B b@sdZddlmZmZddlmZddlmZddlZddl Z ddl Z ddl Z ddl m Z dd lmZdd lmZmZmZdd lmZdd lmZdd lmZddlmZddlmZmZmZddl m!Z!m"Z"m#Z#m$Z$m%Z%ddl&m'Z'ddl(m)Z)m*Z*m+Z+m,Z,ddl-m.Z.e,rddlm/Z/n ddl0m/Z/e1dddZ2e 3de2Z4e 3de2Z5e 3de2Z6e 3de2Z7e 3de2Z8e 3de2Z9e 3de2Z:e 3dZ;e 3d e2e j<Z=e 3d!e2e j<Z>e 3d"e2e j<Z?[2d#d$Z@e)eGd%d&d&eZAdS)'z This module contains classes for parsing and processing Amber parameter files. Author: Jason M. Swails Contributors: Date: Aug. 11, 2015 )divisionprint_function) defaultdict)closingN)AmberOFFLibrary)TINY)ParameterError AmberWarningParameterWarning)ResidueTemplateContainer)Mol2File)FileFormatType) ParameterSet)Masselement_by_mass AtomicNum)AtomTypeBondType AngleType DihedralTypeDihedralTypeList)genopen) add_metaclass string_types iteritemsPY2)map)Sequencez([+-]?(?:\d+(?:\.\d*)?|\.\d+))z(".+?"|'.+?'|[\S]*))ZFLOATREZ FILENAMEREz'(..?)-(..?)\s+%(FLOATRE)s\s+%(FLOATRE)sz-(..?)-(..?)-(..?)\s+%(FLOATRE)s\s+%(FLOATRE)szO(..?)-(..?)-(..?)-(..?)\s+%(FLOATRE)s\s+%(FLOATRE)s\s+%(FLOATRE)s\s+%(FLOATRE)sz8\s*%(FLOATRE)s\s+%(FLOATRE)s\s+%(FLOATRE)s\s+%(FLOATRE)szSCEE=\s*%(FLOATRE)szSCNB=\s*%(FLOATRE)szA(..?)-(..?)-(..?)-(..?)\s+%(FLOATRE)s\s+%(FLOATRE)s\s+%(FLOATRE)sz=({\s*["']([\w\+\-]+)["']\s*["'](\w+)["']\s*["'](\w+)["']\s*})z loadamberparams\s+%(FILENAMERE)szloadoff\s+%(FILENAMERE)sz((\S+)\s*=\s*loadmol[23]\s*%(FILENAMERE)scCsddlm}t|dkr@|d|dhdhdhfkr@|dd}tj|rP|Stj|dd}tjtj|d |rtj|d |Stjtj|d |rtj|d |S|rtjtj|d d |rtj|d d |Std |d S)z Finds an Amber file. Looks in the current directory, then the following locations: - $AMBERHOME/dat/leap/lib - $AMBERHOME/dat/leap/parm r) AMBERHOMEr"'ZdatZleaplibparmZoldffzCannot find Amber file [%s]N)Z parmed.amberr lenospathexistsjoin ValueError)fname search_oldffr Zleapdirr.6lib/python3.7/site-packages/parmed/amber/parameters.py_find_amber_file7s (  r0cseZdZdZeddZfddZed$ddZefd d Z d d Z d dZ ddZ ddZ ddZddZddZddZddZd%ddZd&d"d#ZZS)'AmberParameterSetas Class storing parameters from an Amber parameter set Parameters ---------- filenames : str, list of str, file-like, or list of file-like; optional Either the name of a file or a list of filenames from which parameters should be parsed. Notes ----- Order is important in the list of files provided. The parameters are loaded in the order they are provided, and any parameters that are specified in multiple places are overwritten (that is, the *last* occurrence is the parameter type that is used) See Also -------- :class:`parmed.parameters.ParameterSet` c Cs4tt|d}||}|s\x|rB|sB|}q,W|sLdS|dkr\dS|dkrldS|}t|dkrdSt|ddkrdSyt|ddStk rYnXyt|dWntk rdSXyt|dWnt tfk rt|ddkr|dd r^|dd r|dd |dd }|t krtt |t|ddkr|ddkrtt dt|ddkrdS|ddkrdSnB|t kr\|dt kr tt |dt|ddkr dSdSnJ|dd }|t krNtt |t|ddkrNdS|t krdSnB|dd }|t krtt |t|ddkrdSndSnB|dd }|t krtt |t|ddkrdSndSYnXt|d kr"yt|d dStk rdSXndSWd QRXd S) aT Identifies the file type as either an