B bm@sdZddlmZmZmZddlmZmZddlm Z ddl Z ddl m Z ddl Z ddl Z ddlZyddlmZWn ek rddlmZYnXddlZddlZdd lmZmZdd lmZmZmZdd lmZdd lmZm Z dd l!m"Z"ddl#m$Z$ddl%m&Z&m'Z'm(Z(m)Z)m*Z*m+Z+m,Z,m-Z-m.Z.m/Z/m0Z0m1Z1m2Z2m3Z3m4Z4m5Z5m6Z6m7Z7m8Z8m9Z9m:Z:m;Z;mZ>m?Z?ddl@mAZBddlCmDZDddlEmFZFmGZGmHZHddlImJZJyRddlKZKyeKLe MdZNWneOk rdZNYnXe MZPe QdZRWn:ek r2ddlSZSeSTZNdZPddlUZUeUVZRYnXeWdZXGdddeYZZeFeGddde$Z[d%ddZ\dd Z]d!d"Z^d#d$Z_dS)&zq This module contains functionality relevant to loading a GROMACS topology file and building a Structure from it )print_functiondivisionabsolute_import) OrderedDict defaultdict)closingN)datetime)letters) ascii_letters)TINY DEG_TO_RAD) GromacsErrorGromacsWarningParameterError)FileFormatType) ParameterSet_find_ureybrad_key) GromacsFile) Structure)AtomBondAngleDihedralImproperNonbondedException ExtraPointBondTypeCmap NoUreyBradley AngleType DihedralTypeDihedralTypeList ImproperTypeCmapType RBTorsionTypeThreeParticleExtraPointFrameAtomType UreyBradleyTwoParticleExtraPointFrameOutOfPlaneExtraPointFrameNonbondedExceptionTypeUnassignedAtomType)element_by_mass AtomicNum)unit)genopen) add_metaclass string_types iteritems)rangeZusernamez\[ (\w+) \]\s*$c@s:eZdZdZdddZdd Zd d Zd d ZddZdS) _Defaultsz= Global properties of force fields as implemented in GROMACS r4no?cCst|dkrtdt|dkr(td|dkr8tdt|dkrLtdt|dkr`td t||_t||_||_t||_t||_dS) N)r4r6z(nbfunc must be 1 (L-J) or 2 (Buckingham))r4r6zcomb_rule must be 1, 2, or 3)yesr7zgen_pairs must be 'yes' or 'no'rzfudgeLJ must be non-negativezfudgeQQ must be non-negative)int ValueErrorfloatnbfunc comb_rule gen_pairsfudgeLJfudgeQQ)selfr>r?r@rArBrD8lib/python3.7/site-packages/parmed/gromacs/gromacstop.py__init__fs       z_Defaults.__init__cCsd|j|j|j|j|jfS)NzL<_Defaults: nbfunc=%d, comb-rule=%d, gen-pairs="%s", fudgeLJ=%g, fudgeQQ=%g>)r>r?r@rArB)rCrDrDrE__repr__xsz_Defaults.__repr__cCsf|dkr|d7}|dkr|jS|dkr,|jS|dkr:|jS|dkrH|jS|dkrV|jStd|dS)Nrr4r6r9zIndex %d out of range)r>r?r@rArB IndexError)rCidxrDrDrE __getitem__}sz_Defaults.__getitem__cCs<|j|jko:|j|jko:|j|jko:|j|jko:|j|jkS)N)r>r?r@rArB)rCotherrDrDrE__eq__s     z_Defaults.__eq__cCs|dkr|d7}|dkr8t|dkr,tdt||_n|dkr`t|dkrTtdt||_nx|dkr|d krxtd ||_nX|d krt|dkrtd t||_n0|d krt|dkrtd||_n td|dS)NrrH)r4r6znbfunc must be 1 or 2r4)r4r6r9zcomb_rule must be 1, 2, or 3r6)r:r7zgen_pairs must be "yes" or "no"r9zfudgeLJ must be non-negativerIzfudgeQQ must be non-negativezIndex %d out of range) r;r<r>r?r@r=rArBrJ)rCrKvaluerDrDrE __setitem__s.       z_Defaults.__setitem__N)r4r6r7r8r8) __name__ __module__ __qualname____doc__rFrGrLrNrPrDrDrDrEr5ds  r5cs eZdZdZeddZd@fdd ZdAdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZddZd d!Zd"d#Zd$d%Zd&d'ZdBd(d)Zd*d+Zd,d-Zd.d/ZdCfd1d2 Zfd3d4ZedDd5d6ZdEd8d9Zed:d;Z dd?Z"Z#S)FGromacsTopologyFilea Class providing a parser and writer for a GROMACS topology file Parameters ---------- fname : str The name of the file to read defines : list of str=None If specified, this is the set of defines to use when parsing the topology file parametrized : bool, optional If True, parameters are assigned after parsing is done from the parametertypes sections. If False, only parameter types defined in the parameter sections themselves are loaded (i.e., on the same line as the parameter was defined). Default is True xyz : str or array, optional The source of atomic coordinates. It can be a string containing the name of a coordinate file from which to fill the coordinates (and optionally the unit cell information), or it can be an array with the coordinates. Default is None box : array, optional If provided, the unit cell information will be set from this variable. If