B b@s\dZddlmZmZmZddlZddlZddlZddlmZ ddl m Z ddl m Z ddlmZdd lmZmZdd lmZmZdd lmZdd lmZmZdd lmZmZmZmZm Z m!Z!m"Z"m#Z#m$Z$m%Z%m&Z&ddl'm(Z(ddl)m*Z*m+Z+m,Z,ddl-m.Z.ddl/m0Z0m1Z1e2dZ3Gddde4Z5ddZ6Gddde4Z7Gdddee7Z8ddZ9dS)z This module contains classes for parsing and processing CHARMM parameter, topology, and stream files. Author: Jason M. Swails Contributors: Date: Mar. 26, 2017 )absolute_importdivisionprint_functionN)copy) OrderedDict) combinations)TINY) CharmmErrorParameterWarning) PatchTemplateResidueTemplate) ParameterSet) AtomicNumelement_by_mass) AngleTypeAtomAtomTypeBondTypeCmapType DihedralTypeDihedralTypeList ImproperType NoUreyBradley DrudeAtomDrudeAnisotropy)genopen) integer_types iteritems string_types)zip) CharmmFileCharmmStreamFilezpenalty\s*=\s*([\d\.]+)c@s eZdZdZddZddZdS)_EmptyStringIteratorz Always yields an empty string ccsx dVqWdS)N)selfr&r&7lib/python3.7/site-packages/parmed/charmm/parameters.py__iter__#sz_EmptyStringIterator.__iter__cCsdS)Nr%r&)r'idxr&r&r( __getitem__&sz _EmptyStringIterator.__getitem__N)__name__ __module__ __qualname____doc__r)r+r&r&r&r(r$!sr$cCsjt|tr|S||kr>|ddddddddSd|ddddddddS) N*ZSTR+P-Mz%sLTU) isinstancerupperreplace)namer&r&r( _typeconv)s   $r:c@s eZdZdZddZddZdS)CharmmImproperMatchingMixinz+ Implements CHARMM-style improper matching cCs4||j||||}|dkr0||j||||}|S)z3 Matches an improper type based on atom type names N)_match_improper_with_typemapimproper_typesimproper_periodic_types)r'a1a2a3a4typr&r&r(match_improper_type6sz/CharmmImproperMatchingMixin.match_improper_typec Cs"||||f|kr |||||fS||||f|kr@|||||fStt||||g}|j|d|krt||j|SxTt||||fdD]>\}}} tt||| dg}|j|d|kr||j|SqWxRt||||fdD]<\}}tt||ddg}|j|d|kr||j|SqWdS)NXr)tuplesorted_improper_key_mapgetr) r'Ztypemapr?r@rArBkeyZexact1Zexact2Zexact3r&r&r(r<=s z8CharmmImproperMatchingMixin._match_improper_with_typemapN)r,r-r.r/rDr<r&r&r&r(r;3sr;cseZdZdZfddZedddZfdd Zed d d Z ed dZ ed!ddZ d"ddZ ddZ ddZd#ddZddZddZddZZS)$CharmmParameterSetaQ Stores a parameter set defined by CHARMM files. It stores the equivalent of the information found in the MASS section of the CHARMM topology file (TOP/RTF) and all of the information in the parameter files (PAR) Parameters ---------- *filenames : variable length arguments of str The list of topology, parameter, and stream files to load into the parameter set. The following file type suffixes are recognized: .rtf, .top -- Residue topology file .par, .prm -- Parameter file .str -- Stream file .inp -- If "par" is in the file name, it is a parameter file. If "top" is in the file name, it is a topology file. Otherwise, ValueError is raised. See Also -------- :class:`parmed.parameters.ParameterSet` cstt|}|j|_|S)N)superrL__copy___declared_nbrules)r'other) __class__r&r(rNlszCharmmParameterSet.