B by@sdZddlmZddlmZddlmZmZmZm Z m Z m Z m Z m Z mZmZmZmZmZddlmZmZmZddlmZmZddlmZdd lmZdd lmZm Z dd lm!Z!dd l"Z"dd l#Z#d dZ$Gddde%Z&Gddde'Z(e")da*GdddeZ+ddZ,ddZ-d S)z Provides a Python class for parsing a PSF file and setting up a system structure for it Author: Jason M. Swails Contributors: Date: April 20, 2014 )division)copy) BondAngleDihedralImproper AcceptorDonorGroupCmap UreyBradley NoUreyBradleyAtom DihedralType ImproperTypeUnassignedAtomType) CharmmError CharmmWarningParameterError) needs_openmm Structure)genopen)wraps)ziprange) string_typesNcstfdd}|S)zt Protects a function from raising an index error, and replace that exception with a CharmmError instead c s>y ||Stk r8}ztd|Wdd}~XYnXdS)z Catch the index error zArray is too short: %sN) IndexErrorr)argskwargse)func0lib/python3.7/site-packages/parmed/charmm/psf.pynewfuncs z!_catchindexerror..newfunc)r)r r#r!)r r"_catchindexerrorsr$c@seZdZdZdS)_FileEOFz For control flow N)__name__ __module__ __qualname____doc__r!r!r!r"r%'sr%c@seZdZdZddZdS) _ZeroDicta1 Contains a dict that returns dummy (zero) arguments when a key is not present rather than raising a KeyError. The return value for non-existent items is (0, []). It also special-case sections that have multiple pointers to avoid index errors if those are not present in the PSF file cCsy t||Stk r|drVx"|D]}|dr,t||Sq,WddggfS|drx"|D]}|drft||SqfWddggfSdgfSXdS)NZNGRPrZNUMLP)dict __getitem__KeyError startswith)selfkeykr!r!r"r,1s         z_ZeroDict.__getitem__N)r&r'r(r)r,r!r!r!r"r**sr*z(-?\d+)([a-zA-Z]*)cseZdZdZeddZeddZeddZe dd d Z edd d Z ddZ e dfdd ZdddZddZZS) CharmmPsfFilea4 A chemical :class:`Structure` instantiated from CHARMM files. Parameters ---------- psf_name : str, optional Name of the PSF file (it must exist) Raises ------ IOError : If file ``psf_name`` does not exist CharmmPsfError : If any parsing errors are encountered cCs2y||Stk r,td||fYnXdS)a Converts a string to a specific type, making sure to raise CharmmError with the given message in the event of a failure. Parameters ---------- string : str Input string to process type : type Type of data to convert to (e.g., ``int``) message : str Error message to put in exception if failed zCould not convert %s [%s]N) ValueErrorr)stringtypemessager!r!r"_convertSszCharmmPsfFile._convertcs|d|d}||ddd}d|krN|d|d}t|dkrn|dtd}ntfdd|D}||fS)N!:rpointercsg|]}|tdqS)r;)r7int).0w)clsr!r" ssz7CharmmPsfFile._parse_psf_title_line..)indexsplitstripupperlenr7r<tuple)r?linewordstitlepointersr!)r?r"_parse_psf_title_lineis z#CharmmPsfFile._parse_psf_title_linecs |}x"|s*|s tdq |}q Wd|krD|\}}ntd|}|s|dr|}d|kr|\}}|}g}|dks|dkrxV|r|||}qWn6x4|r|}|fdd|D|}qW|||fS) a This method parses a section of the PSF file Parameters ---------- psf : file Open file that is pointing to the first line of the section that is to be parsed Returns ------- title : str The label of the PSF section we are parsing pointers : (int/tuple of ints) If one pointer is set, pointers is simply the integer that is value of that pointer. Otherwise it is a tuple with every pointer value defined in the first line data : list A list of all data in the parsed section converted to integers zUnexpected EOF in PSF filer8z!Could not determine section titleZNNBNATOMNTITLEcsg|]}|tdqS)zPSF data)r7r<)r=r>)r?r!r"r@sz4CharmmPsfFile._parse_psf_section..) readlinerCr%rKrr.appendrBextend)r?psfrGrIrJdatarHr!)r?r"_parse_psf_sectionxs0       z CharmmPsfFile._parse_psf_sectionNc.Cs~t||dkrdSt|tr0t|d}d}n|}d}z.t|trJ|nd|_|}|dsrtd| | dd}|t }xt||D]0\} }|jt |j!