provided, it must be a collection of 6 floats representing the unit cell dimensions a, b, c, alpha, beta, and gamma, respectively. Default is None. Notes ----- If the ``xyz`` argument is a file name that contains the unit cell information, this unit cell information is set. However, the ``box`` argument takes precedence and will override values given in the coordinate file unless it has its default value of ``None``. c Cstt|}x|D]}|dr4|d|d}|s>q|dr|drTq|dr`q|drlq|drxq|drqd St|}|sd S|\}|d kSWd SQRXdS) aT Identifies the file as a GROMACS topology file Parameters ---------- filename : str Name of the file to check if it is a gromacs topology file Returns ------- is_fmt : bool If it is identified as a gromacs topology, return True. False otherwise ;N#z#ifz#definez#includez#undefz#endifF)atoms atomtypesdefaults moleculetypesystem bondtypes angletypes cmaptypes dihedraltypesbondsangles dihedralscmaps molecules exclusionsnonbond_paramsZposition_restraints)rr/ startswithindexstrip _sectionrematchgroups)filenameflineZrematchZsecrDrDrE id_formats0           zGromacsTopologyFile.id_formatNTcsddlm}tt|d|_tdd|_|dk r|||||dk rt |t r||dd}t |drt|j dkrt d||j |_ |dkrt |d r|j|_n||_ |dk r||_|n|dk s|dk rtd dS) Nr) load_filer:)r@T)Z skip_bonds coordinatesz!File %s does not have coordinatesboxz,Cannot provide coordinates/box and NOT a top)parmedrrsuperrUrF parametersetr5rZread isinstancer1hasattrrs TypeErrorrtZunchanger<)rCfnamedefines parametrizeZxyzrtrrro) __class__rDrErFs*      zGromacsTopologyFile.__init__c7 s^ddlm}t}|_t}|_t}t}t} t} t} g} g} |dkr\tdd}t}tt||j g|d}d}x|D]}| }|sq|ddkr|dd }q|d kr.| \}}t |}||krt d |t|f||<| ||_t}t}t} t} t} q|d krLj|||q|d kr|||j\}}j||dk r$j|j|_q|d kr||| j\}}j||dk r$j|j|_q|dkrn|||| j\}}}}j||dk r&j||dk rDj|j|_|dk r$|tk r$j |j |_q|dkr|!|| |q|dkr|"|j}j#|q|dkr||_$q|dkr*| }t%|dkrt d|ddkr t&'dt(d|_)|ddkrd|_*t+||_,q|dkrX| \}}t |}| ||fq|dkr|-|j\} }!j.| j.|!j/q|dkry|0|j|\}"}#Wnt1k rt dYnXj|"j|#j|#_q|dkrDfdd | D}$x$|$ddD]}%|$d2|%q*Wq|d!krh|3|\}&}'|'|j4|&<q|d"kr| }|dd\}(})d#d$|d%d&D\}*}+|*d'9}*|+t5j67t5j89}+|+|*d(f|j9|(|)f<|+|*d(f|j9|)|(f<|j4|(:|)|*d(|+|j4|):|(|*d(|+q|d)krT|;|\}%}"},|,|j|%|"f<|,|j|"|%f<q|d*kr|<|\}%}"}-},}.|,|j|%|"|-f<|,|j|-|"|%f<|.dk r$|.|j |%|"|-f<|.|j |-|"|%f<q|d+kr|=|\}/}0},}1t>t?|/}2|0d,krD|1s|/|j@kr"tA|,g},|,|j@|/<|,|j@|2<n |/|j@kr|j@|/j|,dd-nT|0d.krZ|,|jB|/<n>|0d/krz|,|jC|/<|,|jC|2<n|0d0kr$|,|jD|/<|,|jD|2<q|d1kr|E|\}(})}3}4}5},|,|jF|(|)|3|4|)|3|4|5f<|,|jF|5|4|3|)|4|3|)|(f<q|d2kr|G|\}%}"},|,|jH|%|"f<|jH|"|%f<qW|jI}6WdQRX| s\x| D]}| |dfqDWx| D]\}}||krt d3|||\}|d%krtJ|rt&'d4|t(n&|d%krtJd%rt&'d4|t(|dkrt&'d5|t(|dkr|||d7}n0|dkr0|||d|7}nt d6||fqbW|6|_K|rZ|LdS)7z3 Reads the topology file into the current instance r)gromacsNr4)ZFLEXIBLE)Zincludesr}[r[z#Duplicate definition of molecule %srXraZpairsrbrccmapr\rZr6zToo few fields in [ defaults ]1z.Unsupported nonbonded type; unknown functionalT)r3 geometricreZsettles)Zvirtual_sites3Zdummies3z7Cannot determine vsite geometry without parameter typesrfcsg|]}jt|dqS)r4)rXr;).0w)moleculerDrE vsz,GromacsTopologyFile.read..rYrgcss|]}t|VqdS)N)r=)rxrDrDrE sz+GromacsTopologyFile.read..r9rH gÚ?r]r^r`normal)overrideimproperimproper_periodic rbtorsionr_Z pairtypesz8Structure contains %s molecules, but no template definedz!nrexcl %d not currently supportedz4Detected addition of 0 %s molecules in topology filezCan't add %d %s molecules)MrurrrwdictrerrrGROMACS_TOPDIRrjsplitr;r rappendnrexclZadd_atom _parse_atoms _parse_bondsrXra bond_typeslist _parse_pairsadjusts adjust_types _parse_anglesrb urey_bradleys angle_typesrurey_bradley_types_parse_dihedrals _parse_cmapsrdtitlelenwarningswarnrunknown_functionalcombining_ruler5rZ_parse_settlesextendclaim_parse_vsites3KeyErrorZexclude_parse_atomtypes atom_typesu kilojouleconversion_factor_to kilocalorie nbfix_typesZ add_nbfix_parse_bondtypes_parse_angletypes_parse_dihedraltypestuplereverseddihedral_typesr!improper_typesimproper_periodic_typesrb_torsion_types_parse_cmaptypes cmap_types_parse_pairtypes pair_typesZincluded_files_any_atoms_farther_thanZitpsr~)7rCr|r}r~gmxparamsrerrub_typesr exc_typesZstructure_contentsZmolnamesZproper_multiterm_dihedralsroZcurrent_sectionrpZmolnamerbond bond_typenbenbetangubangtubtrwordsnamenumZbndsZbndtsbZbtrXaattypetypa1a2sigepstcutkeyZkndreplaceZrkeya3a4a5ZitplistrD)rrErxsb                                                                              zGromacsTopologyFile.readc Cs|}y|j|d}Wntk r2d}YnXt|dkr`|dk rV|j}|j}qd}d}n2t|d}|dk r|jdkr|j}n tt|}t|dkrt|dnd}|dkrt |d|d|d }nt ||d|d||d }||d t |d fS) z7 Parses an atom line. Returns an Atom, resname, resnum r4NrrrI)rtypecharge) atomic_numberrrrmassr9r6) rrrrrrr=r-r,rrr;) rCrprrrrrratomrDrDrErs*     z GromacsTopologyFile._parse_atomsc Cs|}t|ddt|dd}}t|d}|dkrPtdtd|_t||||}||_d} t|dkr|dkrdd |d dD\} } | | f|kr|| | f|_ n6t | t j t j dd| t j } | || | f<|_ || fS) z3 Parses a bond line. Returns a Bond, BondType/None rr4r6z#bond funct != 1; unknown functionalTNrHcss|]}t|VqdS)N)r=)rrrDrDrErsz3GromacsTopologyFile._parse_bonds..r9)rr;rrrrrfunctrrrrkilojoule_per_mole nanometer) rCrprrXrijrrrreqkrDrDrErs&"   z GromacsTopologyFile._parse_bondsc Cs|}t|ddt|dd}}t|d}|dkrPtdtd|_t||||}||_d} |dkrt|dkrt |dd } t |d } | | f|kr|| | f|_ n.t | t j | t j|jj} | || | f<|_ || fS) z> Parses a pairs line. Returns NonbondedException, NEType/None rr4r6z$pairs funct != 1; unknown functionalTNrHr9gÚ?rI)rr;rrrrrrrr=rr*r nanometerskilojoules_per_molerZrB) rCrprrXrrrrrrrrrDrDrErs&"    z GromacsTopologyFile._parse_pairscCs|}dd|ddD\}}}t|d} | dkrJtdtd|_d} } } t||||||} | | _| dkrt||||} | d krt |d ks| dkr&t |d kr&d d |dd D\}}||f|kr|||f| _ n6t |t j t jdd|t j} | |||f<| _ | dkrt |d krdd |d d D\}}|dkr||f|kr|||f| _ n6t|t j t jdd|t j} | |||f<| _ nt| _ | | | | fS)z9 Parse an angles line, Returns Angle, UB/None, and types cSsg|]}t|dqS)r4)r;)rrrDrDrEr!sz5GromacsTopologyFile._parse_angles..Nr9)r4rHz*angles funct != 1 or 5; unknown functionalTrHr4rrcss|]}t|VqdS)N)r=)rrrDrDrEr-sz4GromacsTopologyFile._parse_angles..rIr6css|]}t|VqdS)N)r=)rrrDrDrEr5sr)rr;rrrrrrr'rrrrrradiandegreerrr)rCrprrrXrrrrrrrrrtheteqZubreqZubkrDrDrErs<  ,    z!GromacsTopologyFile._parse_anglesc Cs:|}dd|ddD\}}}} t|d} | dksN| dkrt|dkr|||j|||| || dk\} } |j| | dk r|j| |j| _n| dkr| ||||| |j|\} } |j | | dk r|j | |j | _n:| d kr>| ||||| |j|\} }|j | |dk r&|j||j|_n| dkr|j||j||j||j| f}||kr||} ||| d} nPt|} ||} | | _||<|tt|<|j| |j| |j| _nDtd tt|j||j||j||j| } |j| d |_| dk r6| | _dS) z* Processes a dihedrals line, returns None cSsg|]}t|dqS)r4)r;)rrrDrDrErFsz8GromacsTopologyFile._parse_dihedrals..NrI)r4rI rr6r9z3torsions funct != 1, 2, 3, 4, 9; unknown functionalT)rr;r_process_normal_dihedralrXrcrrr_process_improper impropersr_process_rbtorsion rb_torsionsr_process_dihedral_seriesrrrrrrrrr)rCrprZPMDrrrrrlrdihdihtimptrbtrrDrDrErCs\                       z$GromacsTopologyFile._parse_dihedralsc Cs||}dd|ddD\}}}}}t|d} | dkrNtdtd|_t||||||||||} | | _| S)z! Parses cmap terms, returns cmap css|]}t|dVqdS)r4N)r;)rrrDrDrEr|sz3GromacsTopologyFile._parse_cmaps..NrHr4z#cmap funct != 1; unknown functionalT)rr;rrrrrr) rCrprXrrrrrmrrrDrDrErys  $z GromacsTopologyFile._parse_cmapscCstdd|D}|dkr&td|y&dd|D\}dd|D\}}Wntk rhtdYnXy&|\}}} } t| t| } } Wntk rtdYnXtj} td tj| d | | } td tj| d | | } t ||| t ||| t ||| g| | gfS) z? Parses settles