Amber-style frcmod or parm.dat file. Parameters ---------- filename : str Name of the file to check format for Returns ------- is_fmt : bool True if it is an Amber-style parameter file. False otherwise. rF)MASSBONDANGLEANGLDIHEDIHEDDIHEDRALIMPRIMPROPIMPROPERNONBNONBONNONBOND NONBONDEDTrrrCN)rrreadlinestriprstripsplitr&floatr+ IndexErrorisalphaupperlowerrabs)filenameflinewordskeyr.r.r/ id_formatgs       (, 0(     zAmberParameterSet.id_formatcstt|d|_d|_g|_x|D]}t|tr^t |rR|j t |q| |q&t|trx@|D],}t |r|j t |qn| |qnWq&| |q&WdS)Ng333333?g@)superr1__init__Z default_sceeZ default_scnbtitles isinstancerrrRresiduesupdateparseload_parametersr)self filenamesrMr,) __class__r.r/rTs       zAmberParameterSet.__init__FcCs|}t|tr t|d}d}n|}d}dd}|tdd|}d|}|rX||} d d } x|D]} | d d } t | r| t | d }| t ||qnt | r| t | d }|j tt ||qnt | rnt | \\} }tt ||} t| trBtdtx&| D]}||j |j<q*Wqn| |j | <qnWy| d}Wntk rxd}YnX|td}x@|t|kr||dkr||dkrtd|d7}qW|t|krtdg}d}|d7}xp|t|kr^||}|dkr|d7}n.|dkr:|d8}|d krHPn|dkrHd}|||d7}qWd|}xNt |D]@\}}}}|tkrtd|||j krzt||j |_!qzW|S)a Load a parameter set from a leaprc file Parameters ---------- fname : str or file-like Name of the file or open file-object from which a leaprc-style file will be read search_oldff : bool, optional, default=False If True, search the oldff directories in the main Amber leap folders. Default is False Notes ----- This does not read all parts of a leaprc file -- only those pertinent to defining force field information. For instance, the following sections and commands are processed: - addAtomTypes - loadAmberParams - loadOFF - loadMol2 - loadMol3 r2TFcSslg}g}xJ|D]B}|dr2||ddqn |||d|g}qW|rh|d||S)Nz\ )endswithappendr*)linesnewlinesZ compositerOr.r.r/ joinliness   z0AmberParameterSet.from_leaprc..joinlinescSsd|kr |S|d|dS)N#)index)rOr.r.r/z/AmberParameterSet.from_leaprc..r_cSs0|ddkr|dd}|dddd}|S)Nr)r"r#rr! _BSTOKEN_z\  )replace)r,r.r.r/ process_fname"s  z4AmberParameterSet.from_leaprc..process_fnamez\ rirzSMulti-residue mol2 files not supported by tleap. Loading anyway using names in mol2Z addatomtypes{z z.Unsupported addAtomTypes syntax in leaprc filer} rjz%s is not a recognized element)"rVrrrr*closerKrk _loadparamsrefindallrZr0 _loadoffrerWrXrrY _loadmol2rerr warningswarnr namerfr+r&r rarD _atomtyperer atom_typesZ atomic_number)clsr,r-ZparamsrN own_handlerdrbtextZ lowertextrlrOZresnameZresidueZresidxZatom_types_stricharsZnopenchar_rwZsymbZhybr.r.r/ from_leaprcs~                     zAmberParameterSet.from_leaprccstt|j|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 F)Zallow_unequal_duplicates)rSr1from_structure)rzZstruct)r]r.r/r`sz AmberParameterSet.from_structurecCst|trt|d}d}n|}d}|j|zJxD|D]<}|sV|||S|dkrn|||S|||Sq>WWd|r| XdS)z Load a set of parameters from a single parameter file Parameters ---------- fname : str or file-like Parameter file to parse r2TF)r3r4r5r6r7r8r9r:r;r<r=r>r?r@N) rVrrrUrarCrD _parse_frcmod_parse_parm_datrp)r[r,rNr{rOr.r.r/rZss      z!AmberParameterSet.load_parameterscsXfdd}d}tdd}d}x.