(,mTBBK$66{CCL|##-;N%1--- L)#" NNN4ANNNt8NN,,-- -s - A1A7r)F) rrrrr rr__annotations__r r'r)r0rDrrrrrIs$Gd$$$ "?.?.?.?.?.?.rr) metaclassc jt|tr||_|jdi||S t |tr ||fi|Sn#t $rYnwxYw t ||fi|}n0#t$r#td |wxYw|S)aget an appropiate guesser to the Universe and pass the Universe to the guesser Parameters ---------- u: Universe to be passed to the guesser context: str or Guesser **kwargs : dict, optional Extra arguments are passed to the guesser. Returns ------- Guesser class Raises ------ * :exc:`KeyError` upon failing to return a guesser class .. versionadded:: 2.8.0 zUnidentified guesser type {0}r) isinstancerr r'r6 TypeErrorrrr3format)r ur$guessers r get_guesserrMs.';''''''' g{ + + (71'''' ' (      HGMMOO,Q99&99 HHH6==gFFGGGH NsA AA%B-B0r)rrrcore.topologyattrsrnumpyr9loggingtypingrr) getLoggerr=r r rrMrrrrTs. *))))))),,,,,,  4 5 56666646660s.s.s.s.s.Ls.s.s.s.l%%%%%%r