B b2@sdZddlmZddlmZmZddlmZmZddl m Z ddl m Z m Z mZddlmZddlmZmZdd lmZmZGd d d eZeeGd d d e ZGdddeZddZdddZdS)zE This module contains classes for reading various TINKER-style files ) TinkerError)FileFormatType load_file)element_by_name AtomicNum) Structure)AtomBondResidue)genopen) add_metaclass string_types)rangezipc@s,eZdZdZeeeeeeedZddZdS)KeywordControlFilezC Reads and processes a keyword control file for TINKER simulations ) PARAMETERSzA-AXISzB-AXISzC-AXISALPHABETAGAMMAc Csdddddddd|_xt|dD]}|s0q"|}|d}||dd}y|j|||j|<Wq"tk rYq"tk rt d||j|fYq"Xq"WdS)N)rzA-AXISzB-AXISzC-AXISrrrrrzNMalformed keyword control file! Could not convert the value of %s into type %s) keywordsopenstripsplitupperreplace _datatypesKeyError ValueErrorr)selffnamelinewordskeyresultr&8lib/python3.7/site-packages/parmed/tinker/tinkerfiles.py__init__s   zKeywordControlFile.__init__N)__name__ __module__ __qualname____doc__strfloatrr(r&r&r&r'r s rcs:eZdZdZeddZeddZd fdd ZZS) XyzFilea\ Reads and processes a Tinker XYZ file Parameters ---------- fname : str or file-like Name of the file, or the file object containing the XYZ file contents seq : str, optional Name of the file containing the residue (and chain) sequence. Default is None (so every atom will be part of the same residue) c Cs$t|dkrdSyt|dWntk r4dSXyt|dWn>tk ryt|dWntk rzYnXdSYnXdSydd|ddDWntk rdSXyd d|ddDWntk rYnXdSyd d|dd DWntk rdSXd S) a] Checks that the tokenized line is consistent with an atom record Parameters ---------- words : list of str Result of line.split() on a line of the file Returns ------- is_atom : bool If it is consistent with an atom record, return True. Otherwise, False FrcSsg|] }t|qSr&)r.).0wr&r&r' Zsz.XyzFile._check_atom_record..cSsg|] }t|qSr&)int)r2r3r&r&r'r4_scSsg|] }t|qSr&)r7)r2r3r&r&r'r4fsNT)lenr7rr.)r#r&r&r'_check_atom_record7s:  zXyzFile._check_atom_recordc Cst|d}|}|sdSyt|d}Wnttfk rFdSX|dkrTdS|}t|dkrydd|DWn"tk rt|rdSdSX|}t|S)a! Identify the file as a Tinker XYZ file Parameters ---------- filename : str Name of the file to test whether or not it is a mol2 file Returns ------- is_fmt : bool True if it is a xyz file, False otherwise rFrr0cSsg|] }t|qSr&)r.)r2r3r&r&r'r4sz%XyzFile.id_format..T) r readlinerr7r IndexErrorr8r/r9)filenamefr#natomr&r&r' id_formatks(      zXyzFile.id_formatNc stt|t|tr(t|d}d}n|}d}|dk r@t|}yt| d}Wn t t fk rxt dYnX|dk r|t |jkrt d|| }t |dkrt|sdd |D|_| }td }d |_d|_|dk r|jd}t|d |} ntt|d } t| |d |d d } dd |dd D\| _| _| _|| |j|j|j|j|j dd |ddDg} xt!|D]\} } | }|dk r|j| d j"}t|d |} ntt|d } t| |d |d d } dd |dd D\| _| _| _|| |j|j|j|j|j | #dd |ddDqWxZt$|j| D]J\} }| j%d } x4|D],}|| kr|j&#t'| |j|d qWqjW|dkrx,|jD]"} t | j&dkrt| j| _(qW|r|)dS)NrTFrzBad XYZ file format; first linezISequence file %s # of atoms does not match the # of atoms in the XYZ filer0cSsg|] }t|qSr&)r.)r2r3r&r&r'r4sz$XyzFile.