__copy__r%NcCs^y||Stk rXd||f}|dk r8|d|7}|dk rL|d|7}t|YnXdS)za Converts a data type to a desired type, raising CharmmError if it fails zCould not convert %s to %s Nzinput line %d zinput line: %s ) ValueErrorr )datatypemsg line_indexliner&r&r(_convertqs   zCharmmParameterSet._convertc s:tt|g|_d|_ggg}}}x|D]}|dsH|drT||q0|dsh|drt||q0|dr||q0|drtj |d}d |kr||qd |kr||qt d |q0t d |q0Wx|D]}| |qWx|D]}| |qWx|D]} | | q"WdS) NFz.rtfz.topz.parz.prmz.strz.inpr!partopzUnrecognized file type: %s)rMrL__init__ parametersetsrOendswithappendospathsplitrRread_topology_fileread_parameter_fileread_stream_file) r'argsZtopsZparsZstrsargfnamerZrYZstrf)rQr&r(r[s2           zCharmmParameterSet.__init__Fc s$|}|rddnddtfdd}x0t|jD]"\}}t|j|_||||jqz6CharmmParameterSet.from_parameterset..cSs|S)Nr&)rir&r&r(rjrkcst|trt|}nt|tr0tdd|D}|tkrBt||<n:t|kr`t|||<n|}|t|<|||<dS)Ncss|]}t|VqdS)N)r:).0kr&r&r( szOCharmmParameterSet.from_parameterset..copy_paramtype..)r6rr:rGrid)rKrCdictZnewtype)do_copy id_typemapr&r(copy_paramtypes      z.copy_paramtypez%d-key cmap type detected!)rpratom_types_tupler:r9 atom_typesatom_types_int bond_types angle_typesurey_bradley_typesdihedral_typesr>r= cmap_typeslenAssertionError nbfix_types) clsZparamsrZ new_paramsrsrKZ atom_typetypenamer*rCr&)rqrrr(from_parametersetsB    z$CharmmParameterSet.from_parametersetcCs|tj|ddS)a' Extracts known parameters from a Structure instance Parameters ---------- struct : :class:`parmed.structure.Structure` The parametrized ``Structure`` instance from which to extract parameters into a ParameterSet Returns ------- params : :class:`ParameterSet` The parameter set with all parameters defined in the Structure Notes ----- The parameters here are copies of the ones in the Structure, so modifying the generated ParameterSet will have no effect on ``struct``. Furthermore, the *first* occurrence of each parameter will be used. If future ones differ, they will be silently ignored, since this is expected behavior in some instances (like with Gromacs topologies in the ff99sb-ildn force field). Dihedrals are a little trickier. They can be multi-term, which can be represented either as a *single* entry in dihedrals with a type of DihedralTypeList or multiple entries in dihedrals with a DihedralType parameter type. In this case, the parameter is constructed from either the first DihedralTypeList found or the first DihedralType of each periodicity found if no matching DihedralTypeList is found. F)Zallow_unequal_duplicates)rrfrom_structure)rZstructr&r&r(rsz!CharmmParameterSet.from_structurecCsd|}|dk r|||dk r*||t|tr@||n |dk r`x|D]}||qNW|S)aw Instantiates a CharmmParameterSet from a Topology file and a Parameter file (or just a Parameter file if it has all information) Parameters ---------- tfile : str The name of the Topology (RTF/TOP) file to parse pfile : str The name of the Parameter (PAR/PRM) file to parse sfiles : list(str) Iterable of stream (STR) file names Returns ------- New CharmmParameterSet populated with parameters found in the provided files Notes ----- The RTF file is read first (if provided), followed by the PAR file, followed by the list of stream files (in the order they are provided). Parameters in each stream file will overwrite those that came