line; returns list of Bonds, list of BondTypes cSsg|]}t|ts|qSrD)ryr)rrrDrDrErsz6GromacsTopologyFile._parse_settles..r9z Cannot SETTLE a %d-atom moleculecSsg|]}|jdkr|qS)r)r)rrrDrDrErscSsg|]}|jdkr|qS)r4)r)rrrDrDrErsz"Can only SETTLE water; wrong atomszBad [ settles ] linegAr6) rr r<rr=rrrrr)rCrprXZnatomsoxyhyd1hyd2rrdohdhhZnmZbt_ohZbt_hhrDrDrErs$ z"GromacsTopologyFile._parse_settlescs*|}t|dd}fdd|ddD}t|d}|dkr~t|dt|d}} t|| tkrtdntd |d} || jkrtd t} x|| jD]r} |d| krt | t |df} | j p|j | j | d <|d | krt | j t | jf} | j p|j | j | d <qWx| jD]l}| |jk r@q,|d|ks,|d|kr`q,t |j t |jt |jf} |j p|j| j| d<Pq,WxN|djD]@} |d | krt | j t | jf} | j p|j | j | d<qWtj| |d|d || f| }td|tj}t|| ||fS)z3 Parse vsites3/dummy3 line; returns Bond, BondType rr4csg|]}t|dqS)r4)r;)rr) all_atomsrDrErsz6GromacsTopologyFile._parse_vsites3..rIrHrz&No vsite frames with different weightsz&Only 3-point vsite type 1 is supportedz(Unexpected bond b/w vsite and its parentZdp1r6Zdp2rZd12)rr;r=absr r bond_partnersrra_gettyperrratom1atom2rbatom3rrr%Z from_weightsrr angstromsr)rCrpr rrZvsiterXrrrparentZkwsrrangleZbondlenZbt_vsrD)r rErsJ          z"GromacsTopologyFile._parse_vsites3c CsF|}|d}t|ddkr>|dtkr>d}d}d}d}nxt|ddkrx|dtkrxd}d}t|d }|d}n>d }d}yt|d}d}Wn tk r|d}d}YnXt||}|dkr|dkrtt|}t||d} t||tj } t||dtj } t |d|||| d } | | | d d || fS) z; Parses line from atomtypes section, returns str, AtomType rr9r4rrINrHrr6)rrgÚ?) rrr r;r<r=r-r,rrrr&Z set_lj_params) rCrprrZatnumZsigidxZmassidxrrZchgrrrrDrDrErs:      z$GromacsTopologyFile._parse_atomtypescCsp|}t|dtj}t|ddtjtjd}|ddkrXtdtd|_|d|dt ||fS) z2 Parse bondtypes line. Returns str, str, BondType r9rIr6rz(bondtypes funct != 1; unknown functionalTrr4) rr=rrrrrrrr)rCrprrrrDrDrErs  z$GromacsTopologyFile._parse_bondtypescCs|}t|dtj}t|ddtjtjd}|ddkrd|ddkrdtdtd|_ d }|ddkrt|d }t|d d}|d krt }n(|tj 9}|tjtj d9}t ||}|d |d |dt |||fS)zY Parses angletypes line. Returns str, str, str, AngleType, BondType/None rIrHr6r9r5z.angletypes funct != 1 or 5; unknown functionalTNrrrr4)rr=rdegreesrradiansrrrrrrrr)rCrprthetarrZub0ZcubrDrDrErs"     z%GromacsTopologyFile._parse_angletypesc Cs|}d}d}|ddkr:d}}|dd\}}d} n|dd\}}}}d} d} || dk}|| d k} || d krd }n0|| d krd }n|| dkrtdtd|_|dkr$t|| dtj} t|| dtj} t || d} t | | | d|j j d|j j d}| rd}n|d krt|| dtj}t|| dtjtjdd}t||||g\}}}}t||}np|d kr|dd\}}}}dd|| d| dD\}}}}}}t||||||d|j j d|j j d}||||f|||fS)zA Parse dihedraltypes, returns (str,str,str,str), str, Type, bool Frr6) r2r4r89Z10Z11XNrI)rrrrrrrrr)rrrz!dihedraltypes funct not supportedTr4r9)sceescnbrcss|]}t|tjVqdS)N)r=rr)rrrDrDrErHsz;GromacsTopologyFile._parse_dihedraltypes..r)rrrrrr=rrrr;r rZrBrArsortedr"r$)rCrprrZdtyperrrrZsirphasephi_kperZptyperrc0c1c2c3c4c5rDrDrErsR          $  $ z(GromacsTopologyFile._parse_dihedraltypesc Cs|}|dd\}}}}}t|dt|d}} dd|ddDtj} t| || krltd|| kr|td|||||t|| fS) NrHrrcSsg|] }t|qSrD)r=)rrrDrDrErTsz8GromacsTopologyFile._parse_cmaptypes..rz,CMAP grid dimensions do not match resolutionzOnly square CMAPs are supported)rr;rrrr r#) rCrprrrrrrZres1res2gridrDrDrErOsz$GromacsTopologyFile._parse_cmaptypescCs`|}|dd\}}dd|ddD\}}|tjd9}|tj9}||t|||jjfS)Nr6css|]}t|VqdS)N)r=)rrrDrDrEr_sz7GromacsTopologyFile._parse_pairtypes..r9rHgÚ?)rrrrr*rZrB)rCrprrrZcs6Zcs12rDrDrEr[s  z$GromacsTopologyFile._parse_pairtypesc Cst|||||||||d} d} t|dkrdd|ddD\} } } | | | f|krn|| | | f| _nBt| tj| | tjd|jjd|jj d} | || | | f<| _| | fS)N)rrcss|]}t|VqdS)N)r=)rrrDrDrErmsz?GromacsTopologyFile._process_normal_dihedral..rHr4)rr) rrrr rrrrZrBrA)rCrrXrrrrrimprrr!r"r#rDrDrErhs"    z,GromacsTopologyFile._process_normal_dihedralcCsdd|ddD\}}}t|tj||tjd|jjd|jjd}|dk