__init__..ZSYSr1r6) atomic_numbernametypecSsg|] }t|qSr&)r.)r2r3r&r&r'r4sr5cSsg|] }t|qSr&)r7)r2r3r&r&r'r4scSsg|] }t|qSr&)r.)r2r3r&r&r'r4scSsg|] }t|qSr&)r7)r2r3r&r&r'r4s)*superr/r( isinstancer r rr7r:rrr;rr8atomsr9boxr ZnumberZ_idxZresidues_guess_atomic_numberrrrZxxZxyZxzZadd_atomrAchainZinsertion_codeZsegid enumerateresidueappendridxbondsr r@close)r r!seqZfxyzZown_handle_xyzZ seqstructr>r#rJr@ZatomZbond_idsir"rMrL) __class__r&r'r(sl      "    " "   (  zXyzFile.__init__)N) r)r*r+r, staticmethodr9r?r( __classcell__r&r&)rQr'r/*s  4 'r/c@s.eZdZdZd ddZddZeddZdS) DynFilez' Reads and processes a Tinker DYN file NcCs|dk r||dS)N)read)r r!r&r&r'r(szDynFile.__init__cCs4t|d}z|dkr*td||}t|dd|dd|_|_|dkrttdd d td D|_| }t |d d d |jd<t |d d d |jd<t |d d d |jd<| }t |d d d |jd<t |d d d |jd<t |d d d |jd<|dkr^tddd t|jD|_ t||j |j|}|dkrPd|_dd t|jD|_t||j|j|dkrtddd t|jD|_t||j|j|dkr&tddd t|jD|_t||j|jn|dkrd |_d!d t|jD|_t||j|j|d"krtd#|d$d t|jD|_t||j|j|d%krtd&|d'd t|jD|_t||j|jn td(|Wd|XdS))z Parses the .dyn file rzNumber of Atoms and Title :z'%s is not a recognized TINKER .dyn filerNzPeriodic Box Dimensions :zNo periodic box dimension linecSsg|]}dqS)gr&)r2rPr&r&r'r4sz DynFile.read..r0DEr1r5r6zCurrent Atomic Positions :z No atomic positions in .dyn filecSsg|]}dddgqS)gr&)r2rPr&r&r'r4sz"Current Translational Velocities :TcSsg|]}dddgqS)gr&)r2rPr&r&r'r4szCurrent Angular Velocities :z4Could not find Angular velocity section in .dyn filecSsg|]}dddgqS)gr&)r2rPr&r&r'r4szCurrent Angular Momenta :z3Could not find angular momenta section in .dyn filecSsg|]}dddgqS)gr&)r2rPr&r&r'r4szCurrent Atomic Velocities :FcSsg|]}dddgqS)gr&)r2rPr&r&r'r4szCurrent Atomic Accelerations :z#Could not find accelerations in %s cSsg|]}dddgqS)gr&)r2rPr&r&r'r4 sz Alternate Atomic Accelerations :z&Could not find old accelerations in %scSsg|]}dddgqS)gr&)r2rPr&r&r'r4szNo velocities in %s)rr:rrr7r>titlerrFrrr.rZ positionsrT _read_sectionZ rigidbodyZtranslational_velocitiesZangular_velocitiesZangular_momentaZ velocitiesZ accelerationsZold_accelerationsrN)r r!r=r"r#r&r&r'rUsr *    z DynFile.readc Csxt|D]}|}yXt|ddd||d<t|ddd||d<t|ddd||d<Wq ttfk rtdYq Xq WdS)z Reads a section of an open file into the passed container. The container should be a 2-dimensional list of length natom x 3 rrWrXr1r5z$Could not parse values from dyn fileN) rr:rrr.rr;rr)r=Z containerr>rPr#r&r&r'r\s zDynFile._read_section)N)r)r*r+r,r(rUrRr\r&r&r&r'rTs @rTcCs&y t|dStk r dSXdS)NTF)r.r)thingr&r&r'is_float&s r^NcCs|ddd|D}|dks*t|jdkrpt|dkrpyt|d|dStk rntt|SXtt|S)z Guesses the atomic number rcss|]}|r|VqdS)N)isalpha)r2cr&r&r' 0sz'_guess_atomic_number..Nr1r)joinr8rErrlowerrr)rArJr&r&r'rG-s rG)N)r,Zparmed.exceptionsrZparmed.formats.registryrrZparmed.periodic_tablerrZparmed.structurerZparmed.topologyobjectsrr r Zparmed.utils.ior Zparmed.utils.sixr r Zparmed.utils.six.movesrrobjectrr/rTr^rGr&r&r&r's   'U