before (or simply append to the existing set if they are different) N)rbrcr6rrd)rtfilepfileZsfilesinstsfiler&r&r(load_sets     zCharmmParameterSet.load_setcICstj}t|trd}t|}n d}|}t|ts>|dkr>t}d}d}d}g} d} t} d} d} xt|D]\}}|}y |j }Wnt k r||}YnX|sql| dkr| dr|dd} ql| drd }ql| d rd }ql| d s| d r"d}ql| dsB| drHd}ql| dsh| drnd}ql| drd}ql| drd}} d}| dd}d}xt|D] \}}| dkrydt||d}Wn"ttfk rtdYnX|jrdt|jdkrtt|j\}}t|dj|}|tkrtdn0xft|jD] \}}x|D] }||_q~WqpWn6| dr|jr|jdkrtdd|_d} qWql| drd}ql| drd}ql| drd}ql|dd d kr2d}ql|dkr>qlt|}t|dkrdt|d}nd}| d kr| d!sql| }|d d krqly<||dtd"||d#}|d$ }||dtd%||d#}Wntk rtd&YnXy:|d' } t| d$kr0| d| d} t| }!Wn&tt fk r`tt!|}!YnXt"||||!d(}"|"|j#|"j$<|"|j%|"j&<|"|j'|"j$|"j&f<ql| d kr| }|d d krqlyH|d }#|d }$||d$td)||d#}%||dtd*||d#}&Wntk r.td+YnXt(|#|$t)|#|$f}t*|%|&}'||j+kr|j+||'krt,-d,||j+||'ft.|'|j+|#|$f<|'|j+|$|#f<n|'|j+|#|$f<|'|j+|$|#f<||'_/ql| dkrx| }|d d krqlyT|d }#|d }$|d$ }(||dtd-||d#}%||d'td.||d#})Wntk rdtd/YnXt0|%|)}*|#|$|(f}||j1kr|j1||*krt,-d0||j1||*ft.|*|j1|#|$|(f<|*|j1|(|$|#f<n |*|j1|#|$|(f<|*|j1|(|$|#f<y@||d1td2||d#}+||d3td4||d#},t*|+|,}-||-_/Wntk rNt2}-YnX|-|j3|#|$|(f<|-|j3|(|$|#f<||*_/ql| dk r| }|dj d krqlyv|d }#|d }$|d$ }(|d }.||d'td5||d#}%||d1td6||d#}/||d3td7||d#}0Wntk r4td8YnX|#|$|(|.f}t4|%|/|0}1||1_/||jkrd}2x\t|j|D]J\}}3|3j5|1j5krt|3|1krt,-d9|3|1ft.|1|j||<d}2PqtW|2 s|j|6|1qlt7}|6|1||j|#|$|(|.f<||j|.|(|$|#f<ql| dk r^| }|d d k r:qly`|d }#|d }$|d$ }(|d }.||d'td:||d#}%||d1td;||d#})Wntk rtd8YnXy||d3td;||d#}4Wntk rd}5YnXt|)}5|4})|#|$|(|.f}||j8t9t:|<|5dk r:t;|%|)}6|6|j<|<nt4|%|5|)}6|6|j=|<d|6_>||6_/ql| dk r| }|d d k rqlyd }<||d?td@||d#}=Wntk rvtdAYnX|#|$|(|.|9|:|;||<|;|:|9|.|(|$|#g}?t9t(|>|?}t9t)|>|?}|=} g} YqlXql| dk r| }|dj d k rqly>|d }"||d$tdB||d#}@||dtdC||d#}AWn0ttfk rb| rPxt|D]\}}| dk r ydt||d}Wn"ttfk rtdDYnX|j rtt|j\}}t|dj|}|tk rtdn0xft|jD] \}}x|D] }||_ qW qWn6| d r\|j rL|jdk rLtdd|_d} q\WwlYn.X|j r|jdk r| stdd}d|_y0||d1tdE||d#}B||d3tdF||d#}CWntk rd}B}CYnX|@|A|B|Cg| |"<ql| dkrl| }|d d krqly|d }D|d }Et||d$tdG||d#}F||dtdH||d#}Ay4t||d'tdI||d#}G||d1tdJ||d#}CWntk rd}G}CYnXy4|j#|DB|E|A|F|C|G|j#|EB|D|A|F|C|GWnt k rYnXWntk r$tdKYnX|F|Af|jCt(|D|Et)|D|Ef<qlW|dk rpt@| | }H|H|jA|<|H|jA|<y(x"| D]}|j#|jD| |qxWWn&t k rt,-dL|t.YnX| dk r|jE6| |r|FdS)MaN Reads all of the parameters from a parameter file. Versions 36 and later of the CHARMM force field files have an ATOMS section defining all of the atom types. Older versions need to load this information from the RTF/TOP files. Parameters ---------- pfile : str or list of lines Name of the CHARMM parameter file to read or list of lines to parse as a file comments : list of str, optional List of comments on each of the pfile lines (if pfile is a list of lines) Notes ----- The atom types must all be loaded by the end of this routine. Either supply a PAR file with atom definitions in them or read in a RTF/TOP file first. Failure to do so will result in a raised RuntimeError. TFNrz*>>r!NATOMZATOMSBONDZBONDSZANGLEZTHETAZANGLESDIHEZPHIZ DIHEDRALSZIMPROPERZIMPHICMAPZ NONBONDEDZE14FACzDCould not parse 1-4 electrostatic scaling factor from NONBONDED cardzInconsistent 1-4 scalingsZGEOM geometricz=Cannot combine parameter files with different combining rulesZNBFIXZHBONDTHOLErEENDMASSz atom type)rVrWrz atom masszCould not parse MASS section.)r9numbermass atomic_numberzbond force constantzbond equilibrium distzCould not parse bonds.zReplacing bond %r, %r with %rzangle force constantzangle equilibrium valuezCould not parse angles.zReplacing angle %r, %r with %rzUrey-Bradley force constantr5zUrey-Bradley equil. valuezdihedral force constantzdihedral periodicityzdihedral phasezCould not parse dihedrals.zReplacing dihedral %r with %rzimproper force constantzimproper equil. valuecSsg|] }t|qSr&)float)rlwr&r&r( jsz:CharmmParameterSet.read_parameter_file..rtzCMAP resolutionzCould not parse CMAP data.zvdW epsilon termzvdW Rmin/2 termz.Could not parse electrostatic scaling constantz1-4 vdW epsilon termz1-4 vdW Rmin/2 termz NBFIX Eminz NBFIX RminzNBFIX Emin 1-4zNBFIX Rmin 1-4zCould not parse NBFIX terms.z)Atom type %s not present in AtomType list)GrLrXr6strr"r$rp enumeratestripcommentAttributeError startswithr7rarrR IndexErrorr rOr}r{nextrabssceer combining_rule _penaltyrefindallintlowerrKeyErrorrratom_types_strr9rwrruminmaxrrxwarningswarnr penaltyrryrrzrperr^rrIrGrHrr=r>Zimproperextendrr|Z add_nbfixrZ set_lj_paramsr\close)Ir'rcommentsconv own_handlefsectionZ current_cmapZ current_cmap2Zcurrent_cmap_dataZcurrent_cmap_resZnonbonded_typesZ parametersetZdeclared_geometricirWrZread_first_nonbondedwordsrZword_Zdt0ZdiffrKZdtlZdtZpensrr*r9relemratypeZtype1Ztype2rmreqZ bond_typeZtype3theteqZ angle_typeZubkZubeqZubtypeZtype4nphaseZdihedralZreplacedZdtypeZtmprZimpropZholderZtyZtype5Ztype6Ztype7Ztype8resZk1Zk2epsilonrminZeps14Zrmin14Zat1Zat2ZeminZemin14rCr&r&r(rc<s                                                                        "       z&CharmmParameterSet.read_parameter_filec2 s tj}t|tr"d}tt|}nd}|}d}}t}t}t} t} t|} d} d} y x| r| } | dd dkr| y<|dt d| | d }d  }|d t d | | d }Wn t k rtd |YnXy:d }t|d kr|d|d}t|}Wn&t tfk rLtt|}YnXt||||d}||j|j<||j|j<||j|j|jf<nH| dd dkrn.| dd dkr^| tdkrtdtnttdd}xbt||D]T\}}| dkrd}| dr2|}n"| dkrF|}ntd|qWnv| dd dk r| dd }| d }||jkrtd|t || |<|| |<yt d }Wn(t t!fk rtd|YnX|dkrt"|n"|dkr(t#|nds6t$dd} t|} g}g}x*| rv| %} | dd dkr|rj&'|g}n| dd dkrn| d }d  }t d }dkrHt (dd}d }d!}d"krt (d"d}d#kr2(d#d}t)||||||d$} nt*|||d%} |'| +| n| dd& d'kr| d  }d }!|!dkrj,'|n6|!d(kr܈j-'d dntd)| |!fnt|  r| d d*krtd+d,| ddD}xt||D]\}"}#|dkrd}$| d d-krtd }$j.'|"|#|$fqD|"d.r|#_/qD|#d.r|"_/qD|"d/r؈|#_0qD|#d/r|"_0qD1|"|#qDWnb| dd d0kr"nH| dd d1kr<n.| dd& d2krVn| dd3 d4kr,| ddd }%| s|%d5krtd6dd} Pd d&\}"}#}&}'fd7d8t2d&td D}(|(d9})|(d:}*|(d;}+d| dd  d>kr| dd|'d?d,ddDd@d,ddDfn| dd  dAkrPn| dd dBkr0t| dd}x\t||D]N\}}| dkrd}| dr|| |<n| dr|| |<qWn:| dd dCkrtdDdE| ddD}xdt||||D]R\}"}#}&}'j4'|"|#|&|'f|#dd.ks|&dd.ks|'d.krt|"_/qtWn| ddF dGk rR| fdHd,ddD}.fdId8t2dtd D}(t |(dJ}/t |(dK}0t5|.