rb||d}n>t|tj||tjd|jjd|jjd}t}|||S)Ncss|]}t|VqdS)N)r=)rrrDrDrErysz?GromacsTopologyFile._process_dihedral_series..rHrr4)rr) r rrrrZrBrArr!)rCrZdihtyper!r"r#dtZdtlrDrDrErxs        z,GromacsTopologyFile._process_dihedral_seriesc Cst||||||||}d} t|dkrdd|ddD\} }| |f|krd|| |f|_n6t|tjtjdd| tj} | |_|| |f<|| fS)z7 Processes an improper, returns Improper, ImproperType Nrcss|]}t|VqdS)N)r=)rrrDrDrErsz8GromacsTopologyFile._process_improper..rHr6)rrrr"rrrr) rCrrrrrrXrr,rZpsieqrDrDrErs   z%GromacsTopologyFile._process_improperc Cst||||||||}d} t|dkrdd|ddD\} } } } }}| | | | ||f|kr||| | | | ||f|_n`tj}t| || || || |||||d|jjd|jjd} | || | | | ||f<|_|| fS)N css|]}t|VqdS)N)r=)rrrDrDrErsz9GromacsTopologyFile._process_rbtorsion..rHr4)rr) rrrrrr$rZrBrA)rCrrrrrrXrrbrr$r%r&r'r(r)ZkjpmrDrDrErs " z&GromacsTopologyFile._process_rbtorsionc Csj |jdkrtdt|j}dd}x|jD]}|j|j|_q.Wt}x\|jD]P}|j |j krz| |j |j fn| |j |j f|jdk rqTt |j t |j f}||j kr|j ||_d|j_qT|jjdkr|jdkstd|jd kr&t|j j|j j}t|j j|j j}n6|jd kr\t|j j|j j}d |j j|j j}||jj9}t|d ||jj|jd } |j| | |_d|j_qTtdqTW||j |jt} x|jD]} x| j jD]} xx| j jD]l} tt| | j | j | gdkrq| | jks| | j kr$q| | kr>| | | fn| | | fqWqW| jdk rhqt | j t | j f}||j!kr|j!|| _d| j_ntdqWt| |dkr$tddd|jd }|j|d}x2| |D]&\}}|jt"||||d7}qWt#$d|t%t|| dkrNt#$dt|| t%||j!|j!xf|j&D]\}|jdk rxqdt |j t |j t |j'f}||j(kr|j(||_d|j_ntdqdW||j(|j(x^|j)D]T}|jdk rqt*|}||j+kr$|j+||_|jt,k r,d|j_ntdqWx6t-t.t|j)D] }|j)|jt,krF|j)|=qFW||j+|j+x|j/D]}|jdk rqt |j t |j t |j't |j0f}|j1sdt |j t |j'df}t |j t |j t |j'df}dt |j t |j't |j0f}||j2kr:|j2||_d|j_nn||j2kr\|j2||_d|j_nL||j2kr~|j2||_d|j_n*||j2kr|j2||_d|j_ntdn||j3kr|j3||_d|j_nx|d|d|ddfd|d|d|df|d|dddfdd|d|dfgD](}||j3kr"|j3||_d|j_Pq"WtdqW||j2|j2||j3|j2x*|j4D]}|jdk rqt |j t |j t |j't |j0f}dt |j t |j'df}t |j t |j t |j'df}dt |j t |j't |j0f}||j5kr2|j5||_d|j_nn||j5krT|j5||_d|j_nL||j5krv|j5||_d|j_n*||j5kr|j5||_d|j_ntdqW||j5|j5|6x|j7D]}|jdk rؐqt8t9t |j t |j t |j't |j0g}||j:kr(|j:||_d|j_qxnt |j t |j't |j0fD]F}t8t9t |j |ddg}||j:krtqF|j:||_d|j_PqFWtdqW||j:|j:x|j;D]}|jdk rȐqt |j t |j t |j't |j0t |j<f}|d|d|d|d|d|d|d|df}||j=k rJ|j=||_d|j_ntdqW||j=|j=dS) zj Assign parameters to the current structure. This should be called *after* `read` Nzparametrize called before readcSsbtdd|D}xBt|D]6\}}|js,qt||kr:q|t|||qW|dS)Ncss|]}t|VqdS)N)id)rrrDrDrErszPGromacsTopologyFile.parametrize..update_typelist_from..)setr2usedr0addrr)ZptypestypesZ added_typesrrrDrDrEupdate_typelist_froms z=GromacsTopologyFile.parametrize..update_typelist_fromTr:)rlorentzzUnrecognized combining rulerr6g?gÚ?)rz$Not all pair parameters can be foundrIzNot all bond parameters foundrgr4zp%i 1-4 pairs were missing from the [ pairs ] section and were set to zero; make sure you know what you're doing!ziThe [ pairs ] section contains %i exceptions that aren't 1-4 pairs; make sure you know what you're doing!zNot all angle parameters foundz%Not all urey-bradley parameters foundrz Not all torsion parameters foundr6r9z)Not all improper torsion parameters foundz$Not all R-B torsion parameters foundz!Not all improper parameters foundzNot all cmap parameters found)>rw RuntimeErrorcopyrXrr atom_typer1rrrr3r rr2rZr@rAssertionErrormathsqrtepsilonsigmarAr*rBrrrrar rangle_partnersrrrrrrbrrrrrrrr3rcatom4rrrrrupdate_dihedral_exclusionsrrr rrdatom5r)rCrr5rZgmx_pairZpairrrrZpairtypeZtrue_14rZbpiZbpjZ zero_pairtypeZ num_zero_14rrrrrrZwckeyZwckey1Zwckey2ZanchorrrDrDrEr~sp                                                                                 4   zGromacsTopologyFile.parametrizeFcs$tt|||}t|j|_|S)a Makes a copy of the current structure as an instance of a specified subclass Parameters ---------- cls : Structure subclass The returned object is a copy of this structure as a `cls` instance split_dihedrals : ``bool`` If True, then the Dihedral entries will be split up so that each one is paired with a single DihedralType (rather than a DihedralTypeList) Returns ------- *cls* instance The instance of the Structure subclass `cls` with a copy of the current Structure's topology information )rvrUr8rZ)rCclsZsplit_dihedralsr)rrDrEr8szGromacsTopologyFile.copycs0tt||}t|tr|St|j|_|S)z- See Structure.__getitem__ for documentation )rvrUrLryrr8rZ)rCZ selectionstruct)rrDrErLs  zGromacsTopologyFile.__getitem__c Csddlm}|}|r&||}||j|_|j|_|j|_|j|_|j|_|j|_|j|_|j |_ |j |_ |j |_ |j |_ |j |_ |j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|js|js|js|js|js|js|jrtdt|dr(t |j!t"r(|j!|_!nt#}t#}|j rzx2|j D](}|j$dkrXqD|%d|j$j&qDWd|j!_'nx|jD]}|j$dks|j(rqt |j$t)rxj|j$D].} | j*r|%| j*| j+r|%| j+qWn0|j$j*r|%|j$j*|j$j+r|%|j$j+qWt,t#dd |DdkrBt-d t.|}t.|}t,t#d d |Ddkrd|d|j!_/nd |j!_/t,t#d d |Ddkrd|d|j!_0nd |j!_0|jdkrd|j!_1t2j3|dd|_4|S)a Instantiates a GromacsTopologyFile instance from a Structure Parameters ---------- struct : :class:`parmed.Structure` The input structure to generate from copy : bool, optional If True, assign from a *copy* of ``struct`` (this is a lot slower). Default is False Returns ------- gmxtop : :class:`GromacsTopologyFile` The topology file defined by the given struct r)r8z.GromacsTopologyFile does not support Amoeba FFrZNr4r7css|]}d|VqdS)z%.5fNrD)rrrDrDrErsz5GromacsTopologyFile.from_structure..zAStructure has mixed 1-4 scaling which is not supported by Gromacscss|]}d|VqdS)z%.5fNrD)rrrDrDrErsg?css|]}d|VqdS)z%.5fNrD)rrrDrDrErsrr9T)allow_unequal_duplicates)5r8Zjoin_dihedralsrXresiduesrarbrcrrdrrrrrrrrrrrrrtrZtrigonal_anglesZout_of_plane_bendsZ pi_torsionsZ stretch_bendsZtorsion_torsionsZ chiral_framesZmultipole_framesr{rzryrZr5r1rr3Zchgscaler@ ignore_endr!rrrr rrBrAr?rfrom_structurerw) rCrDr8Z_copyZgmxtopZ scee_valuesZ scnb_valuesadjustZdihedralr-rDrDrErHs            z"GromacsTopologyFile.from_structureinlinecBs(ddlm}ddlm}d}d} tj|dd} t|trPd|} t|d }d}nt |d sbt d d} d} |d krx|} nHt|tr|| kr|} qd} t|d } |} nt |d r|} nt d |rd}d}d}|dkr|}nRt|tr|| kr|}nd}t|d }|}n t |d r(|}|j }nt d|dk rt|tr^|dkrt dnVg}xP|D]HtttfddttdDrt d|qhWz@t}|d| ttt|dtjtj dd|tjtj dd|j!d"tj #d$df |sh|d|d|d|j%j&|j%j'|j%j(|j%j)|j%j*f| dk r|d| |s| dtddt+| j,Drd}nd}t-d dt+| j,Drd}nd}| d!|r| d"|r| d#| d$t.j/0t.j1}xxt+| j,D]j\}}| d%||rR| d&|j2|rh| d'|j3| d(|j4|j5|j6d)|j7|fq&W| d*|sT|8rTt9|j:j;}|j:j,<}|d+t.j=0t.j>}xt|?D]h\}}|d|kr|d|kr|d}|d}||9}|d,9}|d-@|d|d|d.|qW| s<|d k r<| jAr$| d/| d0t}t.j=t.jBd10t.j>t.jCd1d1xlt+| jAD]^\}||krΐq|D||DtEtF|| d2|d|djGd)jHfqW| d*| jIr|j%j(d3kr| d4| d5t.j=0t.j>}t.jB0t.jC}t}xlt+| jID]^\}||krq||D||DtEtF|| d6|d|dj6|j7|fq|W| d*| jJr&| d7| d8t}t.j=t.jKd10t.j>t.jKd1d1t.j=t.jBd10t.j>t.jCd1d1} xt+| jJD]\}||krxqb|D||DtEtF|d9|d|d|d1jLjHf}!|| jMkr| jM|}"| |!d:| d;d,|"jG|"jH| fn| |!d| d*qbW| d*| jNr| d<| d=t}t.j/0t.j1d>}#xt+| jND]\}||kr|qf|D||DtEtF|xJD]B}$| |#|d|d|d1|d?d@|$jO|$jPtQ|$jRfqWqfW| d*| jSr| d<| d=t}t.j10t.j/d>}#x~t+| jSD]p\}||krJq4|D||DtEtF|| |#|d|d|d1|d?dAjOjPtQjRfq4W| d*| jT r<| d<| dBdC}#t.j/0t.j1d1xLt+| jTD]>\}| |#|d|d|d1|d?d1jUjVfqW| d*| sL| jW rL| dDt}t.j/0t.j1xt+| jWD]\}||k r qt|D||DtEtF|| dE|d|d|d1|d?|dFjXjXfjXjX}%xTtd|%d)D]D}&| dGtY|&d)|%}'| d"fdHdt|&|'D qW| dI qtW|dk rd|d||dk r|}(d})g}*t}+x|(D]\},}-t|,jZdk r|,jZdj }.|.|+k r|.}/d1}0x6|.|+k rdJ|/|0f}.|0d7}0 qWndK|)}.|)d7})|*|.|+D|.t[\|,||.| |d k qW|s|dL|j] rN||j]n |dM|dI|dNt^dOd|(D}1d}&x|&|1k r x2t_|(D]\}2\},}3|&|3k rP qWt`dP|&|&}4x"|4|1k r|4|3k r|4d7}4 qW|dQ|*|2|4|&f|4}& qWnt|t r|dk rt[\||dR| |d k|s|dL|j] rh||j]n |dM|dI|dN|dQdSn\|}(t^dTd|(D}5t9}6x*|(D]"\}7}-x|-D]}&|7|6|&< qW qWg}8xp|D]f}9tatQ}:g};xr|9D]j}ntee|;d}>xxt_|;D]l\}&}=|&dk rԐ qtd|=|:k r|:td|=dk st`|:td|=dkr |>|=|:td|=7}>n|>|=7}> qW|8|>|9dt|9f|5t|9d8}5 qW|8jfdVdWdXg}?tat}:d}@d}Axt|5D]}&|&|A}4|@t|8kr|8|@d|4kr|?