| d|j!|dqW||dd td}t|dd|dkrtd t|dd|ft|dd}xZt|||D]J\} }}|j"t#|j!| d|j!|d|j!|dd|j"d!_$q"W||d"d td#}t|d"d|dkrtd$t|d"|ft|d"d}x^t||||D]L\} }}}|j%t&|j!| d|j!|d|j!|d|j!|dqWd|j%_ ||d%d td&} t|d%d| dkr|td't|d%d| ft|d%d}x^t||||D]L\} }}}|j't(|j!| d|j!|d|j!|d|j!|dqW||d(d td)}!t|d(d|!dkr8td*t|d(d|!ft|d(d}x>t||D]0\} }|j)t*|j!| d|j!|dqTW||d+d td,}"t|d+d|"dkrtd-t|d+d|"ft|d+d}x>t||D]0\} }|j+t*|j!| d|j!|dqWy|d.d \}#}$Wntk rVtd/YnX|d.d}%|$|j_,t|d.d|#dkrtd0t|%|#ft|d.d}x6t|||D]&\} }}|jt-|j!| ||qW|d1d}%t.|j!d2d3|j!D}&t|%t|j!kr^|&|%kr2t/0d4t1|d5d \}'}(|'d ksV|(d kr^t2d6||d7d td8})t|d7d|)dkrtd9t|d7|)ft|d7d}xt||||||||D]\} }}}}*}+},}-|j3t45|j!| d|j!|d|j!|d|j!|d|j!|*d|j!|+d|j!|,d|j!|-dqW|6||_7Wd|rx|8XdS):zp Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data. NrTFZPSFz'Unrecognized PSF file. First line is %sr9rMrLrnatomzNonsequential atoms detected!rz%Could not interpret residue number %szresidue numberzpartial chargez atomic mass)namer5chargemass)chaininscodesegidZNBONDznumber of bondszGot %d indexes for %d bondsZNTHETAznumber of angleszGot %d indexes for %d anglesZNPHIznumber of torsionszGot %d indexes for %d torsionsZNIMPHIznumber of improperszGot %d indexes for %d impropersZNDONznumber of donorszGot %d indexes for %d donorsZNACCznumber of acceptorszGot %d indexes for %d acceptorsz NGRP NST2zCould not unpack GROUP pointerszGot %d indexes for %d groupsZMOLNTcSsg|] }|jqSr!)marked)r=ar!r!r"r@Esz*CharmmPsfFile.__init__..zDDetected PSF molecule section that is WRONG. Resetting molecularity.z NUMLP NUMLPHzQCannot currently handle PSFs with lone pairs defined in the NUMLP/NUMLPH section.ZNCRTERMzNumber of cross-termsz%Got %d CMAP indexes for %d cmap terms)9r__init__ isinstancerrr]rNr.rrCrBr*r2rSr%rIr7r<r_resrematchgroupsr3floatrpropsZadd_atomrEiterrbondsrOratomsanglesrZfunct dihedralsr impropersrdonorsr acceptorsnst2r set_moleculeswarningswarnrNotImplementedErrorcmapsr ZextendedZunchangeflagsclose).r/Zpsf_nameZfileobjZ own_handlerGZ psf_flagsZ psfsectionsZsecZptrrRrVirHZatidrbZrematchZresidraZresnamer]Zattyper^r_rlatomZnbonditjZnthetar1ZnphilZnimphiZndonZnaccZngrprutmpZ molecule_listZnumlpZnumlphZncrtermmnopr!r!r"rfs          ,,$$&&     ,$ zCharmmPsfFile.__init__FcCsddlm}|jsF|jsF|jsF|jsF|jsF|jsF|jsF|j sF|j dkrNt d|rZt |}|}|j |_ |j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_|j|_x4|j D]*}||j|_|jt k r||jj!