idZddlmZddlZddlZddlZddlmZm Z ddl m Z ddl m Z Gdd eZGd d e e Zd ZdZdZdS)a Base topology reader classes --- :mod:`MDAnalysis.topology.base` ================================================================ Derive topology reader classes from the base class in this module. All topology readers raise :exc:`IOError` upon failing to read a topology file and :exc:`ValueError` upon failing to make sense of the read data. Classes ------- .. autoclass:: TopologyReaderBase :members: :inherited-members: )reduceN)_PARSERS _PARSER_HINTS)IOBase)utilceZdZdZdZdS) _TopologymetaaInternal: Topology Parser registration voodoo When classes which inherit from TopologyReaderBase are *defined* this metaclass makes it known to MDAnalysis. The optional `format` attribute and `_format_hint` staticmethod are read: - `format` defines the file extension this Parser targets. - `_format_hint` defines a function which returns a boolean if the Parser can process a particular object Eg:: class ThingParser(TopologyReaderBase): format = ['foo', 'bar'] @staticmethod _format_hint(thing): try: import WeirdPackage except ImportError: return False return isinstance(thing, WeirdPackage.Thing) This way there is no strict dependency on "WeirdPackage", but if a user supplies a WeirdPackage.Thing the "ThingParser' will be able to step up and read it. .. versionchanged:: 1.0.0 Added format_hint functionality ctt||| tj|d}|D]9}|}|t |<d|vr|djt|<:dS#t$rYdSwxYw)Nformat _format_hint) type__init__r asiterableupperr__func__rKeyError)clsnamebases classdictfmtfmt_names b/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/base.pyrz_Topologymeta.__init__Qs dD%333 /)H"566C   #>>++%("!Y...7&/"(+       DD sA<< B  B N)__name__ __module__ __qualname____doc__rrr r 2s-<r r ceZdZdZdZdZdS)TopologyReaderBasea|Base class for topology readers Parameters ---------- filename : str name of the topology file universe : Universe, optional Supply a Universe to the Parser. This then passes it to the atom instances that are created within parsers. All topology readers must define a `parse` method which returns a Topology object Raises ------ * :exc:`IOError` upon failing to read a topology file * :exc:`ValueError` upon failing to make sense of the read data .. versionadded:: 0.9.0 .. versionchanged:: 0.9.2 Added keyword 'universe' to pass to Atom creation. c||_dSN)filename)selfr%s rrzTopologyReaderBase.__init__zs   r c td)NzOverride this in each subclass)NotImplementedError)r&kwargss rparsezTopologyReaderBase.parse}s!"BCCCr N)rrrrrr*rr rr"r"bsA.!!!DDDDDr r") metaclassc\tj|dd\}}||fd|DfS)aSquash a child-parent relationship Arguments --------- child_parent_ids - array of ids (unique values that identify the parent) *attributes - other arrays that need to follow the sorting of ids Returns ------- child_parents_idx - an array of len(child) which points to the index of parent parent_ids - len(parent) of the ids *parent_attrs - len(parent) of the other attributes T) return_indexreturn_inversec g|] }| Srr).0attr sort_masks r zsquash_by..s$L$L$LT)_$L$L$Lr )npunique)child_parent_ids attributes unique_residsatom_idxr2s @r squash_byr:sM*,tD***&M9h ]$L$L$L$L$L$L$L LLr c  d}t|d t fdtj|dd|Dst d||}t|dz t j|dt} fd|D}tt|dd |ddD]8\}\}}||||<t||D]\} } | ||d| |<9||fS) a(Squash per atom data to per residue according to changes in resid Parameters ---------- criteria : list of numpy ndarray Arrays which when changing indicate a new residue to_squash : list of numpy arrays Arrays which get squashed according to the criteria arrays Returns ------- residx : numpy array The Residue *index* that each Atom gets assigned to. [len(resids)] squashed : numpy array The to_squash arrays reduced down to per Residue values Example ------- resids = np.array([2, 2, 3, 3, 2, 2]) resnames = np.array(['RsA', 'RsA', 'RsB', 'RsB', 'RsC', 'RsC']) segids = np.array(['A', 'A', 'A', 'A', 'B', 'B']) residx, (new_resids, new_resnames, new_segids) = resid_change_squash( (resids,), (resids, resnames, segids)) # Per atom res index residx: [0, 0, 1, 1, 2, 2] # Per residue record of each attribute new_resids: [2, 3, 2] new_resnames: ['RsA', 'RsB', 'RsC'] new_segids: ['A', 'A', 'B'] ctjttjd|D}dgt |ddzzdgzS)z5Generator of indices to slice arrays when they changec3BK|]}|dd|ddkVdS)Nr)r0as r z5change_squash..get_borders..s6"C"Cq1SbS6QqrrU?"C"C"C"C"C"Cr Nrr?)r4nonzeror logical_orlist)arraysborderss r get_bordersz"change_squash..get_borderssW* 2="C"CF"C"C"C D D  vWQZ!^,,,v55r rc3>K|]}t|kVdSr$)len)r0otherl0s rrAz change_squash..s?"E br r?Nz All arrays must be equally sizeddtypecFg|]}tj|jS)rL)r4zerosrM)r0onress rr3z!change_squash..s*CCCA"(4qw///CCCr r>) rIall itertoolschain ValueErrorr4 zeros_likeint enumeratezip) criteria to_squashrGrFresidx new_othersixyoldnewrKrQs @@r change_squashrcseF666 Xa[  B &/ohqrrlI&N&N  =;<<<k8$G w<>!! 6Aqqs Iz22 ! !HC1Xa[CFF ! : r cVt|dkr|dSt|S)zReturns the value in an array of length 1, or the tuple of an array with a longer lengh. Parameters ---------- values: array-like Array to squash Returns ------- values: tuple or single value r?r)rItuple)valuess rreduce_singularrgs+ 6{{aayV}}r )r functoolsrrSnumpyr4warningsrrcoordinates.baserlibrrr r"r:rcrgrr rrns#. &&&&&&&&%%%%%%-----D---`DDDDD=DDDD>MMM,DDDNr