|/|0dL|.d_6n| dd dMk rjPt|} qNW| rj&'|t7|| rqbqb|dk r||<qb|dk rƈ||<qbdsbt$dqbt|} | d7} qbWWnt8k rYnX|j9:|xt;|D]\}| |}1|1dk rhy|j9|1_dS)Oa Reads _only_ the atom type definitions from a topology file. This is unnecessary for versions 36 and later of the CHARMM force field. Parameters ---------- tfile : str Name of the CHARMM topology file to read TFNrrrr!z atom type)rVrWrrEz atom massz"Could not parse MASS section of %s)r9rrrZDECLZDEFArz#DEFA line has %d tokens; expected 5ZNONEZFIRSZLASTzDEFA patch %s unknown)RESIPRESzReplacing residue {}zNo charge for %srrzrestype != RESI or PRESZGROUPrZALPHAg?ZDRUDrZTYPE)r9rTchargealphathole drude_type)r9rTrr5ZDELETEIMPRz7WARNING: Ignoring "%s" because entity type %s not used.)rDOUBLEcSsg|] }|qSr&)r7)rlrr&r&r(rssz9CharmmParameterSet.read_topology_file..rr3r1rZDONORZACCEPTrtZLONEPAIR)ZBISEZRELAzDLONEPAIR type %s not supported; only BISEctor and RELAtive supportedcs.i|]&}t|d|ddqS)r!rr)rr7)rlindex)rr&r( sz9CharmmParameterSet.read_topology_file..ZDISTZANGLrZbisectorZrelativeZICcSsg|] }|qSr&)r7)rlrr&r&r(rscSsg|] }t|qSr&)r)rlrr&r&r(rsrZPATCH)rZIMPHcss|]}|VqdS)N)r7)rlrr&r&r(rnsz8CharmmParameterSet.read_topology_file.. Z ANISOTROPYcsg|] }|qSr&r&)rlr9)rr&r(rscs&i|]}t|d|qS)r!)rr7)rlr)rr&r(rsZA11ZA22)a11a22)rrrzPatch %s not found)?rLrXr6riterr"rrrr7rarrrr r}rrrrrrr9rwrrurrr rresiduesformatr rRr r r~lstripgroupsr^rrrZadd_atomZ delete_atomsZdelete_impropersZ add_bondsheadtailZadd_bondrangeZ lonepairsZ_imprrZ anisotropy _fit_IC_table StopIterationpatchesupdaterZ first_patchZ last_patchr)2r'rrrrZhpatchZtpatchrrZhpatchesZtpatchesrWrVZskip_adding_residuer*r9rrrrittokvalZrestypeZresnamergroupictablerTrrratomZ entity_typer?r@orderZlptype_keywordrArBkeywordsrZthetaZphiZlptypesZlonepairZatomsrrZ patch_namer&)rrr(rbs                           $             &              z%CharmmParameterSet.read_topology_filecCst|tr|}nt|}|\}}}xd|dk r|dk r|}|ddkr`|t|n|ddrz||||\}}}q(WdS)a Reads RTF and PAR sections from a stream file and dispatches the sections to read_topology_file or read_parameter_file Parameters ---------- sfile : str or CharmmStreamFile Stream file to parse Nr!ZrtfZpara) r6r#Z next_sectionrrarbrrrc)r'rrtitlerrrr&r&r(rds    z#CharmmParameterSet.read_stream_filecCs |dkr|dkrtd|dk rnt|tr:t|d}d}n|}d}|d|d||d|rn||dk rt|trt|d}d}n|}d}|d|d |||r||dk rt|trt|d}d}n|}d}|||r|dS) a Write a CHARMM parameter set to a file Parameters ---------- top : str or file-like object, optional If provided, the atom types will be written to this file in RTF format. par : str or file-like object, optional If provided, the parameters will be written to this file in PAR format. Either this or the ``str`` argument *must* be provided str : str or file-like object, optional If provided, the atom types and parameters will be written to this file as separate RTF and PAR cards that can be read as a CHARMM stream file. Either this or the ``par`` argument *must* be provided Raises ------ ValueError if both par and str are None Nz Must specify either par *or* strrTFz4*>>>> CHARMM Topology file generated by ParmEd <<<< z* z5*>>>> CHARMM Parameter file generated by ParmEd <<<< z* ) rRr6rrwrite _write_top_tor _write_par_to _write_str_to)r'rZrYrrZ ownhandler&r&r(rsB              zCharmmParameterSet.writecCs.