|j_!qW|jsx^|jD]T}t"dd|D}|dkrh|j#t$|dddn|j#t$|dd dq.Wd|j_%|S) ay Instantiates a CharmmPsfFile from an input Structure instance. This method makes sure all atom types have uppercase-only names Parameters ---------- struct : :class:`parmed.structure.Structure` The input structure to convert to a CharmmPsfFile instance copy : bool, optional If True, a copy of all items are made. Otherwise, the resulting CharmmPsfFile is a shallow copy Returns ------- psf : :class:`CharmmPsfFile` CHARMM PSF file Raises ------ ValueError if the functional form is not recognized or cannot be implemented through the PSF and parameter/stream files Notes ----- If copy is False, the original object may have its atom type names changed if any of them have lower-case letters r) _typeconvrWz*Unsupported functional form for CHARMM PSFcss|] }|jVqdS)N)r^)r=rer!r!r" sz/CharmmPsfFile.from_structure..g-C6?r9r)&Zparmed.charmm.parametersrZ rb_torsionsZtrigonal_anglesZout_of_plane_bendsZ pi_torsionsZ stretch_bendsZtorsion_torsionsZ chiral_framesZmultipole_framesZnrexclr3_copyroZresiduesrnrp urey_bradleysrqrrrtrsrjrz bond_types angle_typesurey_bradley_typesdihedral_typesimproper_types cmap_typesr5 atom_typerr]sumrOr ru)r?ZstructrZtypeconvrQr~ZresidueZchgr!r!r"from_structureesN           zCharmmPsfFile.from_structurecCs|jS)N)r])r/r!r!r"__str__szCharmmPsfFile.__str__cs$|dk r||tt|j||S)a Creates an OpenMM System object from the CHARMM PSF file. This is a shortcut for calling `load_parameters` followed by Structure.createSystem. If params is not None, `load_parameters` will be called on that parameter set, and Structure.createSystem will be called with the remaining args and kwargs Parameters ---------- params : CharmmParameterSet=None If not None, this parameter set will be loaded See Also -------- :meth:`parmed.structure.Structure.createSystem` In addition to `params`, this method also takes all arguments for :meth:`parmed.structure.Structure.createSystem` N)load_parameterssuperr2 createSystem)r/Zparamsrr) __class__r!r"rs zCharmmPsfFile.createSystemTc Cs(|r t|}|j|_x~|jD]t}y.t|jtr<|j|j}n|j|j}Wn"t k rpt d|jYnX||_ t |j |_|j |_ qWxl|jD]b}t|jj|jjt|jj|jjf}y|j||_Wn t k rt d|YnXd|j_qW|jdd=x>|jD]4}|jjr(qd|j_|j|j|j|j_qW|jdd=x|jD]}t|jj|jj|jjt|jj|jjf}yN|j||_d|j_|j|}|tk rt|j|j|} |j| d|_Wn"t k rt d|YnXqbW|jdd=|jdd=x>|jD]4} | jjr:q(d| j_|j| j|j| j_q(Wx>|jD]4}|jjrzqhd|j_|j|j|j|j_qhWt} x|jD]} | j| j| j| j f\} } }}| j| j|j|jf}||j!krd| j|jdf}||j!krt d| |j!|| _d| j_| jj"| j j"f}| j| j j#ksZ| j| j j$krbd| _%n2|| krtd| _%n | &|| &| j j"| jj"fqW|j!dd=x>|jD]4}|jjrqd|j_|j!|j|j!|j_qWxj|j'D]`}|jj|jj|jj|j jf\} } }}|(| | |||_|jdkrDt d | | ||d|j_qW|j)dd=x|j'D]z}|jjrxqfd|j_t|jt*r|j)|j|j)|j_n6t|jt+r|j!|j|j!|j_ndsft,d qfWxpt-t.t/|j'D]Z}t|j'|jt+r|j'0|}t1|j|j|j|j dd|jd } |2|j| qWx|j3D]v}|jj|jj|jj|j j|jj|jj|j j|j4jf}y|j5||_Wn"t k rt d |YnXd|j_q^W|j5dd=x>|j3D]4}|jjrqd|j_|j5|j|j5|j_qWdS) a) Loads parameters from a parameter set that was loaded via CHARMM RTF, PAR, and STR files. Parameters ---------- parmset : :class:`CharmmParameterSet` List of all parameters copy_parameters : bool, optional, default=True If False, parmset will not be copied. WARNING: ------- Not copying parmset will cause ParameterSet and Structure to share references to types. If you modify the original parameter set, the references in Structure list_types will be silently modified. However, if you change any reference