i5dZddlZddlZddlmZddlZddlmZm Z ddl m Z m Z m Z ddlmZmZmZmZmZmZmZmZmZmZmZmZmZdd lmZejd ZGd d e Z dS) a! PSF topology parser =================== Reads a CHARMM/NAMD/XPLOR PSF_ file to build the system. The topology will contain atom IDs, segids, residue IDs, residue names, atom names, atom types, charges and masses. Bonds, angles, dihedrals and impropers are also read from the file. It reads both standard and extended ("EXT") PSF formats and can also parse NAMD space-separated "PSF" file variants. .. _PSF: http://www.charmm.org/documentation/c35b1/struct.html Classes ------- .. autoclass:: PSFParser :members: :inherited-members: N)ceil)openanyatoi)TopologyReaderBase squash_by change_squash) Atomids Atomnames AtomtypesMassesChargesResidsResnumsResnamesSegidsBondsAngles Dihedrals Impropers)TopologyzMDAnalysis.topology.PSFc.eZdZdZdZdZdZdZdZdS) PSFParseraRead topology information from a CHARMM/NAMD/XPLOR PSF_ file. Creates a Topology with the following Attributes: - ids - names - types - masses - charges - resids - resnames - segids - bonds - angles - dihedrals - impropers .. _PSF: http://www.charmm.org/documentation/c35b1/struct.html .. versionchanged:: 2.8.0 PSFParser now reads string resids and converts them to integers. PSFc t|j5}t|}|dsDd|j|}t |t||dd}d|vrd|_ nd|vrd|_ nd|_ t|t|}|d d ksCd |j}t |t|tt|d D]}t|t d |j|j | |dd d |jf}tddd|jfft"ddd|jfft$ddd|jfft&ddd|jfff} | D]F\} } t||| | || Gn`#t*$rStt"t$t&fD]5} t-|| js|| g6YnwxYwdddn #1swxYwY|S)zkParse PSF file into Topology Returns ------- MDAnalysis *Topology* object rz({0} is not valid PSF file (header = {1})NNAMDEXTEXTENDEDSTANDARDrz!NTITLEz{0} is not a valid PSF filerzPSF file {0}: format {1}NATOMNBONDrNTHETANPHINIMPHI)rfilenamenext startswithformatloggererror ValueErrorsplit_formatrangeintdebug _parse_sec _parseatomsr _parsesectionrrradd_TopologyAttr StopIterationhasattrattrname) selfkwargspsffileheadererr header_flagstitle_topsectionsattrinfos g/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/PSFParser.pyparsezPSFParser.parsedsT] # #4 7w']]F$$U++ &CJJM6 S!!! oo%!!"":++--L%%% ,&&) ) MMMMM''))E!H ))3::4=II S!!! oo%3uQx==))  W LL6$-66    //'GQ4;K+LMMC!Q(:;<(Aq$*<=>VQ4+=>?Xq!T-?@A H 7"*OOJD$MMM((doogt.L.L)M)MNNNNO! 7 7 7"FIyA77D"3 667,,TT"XX66677 7a4 74 74 74 74 74 74 74 74 74 74 74 74 74 74 7l s8G4K A IKAJ1.K0J11KKKcJ|\}}}}t|}|dkr't|}|dk'|}t|d}|dd} | |ks?d|| } t | t| tt||z } tj t|} || || S)zzParse a single section of the PSF Returns ------- A list of Attributes from this section rrz!:z"Expected section {0} but found {1}) r)stripr/floatr+r,r-r.r2r functoolspartial) r;r= section_infodesc atoms_perper_line parsefuncr>num sect_typer?numlines psffile_nexts rGr4zPSFParser._parse_secs0<,i9gllnn""']]Fllnn""F1I1IOOD)) D  9@@iC LL   S// !tC(N++,, (w77 yy(;;;cdddd}||j}d}tj|tj}tj|t}tj|tj} tj|t} tj|t} tj|t} tj|tj} tj|tj}t|D]E} |}nB#t$r5|j d}t |t|dwxYw |||}n#t$ry|d }|||}t d td ||YnwxYw|d ||<|d ||<|d| |<|d| |<|d| |<|d| |<|d| |<|d||<Gt#|}t%| } t'| } t)| } t+|}t-| | |f| | |f\}\}}}t/|}t1|}t5|}t7|dd\}}t9|}t;t=|t=|t=||| | | |||||g ||}|S)aParses atom section in a Charmm PSF file. Normal (standard) and extended (EXT) PSF format are supported. CHEQ is supported in the sense that CHEQ data is simply ignored. CHARMM Format from ``source/psffres.src``: CHEQ:: II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I),ECH(I),EHA(I) standard