i%dZddlZddlZddlmZddlmZddlm Z ddl m Z m Z m Z mZmZmZmZmZmZmZmZGdd eZGd d eZdS) aOpenMM topology parser :mod:`MDAnalysis.converters.OpenMMParser` =================================================================== .. versionadded:: 2.0.0 .. versionchanged:: 2.8.0 Removed type and mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API) Converts an `OpenMM topology `_ :class:`openmm.app.topology.Topology` into a :class:`MDAnalysis.core.Topology`. Also converts some objects within the `OpenMM Application layer `_ - `openmm.app.pdbfile.PDBFile `_ - `openmm.app.simulation.Simulation `_ - `openmm.app.modeller.Modeller `_ - `openmm.app.pdbxfile.PDBxFile `_ The :class:`OpenMMTopologyParser` generates a topology from an OpenMM Topology object. Classes ------- .. autoclass:: OpenMMTopologyParser :members: :inherited-members: .. autoclass:: OpenMMAppTopologyParser :members: :inherited-members: N)TopologyReaderBase)SYMB2Z)Topology) Atomids Atomnames AtomtypesBondsChainIDsElementsMassesResidsResnumsResnamesSegidsc4eZdZdZedZdZdZdS)OpenMMTopologyParserOPENMMTOPOLOGYc ddlm}t||jS#t$r ddlm}YdS#t$rYYdSwxYwwxYwz$Can this Parser read object *thing*?r)appFN)openmmr isinstancer ImportError simtk.openmmthingrs l/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/converters/OpenMMParser.py _format_hintz!OpenMMTopologyParser._format_hintUs 3 " " " " " "eS\22 2     ,,,,,,,,,   uuu  s" A1 AAAAc  ddlm}n7#t$r* ddlm}n#t$rd}t|wxYwYnwxYwd|D}d|D}d|D}d|D}d|D}d |D} d |D} | } d |D} d |D} d |D}d|D}ttj |tj ttj |tt| ||dt!tj |tt#| t%| t'| t)| g}g}g}g}|D]}|j}||jt0vr||jn|d||j||j||d|d|dt9|st;|r}t=jdt;d|Drt=jd|tAtj |tnRd}t=j|n;|tAtj |t|tCtj |t|tEtj |tG|}tG| }tG| }tI||||||}|S)a Construct mda topology from omm topology Can be used for any openmm object that contains a topology object Parameters ---------- omm_topology: openmm.Topology Returns ------- top : MDAnalysis.core.topology.Topology When partial elements are present, values from available elements are used whereas the absent elements are assigned an empty string with their atomtype set to 'X' and mass set to 0.0. For elements with invalid and unreal symbols, the symbol is used as it is for atomtypes but an empty string is used for elements. .. versionchanged:: 2.2.0 The parser now works when element attribute is missing in some or all the atoms. r)daltonsz{OpenMM is required for the OpenMMParser but it's not installed. Try installing it with conda install -c conda-forge openmmc&g|]}|jjS)residueindex.0as r zHOpenMMTopologyParser._mda_topology_from_omm_topology..sGGGQGGGc&g|]}|jjSr#)chainr%r'rs rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..sKKKaAGMKKKr*cg|] }|j Sr#)idr&s rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..s666A14666r*cg|] }|j Sr#namer&s rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..s:::QV:::r*c0g|]}|jjjSr#)r$r,r0r&s rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..sEEE1AIO&EEEr*cg|] }|j Sr#r2r-s rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..s<<.s???!!'A+???r*c6g|]}t|jSr#)strr%)r'cs rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..s >>>1#ag,,>>>r*c>g|]}|jj|jjfSr#)atom1r%atom2r'bs rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..s%NNNA!'-/NNNr*cg|] }|j Sr#)orderr>s rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..s===1qw===r*cg|] }|j Sr#)typer>s rr)zHOpenMMTopologyParser._mda_topology_from_omm_topology..s;;;af;;;r*)dtypeF)typesrAguessedNgXzZElement information missing for some atoms. These have been given an empty element record c3"K|] }|dkV dS)rHNr#)r'is r zGOpenMMTopologyParser._mda_topology_from_omm_topology..s&33AqCx333333r*a For absent elements, atomtype has been set to 'X' and mass has been set to 0.0. If needed these can be guessed using universe.guess_TopologyAttrs(to_guess=['masses', 'types']). (for MDAnalysis version 2.x this is done automatically, but it will be removed in 3.0).aElement information is missing for all the atoms. Elements attribute will not be populated. Atomtype attribute will be guessed using atom name and mass will be guessed using atomtype.For MDAnalysis version 2.x this is done automatically, but it will be removed in MDAnalysis v3.0. These can be guessed using universe.guess_TopologyAttrs(to_guess=['masses', 'types']) See MDAnalysis.guessers.)attrs atom_resindexresidue_segindex)% openmm.unitr!r simtk.unitatomsresiduescopychainsbondsrnparrayint32robjectr r rrrrelementsymbol capitalizerappendmass value_in_unitallanywarningswarnr r r lenr)self omm_topologyr!msgrMrNatomids atomnameschainidsresnamesresidsresnumssegidsrU bond_orders bond_typesrLvalidated_elementsmasses atomtypesr(elemwmsgn_atoms n_residues n_segmentstops r_mda_topology_from_omm_topologyz4OpenMMTopologyParser._mda_topology_from_omm_topologybs6 ' + + + + + + + ' ' ' '....... ' ' ': "#&&&  '/. 'HG,2D2D2F2FGGG KK<3H3H3J3JKKK66!3!3!5!5666::\%7%7%9%9::: EE 0B0B0D0DEEE<'>???++-->> (;(;(=(=>>>NN9K9K9M9MNNN== (:(:(<(<=== ;;l&8&8&:&:;;;  BHWBH555 6 6 bhy777 8 8 %ze L L L RXhf555 6 6 6NN G   X   6NN    ##%% & &A9D;))++v55&--dk::::&--b111  --- di55g>>????"))"--- c"""  %%%%%&&& O%&&# $ E3333333 M;    RX&8GGGHH / d#### LL"(+=V"L"L"LMM N N N Yrx @@@AABBB VBHV,,--...g,,[[ [[    '-     s ==7==c >|j}||}|SN)filenamerzrekwargsrfrys rparsezOpenMMTopologyParser.parses!} 22<@@ r*N)__name__ __module__ __qualname__format staticmethodrrzrr#r*rrrRsT F 3 3\ 3GGGRr*rc.eZdZdZedZdZdS)OpenMMAppTopologyParser OPENMMAPPc ddlm}t||j|j|j|jfS#t$r ddlm}YdS#t$rYYdSwxYwwxYwr) rrrPDBFileModeller SimulationPDBxFilerrrs rrz$OpenMMAppTopologyParser._format_hints  " " " " " "clCNCLI      ,,,,,,,,,   uuu  s&0 AA AAAAc |j}n#t$r|jj}YnwxYw||}|Sr|)r} getTopologyAttributeErrortopologyrzr~s rrzOpenMMAppTopologyParser.parses] 2=4466LL 2 2 2=1LLL 222<@@ s 55N)rrrrrrrr#r*rrrsA F  \ r*r)__doc__numpyrVrb topology.baserguesser.tablesr core.topologyrcore.topologyattrsrrr r r r r rrrrrrr#r*rrsH0##J......######$$$$$$                          ]]]]]-]]]@2r*