|D]"s@q,drRd}q,njdrdd}q,nXdrvd }q,nFd rd }q,n4d rd }q,n"drd}q,ndrd}q,|dkr|q,|dkr|q,|d kr|q,|d kr|||}q,|d kr(|q,|dkr>|q,|dkr,| q,WdS)z0 Parses an frcmod file from an open file object c3sVxD] }|Vq WdS)Nr.)l)rNrOr.r/fiters z.AmberParameterSet._parse_frcmod..fiterNcSsdS)NTr.r.r.r.r/rgrhz1AmberParameterSet._parse_frcmod..r3r4r6r5r7r9r:r<r=r?LJEDITZNBFIX) rrE startswith_process_mass_line_process_bond_line_process_angle_line_process_dihedral_line_process_improper_line_process_nonbond_line_process_nbfix_line)r[rNrOrZsectionfinished_dihedsrQr.)rNrOr/rsV                zAmberParameterSet._parse_frcmodcsfdd}|}t|}tdd}x(|rP|s|sP} x4| d dD]$}| d| |<| | d|q Wt|}qWt|} t| d krbt d | d d kr|t dt|}x.|r|sP|t|}qWxt| D]\}}|j|}||jkr|j|jdk rb|j|jdk rbt|j|j|jtks8t|j|j|jtkrbtd|j|ft| |j|q|j||j|jqWt|dkrt|}x0|r|sP|| t|}qWdS)z: Internal parser for parm.dat files from open file handle c3s$VxD] }|Vq WdVdS)Nr_r.)r)rNrOr.r/rs z0AmberParameterSet._parse_parm_dat..fitercSsdS)NTr.r.r.r.r/rgrhz3AmberParameterSet._parse_parm_dat..NzTrouble parsing 10-12 termsrz<10-12 potential not supported in AmberParameterSet currentlyrrzHCould not parse the kind of nonbonded parameters in Amber parameter fileZREz&Only RE nonbonded parameters supportedzBEquivalency defined between %s and %s but parameters are not equalr)nextrrDrrrrrrFrGr+r dictlistrar&rJrrryrminepsilonrLr rurvrwr remove set_lj_paramsr)r[rNrOrZrawlinerrQa1a2ZacoefZbcoefZequivalent_ljtypesZequivalent_typesrPtypatypZotypr.)rNrOr/rs                  z!AmberParameterSet._parse_parm_datcCs|}yt|d}Wn>tk r<td|dYntk rVtdYnX|d|jkrx||j|d_nj|ddkrt|dt|jd|d}||j|d<n2t|dt|jd|t t |}||j|d<dS)Nrz$Could not convert mass to float [%s]z*Error parsing MASS line. Not enough tokensr)ZEPZLP) rFrGr+r rHrymassrr&rr)r[rOrPrZatyper.r.r/r;s z$AmberParameterSet._process_mass_linecCslt|}|std||\}}}}|}|}tt|t|}||j||f<||j||f<dS)Nz#Could not understand BOND line [%s])_bondrematchr groupsrDrrG bond_types)r[rOrematchrrkeqrr.r.r/rOs  z$AmberParameterSet._process_bond_linec Cszt|}|std||\}}}}}|}|}|}tt|t|}||j|||f<||j|||f<dS)Nz$Could not understand ANGLE line [%s])_anglererr rrDrrG angle_types) r[rOrrra3rrrr.r.r/rYs  z%AmberParameterSet._process_angle_linecCst|}|s$|dkr$td|n|st|}|sBtd||\}}}}|} tt| } | |ksnt|| r~tdn|\} } } }}}}}| | | |f\} } } }| | | |f} || | | f} |dk r|| kr|| krt d|| ft ddt |Dp dg}ddt |Dpsz.g333333?cSsg|] }t|qSr.)rG)rrr.r.r/rsg@r)_dihedrerr _dihed2rertuplereversedAssertionErrorrDrurvr _sceererr_scnbrerGrrLrradihedral_types)r[rOrZlast_keyrZdivrphiperrQZrkeyrrra4sceescnbrZtypsr.r.r/rcsH       $     z(AmberParameterSet._process_dihedral_linec Cst|}|std||\}}}}}}} |}|}|}|}t|||g\}}}||||f} tt|t| t||j| <dS)Nz'Could not understand IMPROPER line [%s]) _improprerr