|d||d|d||dS)z: Private method to write stream items to open file object z/read rtf card * Topology generated by ParmEd * Tz3 read para card * Parameters generated by ParmEd * N)rrr)r'rr&r&r(r=s   z CharmmParameterSet._write_str_tocCsf|r|d|dx:tt|jD](\}\}}|d|d|j|jfq(W|rb|ddS)z< Private method to write topology items to open file object z36 1  zMASS %5d %-6s %9.5f r!z END N)rrrrvr9r)r'rZ write_versionrrrr&r&r(rDs   z CharmmParameterSet._write_top_toc Cstt}}xHt|jD]:\}}x0|D](}|jr>||j|jr(||jq(WqWt|dkspt|dkrxtd|sdn|}|sdn|}| d| |d| dt}x^t|j D]P\}}||krq|||t t || d|d|d|j|jfqW| d t}xjt|jD]\\}}||krPq:|||t t || d |d|d|d |j|jfq:W| d t}xt|jD]z\}}||kr̐q|||t t |xD|D]<} | d |d|d|d |d| jt| j| jfqWqW| dt}xZtt|jdddD]@\}}| d |d|d|d |d|jt|j|jfq\WxHt|jD]:\}}| d |d|d|d |d|jd|jfqW|jr| dt}xt|jD]\}}||kr(q|||t t || d|d|d|d |d|d|d|d|d|jf d} x|jD]x} | r| ddkr| d| |jdkr| dd} n| |jdkr| dd} | d7} | d| qW| dqW| dd||jdkr:dnd fxt|jD]\}}| d!|d"t |j! |j"f|j!|j#kr|j"|j$kr| d#dt |j! ||j"fn| d#dt |j# |j$fqPW| d$d%S)&z= Private method to write parameter items to open file object r!zMixed 1-4 scaling not supportedg?zATOMS Fz BONDS z%-6s %-6s %7.2f %10.4f rz ANGLES z%-6s %-6s %-6s %7.2f %8.2f rz DIHEDRALS z%%-6s %-6s %-6s %-6s %11.4f %2d %8.2f rEz IMPROPERS cSs|dS)Nrr&)rir&r&r(rjxrkz2CharmmParameterSet._write_par_to..)rKz CMAPS z-%-6s %-6s %-6s %-6s %-6s %-6s %-6s %-6s %5d rrr5rrz z %13.6fz z NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac %s wmin 1.5%s rz GEOMr%z%-6s %14.6f %10.6f %14.6fgz%10.6f %10.6f %14.6f z END N)%setrr{raddscnbr}rRpoprrrxrGreversedrmrryrZphi_krrrrHr>r=Zpsi_kZpsi_eqr|Z resolutionZgridrrvrrrZ epsilon_14Zrmin_14) r'rrrrrCtZwrittenrKZtorrrr&r&r(rOs          .    <  60   *      $$z CharmmParameterSet._write_par_to)r%NN)F)NNN)N)NNN)r,r-r.r/rN staticmethodrXr[ classmethodrrrrcrbrdrrrr __classcell__r&r&)rQr(rLUs*   " L # ( ;y 7 rLcCs$x|D]}d|_|_|_qWdS)a Determines cartesian coordinates from an internal coordinate table stored in CHARMM residue topology files Parameters ---------- res : ResidueTemplate The residue template for which coordinates are being determined ictable : list[tuple(atoms, measurements)] The internal coordinate table Notes ----- This method assigns an xx, xy, and xz attribute to ``res``. For the time being, this is just a placeholder, as its functionality has not yet been implemented (CHARMM does not use a 'traditional' Z-matrix, and I don't know of any existing code that will compute the proper cartesian coordinates from the form used by CHARMM) gN)ZxxZxyZxz)rrrr&r&r(rs r):r/Z __future__rrrr_rerrrh collectionsr itertoolsrZ constantsr exceptionsr r Zmodellerr r Z parametersrZperiodic_tablerrZtopologyobjectsrrrrrrrrrrrZutils.iorZ utils.sixrrrZutils.six.movesr Z _charmmfiler"r#compilerobjectr$r:r;rLrr&r&r&r(s>     4    "U