|8|@dt|&gg|A|8|@d1d7}A|@d7}@nft|:td|6|4dkr@|:td|6|4D|&|?|6|4|:td|6|4gn|:td|6|4D|&qWd})g}*t}+x|?D]\},}-t|,jZdkr|,jZdj }.|.|+kr|.}/d1}0x6|.|+krdJ|/|0f}.|0d7}0qWndK|)}.|)d7})|*|.|+D|.t[\|,||.| |d kqpW|s|dL|j]r4||j]n |dM|dI|dNt^dYd|?D}1d}&x|&|1krx2t_|?D]\}2\},}3|&|3kr~Pq~Wt`dP|&|&}4x"|4|1kr|4|3kr|4d7}4qW|dQ|*|2|4|&f|4}&qjWWd|r|g| r| g|r"|gXdS)ZaY Write a Gromacs Topology File from a Structure Parameters ---------- dest : str or file-like The name of a file or a file object to write the Gromacs topology to combine : 'all', None, or list of iterables, optional If None, no molecules are combined into a single moleculetype. If 'all', all molecules are combined into a single moleculetype. Otherwise, the list of molecule indices (start from 0) will control which atoms are combined into single moleculetype's. Default is None parameters : 'inline' or str or file-like object, optional This specifies where parameters should be printed. If 'inline' (default), the parameters are written on the same lines as the valence terms are defined on. Any other string is interpreted as a filename for an ITP that will be written to and then included at the top of `dest`. If it is a file-like object, parameters will be written there. If parameters is the same as ``dest``, then the parameter types will be written to the same topologyfile. molfile : None or str of file-like object, optional If specified as other than None, the molecules will be written to a separate file that is included in the main topology file. The name of this file will be the provided srting. If None or the same as the ``dest'', the molecules will be written into the body of the topology file. If it is a file-like object, the molecules will be written there. Using this option can make it easier to combine multiple molecules into the same topology. This will change where the following topology sections are written: moleculetype, atoms, bonds, pairs, angles, dihedrals, cmap, settles, virtual_sites2, virtual_sites3 and exclusions. itp : bool, optional If True the following topology sections are not written: defaults, atomtypes, nonbond_params, bondtypes, pairtypes, angletypes, dihedraltypes, cmaptypes, system and molecules Thus only the individual molecules will be written in a stand-alone fashion, i.e. an itp-file. If True the molfile parameter will be set to None Raises ------ ValueError if the same molecule number appears in multiple combine lists TypeError if the dest input cannot be parsed ValueError if the combine, parameters, or molfile input cannot be parsed rN) __version__FT)rEz%s rwritez,dest must be a file name or file-like objectrJz?parameters must be "inline", a file name, or a file-like objectz9molfile must be "top", a file name, or a file-like objectallz/combine must be None, list of indices, or "all"c3s&|]}|d|dkVqdS)r4NrD)rr)indicesrDrErsz,GromacsTopologyFile.write..r4z#Can only combine adjacent moleculesz; ; File %s was generated ; By user: %s (%d) ; On host: %s ; At date: %s ; ; This is a standalone topology file ; ; Created by: ; ParmEd: %s, VERSION %s ; Executable: %s ; Library dir: %s ; Command line: ; %s ; z%a. %B %w %X %Y Zunicode_escapezutf-8z [ defaults ] z@; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ z#%-15d %-15d %-15s %-12.8g %-12.8g z#include "%s" z[ atomtypes ] css|]\}}|jdk VqdS)N)Z _bond_type)rrrrDrDrErscss|]\}}|jdkVqdS)rN)r)rrrrDrDrErsz ; name z bond_type