rrDsortedrrGimproper_periodic_types) r[rOrrrrrrrrrQr.r.r/rs  z(AmberParameterSet._process_improper_linecCsy|dd\}}}Wn tk r:td|YnXy|j|t|t|WnBtk rztd|Yn$tk rtd||fYnXdS)NrBz0Could not understand nonbond parameter line [%s]z)Atom type %s not present in the database.z7Could not convert nonbond parameters to floats [%s, %s])rFr+r ryrrGKeyError)r[rOrrepsr.r.r/rs z'AmberParameterSet._process_nonbond_lineNc Csy |dd\}}}}}}Wn tk r@td|YnXy$t|}t|}t|}t|}Wntk rtdYnXt||||f|jt||t||f<|dk rx<||D]0} t||||f|jt| |t| |f<qWx>||D]2} t||||f|jt|| t|| f<qWxR||D]F} x>||D]2} t||||f|jt| | t| | f<qPWqBWdS)Nz%Could not understand LJEDIT line [%s]z.Could not convert LJEDIT parameters to floats.) rFr+r rGmathZsqrt nbfix_typesminmax) r[rOZ equivalentsrrZrmin1Zeps1Zrmin2Zeps2Zoa1Zoa2r.r.r/rs(  , 02z%AmberParameterSet._process_nbfix_lineCreated by ParmEdfrcmodcCst|trt|d}d}n|}d}|dkr6td|||d|d|dx0t|jD]"\}}|d |d |j fqfW|d|d t }x\t|j D]N\\} } }t ||krq| t ||d | d | d |j|jfqW|d|dt }xlt|jD]^\\} } } }t ||krJq*| t ||d| d | d | d |j|jfq*W|d|dt }x`t|jD]P\\} } } } }t ||krؐq| t |t|tst|dkrZt|ts|d}|d| d | d | d | d d|j|j|j|j|jf nx\|ddD]L} |d| d | d | d | d d| j| j| j | j| jf qhW|d} |d| d | d | d | d d| j| j| j| j| jf qW|d|dt}xt|jD]\\} } } } }| dkrt| dks^td| | | | f\} } } } n| dkr| | | | f\} } } } t| | | g\} } } | | | | f|kr|| | | | f|kr2tdq2|d| d | d | d | d |j|j|jf||| | | | f<q2W|d|dx6t|jD](\}}|d|d |j|jfqJW|d|j r|dxNt|j D]@\\} } \}}|d| d | d ||d ||d fqW|r|!dS)a Writes a parm.dat file with the current parameters Parameters ---------- dest : str or file-like The file name or file-like object to write the parameters to title : str, optional The title of the frcmod to write. Default is 'Created by ParmEd' style : str, optional If 'frcmod', the parameters are written in frcmod-format. If 'parm', the parameters are written in parm.dat-format. Default is 'frcmod' wTF)rr%z+style must be either frcmod or parm, not %sz rozMASS z%s%6.3f rzBOND z%s-%s %8.3f %6.3f rzANGLE z%s-%s-%s %8.3f %6.3f zDIHE rrz6%s-%s-%s-%s %4i %14.8f %8.3f %5.1f SCEE=%s SCNB=%s Nr!z IMPROPER XzMalformed generic improper!z5Multiple impropers with the same atom set not allowedz%s-%s-%s-%s %14.8f %8.3f %5.1f zNONB z%s %12.8f %12.8f zLJEDIT z"%s %s %12.8f %12.8f %12.8f %12.8f )"rVrrr+writerErryljustrsetridaddrZreqrZtheteqrrr&Zphi_kZphaserrrrrrrrrrrp)r[desttitleZstyleZoutfiler{ZatomrZdonerrrrZdtypZwritten_impropersrrr.r.r/rs        *      &"$&    $  $  .zAmberParameterSet.write)F)N)rr)__name__ __module__ __qualname____doc__ staticmethodrRrT classmethodrrrZrrrrrrrrrr __classcell__r.r.)r]r/r1Os" n  s2w  @ r1)BrZ __future__rr collectionsr contextlibrrr'reruZofflibrZ constantsr exceptionsr r r Zmodeller.residuer Z formats.mol2rZformats.registryrZ parametersrZperiodic_tablerrrZtopologyobjectsrrrrrZutils.iorZ utils.sixrrrrZutils.six.movesrrZcollections.abcrZsubscompilerrrrrrrrxIrqrsrtr0r1r.r.r.r/sT