irdZddlZddlmZddlmZddlmZddl m Z m Z m Z m Z mZmZGd d eZdS) a FHI-AIMS Topology Parser --- :mod:`MDAnalysis.topolgy.FHIAIMSParser` ==================================================================== Reads an `FHI-AIMS`_ ``.in`` file and pulls the atom information from it. Because an FHI-AIMS input file only has atom name information, any information about residues and segments will not be populated. .. _`FHI-AIMS`: https://aimsclub.fhi-berlin.mpg.de/ See Also -------- :mod:`MDAnalysis.coordinates.FHIAIMS` Classes ------- .. autoclass:: FHIAIMSParser :members: :inherited-members: N)openany)TopologyReaderBase)Topology) AtomnamesAtomidsResidsResnumsSegidsElementsc eZdZdZddgZdZdS) FHIAIMSParseraParse a list of atoms from an FHI-AIMS file Creates the following attributes: - Atomnames .. note:: By default, atomtypes and masses will be guessed on Universe creation. This may change in release 3.0. See :ref:`Guessers` for more information. .. versionchanged:: 2.8.0 Removed type and mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API). INFHIAIMSc lg}gd}t|j5}|D]dr.|dYt fd|Drutd|jtj |}t|}dddn #1swxYwYt|ttj|dzttjdgt#tjdgt%tjdgt& t)|g}t+|dd| }|S) ztRead the file and return the structure. Returns ------- MDAnalysis Topology object )#lattice_vectorinitial_momentvelocityatomc:g|]}|S) startswith).0taglines k/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/FHIAIMSParser.py z'FHIAIMSParser.parse..cs%BBB,,BBBz4Non-conforming line: ({0})in FHI-AIMS input file {0}NrSYSTEM)dtype)attrs)rfilenamestriprappendsplitany ValueErrorformatnpasarraylenrr aranger arrayr r objectr r) selfkwargsnames skip_tagsinfnatomsr$toprs @rparsezFHIAIMSParser.parseSsIII T] # # s  zz||??6**LLb!1222BBBB BBBCC JQQdm Ju%%EZZF               $ e   BIf%%) * * 28QC== ! ! BHaSMM " " 28XJf555 6 6 UOO  vq!5111 sCC++C/2C/N)__name__ __module__ __qualname____doc__r+r9rr!rrr?s9"I F&&&&&r!r)r=numpyr,lib.utilrbaser core.topologyrcore.topologyattrsrr r r r r rrr!rrCs00$$$$$$$$$$$$:::::&:::::r!