z at.num z)mass charge ptype sigma epsilon z%-7s z%-8s z%8d z %10.6f %10.8f A %14.8g %14.8g r z[ nonbond_params ] g?z{0} {1} 1 {2} {3} gÚ?z[ bondtypes ] z$; i j func b0 kb r6z%-5s %-5s 1 %.5f %f r7z[ pairtypes ] zF; i j func sigma1-4 epsilon1-4 ; ; THESE ARE 1-4 INTERACTIONS z%-5s %-5s 1 %.9f %.9f z[ angletypes ] z<; i j k func th0 cth rub kub z'%-5s %-5s %-5s %%d %12.7f %12.7frHz %12.7f %12.7f z[ dihedraltypes ] z.;i j k l func phase kd pn z+%-6s %-6s %-6s %-6s %d %.2f %.6f %d r9rrIz/; i j k l func q0 cq z(%-6s %-6s %-6s %-6s %d %.6f %.6f z[ cmaptypes ] z&%-6s %-6s %-6s %-6s %-6s 1 %4d %4drz\ c3s |]}tj|VqdS)N)strr+)rr)convparamrDrErGsz z%s%dzsystem%dz[ system ] ; Name z Generic titlez%[ molecules ] ; Compound #mols css|]}t|dVqdS)r4N)r)rrrDrDrErlsz"Could not find molecule %d in listz %-15s %6d r\)r\r4css|]}t|dVqdS)r4N)r)rrrDrDrErszMolecule ID out of rangecSs|dS)Nr4rD)rrDrDrEz+GromacsTopologyFile.write..)rcss|]}t|dVqdS)r4N)r)rrrDrDrErs)hZparmed.gromacsrrurKrrHryr1r/rzr{rjr<rlowerr r1anyr3rrrnowrM _username_userid_unameZstrftimeospathrsysargvrjoinencodedecoderZr>r?r@rArBr2rrNr kilocaloriesr kilojoulesrrrrr>r=Z has_NBFIXrrwrkeysrritemsformatrangstromrr3rrrrrrrrrrr!r"r;r#rrpsi_eqpsi_krZ resolutionminrFrU_write_moleculersum enumerater:rrrJr0r8sortclose)BrCdestZcombineZ parametersZmolfileZitprrKZ own_handler|rZown_parfile_handleZinclude_parfileZparfileZown_molfile_handleZinclude_molfileZ_molfileZ combine_listsrYZprint_bond_typesZ print_atnumeconvrr9ZtypemapZtypes_in_systemZeps_conversionvalrrZ used_keyslconvZbconvpartrZfmtr-r*rendreZsysnumnamesZnamesetrrrZorigZsfxZ total_molsrZlstZiiZnmolsZ moleculedictrZcombined_moleculesZclZcountsZ mols_in_molZmolidZmolZcombmolZ new_moleculesZcmcr3rD)rSrOrTrErMs-                                       $                   $                                       $              zGromacsTopologyFile.writec-Cs|d|d||jf|d|dd}x|jD]}|d|jd|j|jtdd |DfxR|D]J}||j7}|d |jd|j|jd|j|j|jd|j|j|f qvWq>W|d d d |j D}d} t |j t |dkrDy.dd |j D\} dd |j D\} } d} Wnt k rBYnX|j rzt jt jdt jt jdd} | r|d|d|ddx|j D]}t|jtst|jtrƐq|d|jjd|jjd|jf|jdkr|d qt|jt|jf}|s>||jks>|j|j|kr`|d|jjd|jj| f|d qW|d |jrz|d|ddt jt j}t jt j}x|jD]}t|jt|jf}|d|jjd|jjd|jf|j j!dkr\|s.||j"ks.|j|j"|kr\|jdk r\|d|jj#||jj$|f|d qW|d n |j%r|d|dd|&t jt j}t jt j}x|j%D]}|j's|j(rސq|j|j)}}||j*ks||j+krq|d|jd|jddf|j j!dkrj|dd|j,|j,|t-.|j/|j/|f|d qW|d |j0r>t jt j1dt jt j1dd} t jt jdt jt jdd}|d |d!d"x@|j0D]4}|d#|jjd|jjd|j2jd|jf|jdkrJ|d qt|jt|jt|j2f}|j34||jk}|jd$krx4|j5D]&}|j|kr|j2|kr|j}PqWt6}|o|j74||k}|s|s$|d%|jj8|jj| f|jd$kr$|d&|jd|j|f|d qW|d |j%r$|d'|d(d)|d t jt j} x|j%D]}|d*|jjd|jjd|j2jd|j)jd|jf|jdkr|d q|j(r|j9}n|j:}t|jt|jt|j2t|j)f}|s6||ks6t;|j||r t|jt<r|d+|jdj=|jdj>| t?|jdj@fx|jddD]T}|d,|jjd|jjd|j2jd|j)jd|j|j=|j>| t?|j@fqWn(|d-|jj=|jj>| t?|jj@f|d qW|d |jA rn|d'|d(d)|d t jt j} d.}x|jAD]}|d*|jjd|jjd|j2jd|j)jd|jf|jdkr|d qjt|jt|jt|j2t|j)f}| s ||jBk s |jB||jkrj|||jjC| |jjD| |jjE| |jjF| |jjG| |jjH| f|d qjW|d |jI r8|d'|d/d0|d t jt jd} x|jID]x}|d*|jjd|jjd|j2jd|j)jd|jf|jdk r |d  q|d1|jjJ|jjK| f qW|d |jL r|d2|d3d4xT|jLD]J}|d5|jjd|jjd|j2jd|j)jd|jMjd|jf q`W| r|d6|d7|d8x8| j D].}| |k r|jdk rd9n |jjd} P qWx| j D].}| |k r|jdk r2d:n |jjd}!P qWxb| j0D]P}"| |"k rN| |"k rN|"jj8tN}#t-.d| | d| | t-O|#}!P qNWtPd;|d<| |!f| rxtQd=d |D}$x|$D]}%|%tRk rp|d>|d?x`|D]X}&t|&jS|% s q|&jST\}}|d@|&jd|jd|jdd|&Udf qW|d  q|%tVtWfk r|dA|dBx|D]}&t|&jStV r|&jST\}}}'|&jSU\}(})}*|dC|&jd|jd|jd|'jdd|)|*fnbt|&jStW r|&jST\}}}'|&jSU\})}*}+|dD|&jd|jd|jd|'jd|)|*|+f qW|d  qW| s| r|dExtX|j D]r\},}|dF|,dx$|j*D]}"|dG|"jd qWx$|j+D]}"|dG|"jd qW|d  qW|d dS)HNz+ [ moleculetype ] ; 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