in the parameter set, then that reference will no longer be shared with structure. Example where the reference in ParameterSet is changed. The following will NOT modify the parameters in the psf:: psf.load_parameters(parmset, copy_parameters=False) parmset.angle_types[('a1', 'a2', a3')] = AngleType(1, 2) The following WILL change the parameter in the psf because the reference has not been changed in ``ParameterSet``:: psf.load_parameters(parmset, copy_parameters=False) a = parmset.angle_types[('a1', 'a2', 'a3')] a.k = 10 a.theteq = 100 Extra care should be taken when trying this with dihedral_types. Since dihedral_type is a Fourier sequence, ParameterSet stores DihedralType for every term in DihedralTypeList. Therefore, the example below will STILL modify the type in the :class:`Structure` list_types:: parmset.dihedral_types[('a', 'b', 'c', 'd')][0] = DihedralType(1, 2, 3) This assigns a new instance of DihedralType to an existing DihedralTypeList that ParameterSet and Structure are tracking and the shared reference is NOT changed. Use with caution! Notes ----- - If any dihedral or improper parameters cannot be found, I will try inserting wildcards (at either end for dihedrals and as the two central atoms in impropers) and see if that matches. Wild-cards will apply ONLY if specific parameters cannot be found. - This method will expand the dihedrals attribute by adding a separate Dihedral object for each term for types that have a multi-term expansion Raises ------ ParameterError if any parameters cannot be found zCould not find atom type for %szMissing bond type for %rFNTzMissing angle type for %rXz#No dihedral parameters found for %rz'No improper type for %s, %s, %s, and %szShould not be here)improper ignore_endr5zNo CMAP parameters found for %r)6rZcombining_rulerorgr5r<Zatom_types_intZatom_types_strrDr-rrstrZ atomic_numberrnminZatom1Zatom2maxrZusedrOlistrrpZatom3rrr r setrqZatom4ridx bond_partnersZangle_partnersraddrrZmatch_improper_typerrrAssertionErrorreversedrrEpoprdeleterzZatom5r)r/ZparmsetZcopy_parametersr~ZatypeZbondr0ZangZubtZubZactive_dih_listZdihZa1Za2Za3Za4ZpairZdihedralimprr}Zcmapr!r!r"rs@                               $           zCharmmPsfFile.load_parameterscCs|jdd=dS)zD Clear the cmap list to prevent any CMAP parameters from being used N)rz)r/r!r!r" clear_cmapszCharmmPsfFile.clear_cmap)N)F)N)T)r&r'r(r) staticmethodr7 classmethodrKrSr$rfrrrrrr __classcell__r!r!)rr"r2Es    ; 2 L Or2cCsddlm}m}|tt|||g}d}xLtt|D]<}||jsB|g}t||||| | ||d7}qBW|S)zN Correctly sets the molecularity of the system based on connectivity. r)setrecursionlimitgetrecursionlimitr9) sysrrrrEZunmarkrrd _set_ownersortrO)rorrownerZmolecule_numberr}rr!r!r"rvs    rvcCsV|||_xF||jD]8}|js<||jt|||j||j|kstdqWdS)zB Recursively sets ownership of given atom and all bonded partners zAtom in multiple molecules!N)rdrrOrrr)roZ owner_arrayZatmZmol_idZpartnerr!r!r"rs   r).r)Z __future__rrrZtopologyobjectsrrrrr r r r r rrrr exceptionsrrrZ structurerrZutils.iorZ utils.sixrZutils.six.movesrrrrerwr$ Exceptionr%r+r*compilerhr2rvrr!r!r!r"s,  <    c(