format: (I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8,2G14.6) (I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR expanded format EXT: (I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6) (I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR no CHEQ:: II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I) standard format: (I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8) (I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8) XPLOR expanded format EXT: (I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8) (I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8) XPLOR NAMD PSF space separated, see release notes for VMD 1.9.1, psfplugin at http://www.ks.uiuc.edu/Research/vmd/current/devel.html : psfplugin: Added more logic to the PSF plugin to determine cases where the CHARMM "EXTended" PSF format cannot accomodate long atom types, and we add a "NAMD" keyword to the PSF file flags line at the top of the file. Upon reading, if we detect the "NAMD" flag there, we know that it is possible to parse the file correctly using a simple space-delimited scanf() format string, and we use that strategy rather than holding to the inflexible column-based fields that are a necessity for compatibility with CHARMM, CNS, X-PLOR, and other formats. NAMD and the psfgen plugin already assume this sort of space-delimited formatting, but that's because they aren't expected to parse the PSF variants associated with the other programs. For the VMD PSF plugin, having the "NAMD" tag in the flags line makes it absolutely clear that we're dealing with a NAMD-specific file so we can take the same approach. c *|dd|ddpd|dd|dd|d d |d d |d d|ddfS)N SYSTEM!"0>rKls rGz'PSFParser._parseatoms..s"1"!B$ +8"R%"R%  "R%  "R%  "R%"R% #rXc *|dd|ddpd|dd|dd|d d |d d |d d|ddfS)N rar^rdre%&./34BFrjrks rGrmz'PSFParser._parseatoms..s#2#"R%  ,H"R%"R%  "R%  "R%  "R%"R% #rXc:|ddS)Nr[)r/rks rGrmz'PSFParser._parseatoms.. saggiimrX)r!r rc t|ddz |dpdt|d|d|d|dt|dt|d fS) Nrrr^rrr$)r2rrL)xs rGrmz'PSFParser._parseatoms..sb !IIM aD H 1JJ aD aD aD !A$KK !A$KK  rX)dtypez is not valid PSF fileNrzWGuessing that this is actually a NAMD-type PSF file... continuing with fingers crossed!zFirst NAMD-type line: {0}: {1}rrrrr$r|r}r~)attrs atom_resindexresidue_segindex)r0npzerosint32objectfloat32float64r1r8r(r,r-r.warningr3r+rstripr r r rrr rrcopyrr rrlen)r;linesrQrV atom_parsers atom_parserset_typeatomidssegidsresidsresnames atomnames atomtypeschargesmassesiliner?valsresidx new_resids new_resnames perres_segids residueids residuenums residuenamessegidx perseg_segidsrCs rGr5zPSFParser._parseatomssh    ,+/  2#4<0    .(828444(&111("(3338HF333HXV444 HXV444 (82:666("*555x  A 0uww  0 0 0>>> S!!! oo4/ 0 x D 1 122   +62 x D 1 1228  va// aGAJQF1IQF1Iq'HQK7IaL7IaLaGAJQF1II'""i(( i(( '""=J Xv &6(B= = 99\=J'' joo//00  -- !*- 8 8! <  && LL  OO KK !#!   & s D$$?E#'E<G?c ,g}t|D]}tj|dz }tdt ||D]/}|t ||||z0|S)Nrr)r1rint64r/rappendtuple)r;rrQrVsectionrfieldsjs rGr6zPSFParser._parsesectionysx A AAXeeggmmoo..2F1c&kk955 A AuVAI ,=%>??@@@@ ArXN) __name__ __module__ __qualname____doc__r+rHr4r5r6rXrGrrJsf.F>>>@<<<8wwwrrXr)!rloggingrMmathrnumpyrlib.utilrrbaserr r core.topologyattrsr r r rrrrrrrrrr core.topologyr getLoggerr,rrrXrGrsv0,$$$$$$$$>>>>>>>>>>%$$$$$  4 5 5wwwww"wwwwwrX