i+dZddlZddlZddlZddlmZddlmZddl m Z ddl m Z ddlmZdd l mZmZmZmZmZmZmZmZGd d e ZdS) aTXYZ topology parser ==================== Tinker_ topology parser: reads information from .txyz and .arc files. Atom types are read from column 6, while bond connectivity is read from column 7 onwards. .. _Tinker: https://dasher.wustl.edu/tinker/ See Also -------- MDAnalysis.coordinates.TXYZ : further documentation on the Tinker format Classes ------- .. autoclass:: TXYZParser :members: :inherited-members: N)SYMB2Z)openany)TopologyReaderBase)Topology) AtomnamesAtomids AtomtypesBondsResidsResnumsSegidsElementsc eZdZdZddgZdZdS) TXYZParsera{Parse a list of atoms from a Tinker XYZ file. Creates the following attributes: - Atomnames - Atomtypes - Elements (if all atom names are element symbols) .. note:: By default, masses will be guessed on Universe creation. This may change in release 3.0. See :ref:`Guessers` for more information. .. versionadded:: 0.17.0 .. versionchanged:: 2.4.0 Adding the `Element` attribute if all names are valid element symbols. .. versionchanged:: 2.8.0 Removed mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API). TXYZARCc t|j5}t|d}t j|t}t j|t}t j|t}g}|} t|d|}n#t$rYnwxYwtt|tj |g|D]x\} } | } | d|| <| d|| <| d|| <| dd} | D]1} t| dz } | | kr|| | f2y dddn #1swxYwYt|t!|t#|t%t'|t)t jdgt-t jdgt/t jdgtg} t1d|Dr<| t3t j|tnt5jd t9|dd| }|S) ztRead the file and return the structure. Returns ------- MDAnalysis Topology object r)dtyperNSYSTEMc3LK|]}|tvV dS)N) capitalizer).0ns h/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/TXYZParser.py z#TXYZParser.parse..s/77Aq||~~'777777zElement information is missing, elements attribute will not be populated. If needed these can be guessed using universe.guess_TopologyAttrs(to_guess=['elements']).)attrs)rfilenameintreadlinesplitnpzerosobjectfloat ValueErrorziprange itertoolschainappendr r r r tupler arrayrrallrwarningswarnr)selfkwargsinfnatomsatomidsnamestypesbondsflineiline bonded_atoms other_atomr!tops rparsezTXYZParser.parse]sT] # # 6s--//233FhvS111GHV6222EHV6222EELLNNE 'ekkmmA&'''      uV}}iougs.K.KLL 6 64zz||!!W 7a7a#ABBx ".66J!$Z1!4J:~~ a_5556 6/ 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6F e   G   e   %,,   28QC== ! ! BHaSMM " " 28XJf555 6 6  77777 7 7  LL"(5"?"?"?@@ A A A A M*   vq!5111 s7B!F:7'C3F:3 D=F:?DB-F::F>F>N)__name__ __module__ __qualname____doc__formatrCr rrrCs8.e_F?????r r)rGr-numpyr&r3guesser.tablesrlib.utilrbaser core.topologyrcore.topologyattrsr r r r r rrrrrIr rrPs/..######$$$$$$$$$$$$######                    YYYYY#YYYYYr