i*dZdZdZddlmZddlmZddlmZ ddl m Z dd l m Z d d lZejd ZGd de Zd S)a*Gromacs portable run input TPR format parser ============================================ The :mod:`~MDAnalysis.topology.TPRParser` module allows reading of a Gromacs_ portable run input file (a `TPR file`_). Because the file format of the TPR file is changing rapidly, not all versions are currently supported. The known working versions and the approximate Gromacs release numbers are listed in the table :ref:`TPR format versions `. .. _`TPR-format-table`: .. table:: TPR format versions and generations read by :func:`MDAnalysis.topology.TPRParser.parse`. ========== ============== ==================== ===== TPX format TPX generation Gromacs release read ========== ============== ==================== ===== ?? ?? 3.3, 3.3.1 no 58 17 4.0, 4.0.2, 4.0.3, yes 4.0.4, 4.0.5, 4.0.6, 4.0.7 73 23 4.5.0, 4.5.1, 4.5.2, yes 4.5.3, 4.5.4, 4.5.5 83 24 4.6, 4.6.1 yes 100 26 5.0, 5.0.1, 5.0.2, yes 5.0.3,5.0.4, 5.0.5 103 26 5.1 yes 110 26 2016 yes 112 26 2018 yes 116 26 2019 yes 119 27 2020[*]_ yes 122 28 2021 yes 127 28 2022 yes 129 28 2023 yes 133 28 2024.1 yes 134 28 2024.4 yes 137 28 2025.0 yes ========== ============== ==================== ===== .. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported. See `Issue 2428`_ for more details. For further discussion and notes see `Issue 2`_. Please *open a new issue* in the `Issue Tracker`_ when a new or different TPR file format version should be supported. Bonded interactions available in Gromacs are described in table 5.5 of the `Gromacs manual`_. The following ones are used to build the topology (see `Issue 463`_): * bonds: regular bonds (type 1), G96 bonds (type 2), Morse (type 3), cubic bonds (type 4), connections (type 5), harmonic potentials (type 6), FENE bonds (type 7), restraint potentials (type 10), tabulated potential with exclusion/connection (type 8), tabulated potential without exclusion/connection (type 9), constraints with exclusion/connection (type 1), constraints without exclusion/connection (type 2), SETTLE constraints * angles: regular angles (type 1), G96 angles (type 2), cross bond-bond (type3), cross-bond-angle (type 4), Urey-Bradley (type 5), quartic angles (type 6), restricted bending potential (type 10), tabulated angles (type 8) * dihedrals: proper dihedrals (type 1 and type 9), Ryckaert-Bellemans dihedrals (type 3), Fourier dihedrals (type 5), restricted dihedrals (type 10), combined bending-torsion potentials (type 11), tabulated dihedral (type 8) * impropers: improper dihedrals (type 2), periodic improper dihedrals (type 4) Classes ------- .. autoclass:: TPRParser :members: :inherited-members: See Also -------- :mod:`MDAnalysis.topology.tpr` Development notes ----------------- The TPR reader is a pure-python implementation of a basic TPR parser. Currently the following sections of the topology are parsed: * Atoms: number, name, type, resname, resid, segid, chainID, mass, charge, element [residue, segment, radius, bfactor, resnum, moltype] * Bonds * Angles * Dihedrals * Impropers This tpr parser is written according to the following files - :file:`{gromacs_dir}/src/kernel/gmxdump.c` - :file:`{gromacs_dir}/src/gmxlib/tpxio.c` (the most important one) - :file:`{gromacs_dir}/src/gmxlib/gmxfio_rw.c` - :file:`{gromacs_dir}/src/gmxlib/gmxfio_xdr.c` - :file:`{gromacs_dir}/include/gmxfiofio.h` or their equivalent in more recent versions of Gromacs. The function :func:`read_tpxheader` is based on the `TPRReaderDevelopment`_ notes. Functions with names starting with ``read_`` or ``do_`` are trying to be similar to those in :file:`gmxdump.c` or :file:`tpxio.c`, those with ``extract_`` are new. Versions prior to Gromacs 4.0.x are not supported. .. Links .. _Gromacs: http://www.gromacs.org .. _`Gromacs manual`: http://manual.gromacs.org/documentation/5.1/manual-5.1.pdf .. _TPR file: http://manual.gromacs.org/current/online/tpr.html .. _`Issue Tracker`: https://github.com/MDAnalysis/mdanalysis/issues .. _`Issue 2`: https://github.com/MDAnalysis/mdanalysis/issues/2 .. _`Issue 463`: https://github.com/MDAnalysis/mdanalysis/pull/463 .. _TPRReaderDevelopment: https://github.com/MDAnalysis/mdanalysis/wiki/TPRReaderDevelopment .. _`Issue 2428`: https://github.com/MDAnalysis/mdanalysis/issues/2428 .. versionchanged:: 2.0.0 The `elements` topology attribute is now exposed if at least one atom has a valid element symbol. In that case, atoms for which the element is not recognized have their element attribute set to an empty string. If none of the elements are recognized, then the `elements` attribute is not set in the topology. .. versionchanged:: 2.7.0 If the TPR molblock is named "Protein_chain_XXX" then we assume that XXX is describing the chain of a protein (in the sense of the PDB chainID) and set the topology attribute `chainID` to "XXX". In all other cases, the chainID remains the full molblock name. The `segID` is never changed. z Zhuyi XuezGNU Public Licence, v2)openany)utils)setting)TopologyReaderBase)ResnumsNzMDAnalysis.topology.TPRparserc$eZdZdZdZddZdZdS) TPRParserzRead topology information from a Gromacs_ `TPR file`_. .. _Gromacs: http://www.gromacs.org .. _TPR file: http://manual.gromacs.org/current/online/tpr.html TPRTc t|jd5}|}dddn #1swxYwYtj|} tj|}nH#t tf$r4|jd}t |t|wxYw| ||j tjkr|jdkrt!||z }|d|jzkr+d}t |t|tj|}|j} |jrtj||j | dkr5|j d krtj|| tj|| |jr#tj||j ||j } n3|jd }t |t|| t=| jj !| S) aParse a Gromacs TPR file into a MDAnalysis internal topology structure. Parameters ---------- tpr_resid_from_one: bool (optional) Toggle whether to index resids from 1 or 0 from TPR files. TPR files index resids from 0 by default, even though GRO and ITP files index from 1. Returns ------- structure : dict .. versionchanged:: 1.1.0 Added the ``tpr_resid_from_one`` keyword to control if resids are indexed from 0 or 1. Default ``False``. .. versionchanged:: 2.0.0 Changed to ``tpr_resid_from_one=True`` by default. rb)modeNz*: Invalid tpr file or cannot be recognizedzHTPR files produced with beta versions of gromacs 2020 are not supported.r E)tpr_resid_from_one precisionz: No topology found in tpr file)"rfilenameread tpr_utils TPXUnpackerread_tpxheaderEOFError ValueErrorloggercriticalIOError _log_headerfverStpxv_AddSizeFieldfgenlen get_buffer get_position sizeOfTprBodyTPXUnpacker2020 from_unpackerngtcbBoxextract_box_infondo_realbTopdo_mtopradd_TopologyAttrrresidsvaluescopy) selfrkwargsinfiletprfdatathmsgactual_body_size state_ngtctpr_tops g/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.pyparsezTPRParser.parses*T] . . . !&;;==D ! ! ! ! ! ! ! ! ! ! ! ! ! ! !$T** )$//BB*%   ]NNNC OOC #,,    7a) ) )bgmm"4??#4#4558I8I8K8KK 1r'7#777)$$$cll",::4@@DW 7 6  &tRW 5 5 5 >>w||"4444  j    7 '#5, GG]CCCC OOC #,,   )>)C)C)E)E!F!FGGGs8<<A--AB2ctd|jtd|jtd|jtd|jtd|jtd|jtd|jtd|j td |j t d |j t d |j t d |jt d |jt d|jt d|jdS)NzGromacs version : ztpx version : ztpx generation : ztpx precision : ztpx file_tag : ztpx natoms : ztpx ngtc : ztpx fep_state : ztpx lambda : ztpx bIr (input record): ztpx bTop : ztpx bX : ztpx bV : ztpx bF : ztpx bBox : )rinfover_strr r#rfile_tagnatomsr* fep_statelambdebugbIrr.bXbVbFr+)r4r9s r>rzTPRParser._log_header s 72:77888 42744555 42744555 92<99::: 82;88999 62966777 42744555 92<99::: 42744555 888999 42744555 22522333 22522333 22522333 4274455555N)T)__name__ __module__ __qualname____doc__formatr?rrLr>r r sM FHHHHT66666rLr )rP __author__ __copyright__lib.utilrtprrrrr!basercore.topologyattrsrlogging getLoggerrr rRrLr>r[s:IIT ( ######$$$$$$((((((  : ; ;b6b6b6b6b6"b6b6b6b6b6rL