B b7@sdZddlmZmZmZddlmZddlmZddl m Z ddl m Z ddl mZmZmZddlmZmZmZdd lmZdd lmZmZdd lmZdd lmZdd lm Z m!Z!Gddde"Z#e e Gddde"Z$dS)z This module contains functionality relevant to loading and parsing GROMACS GRO (coordinate) files and building a stripped-down Structure from it )print_functiondivisionabsolute_import)closing)TINY) GromacsError)FileFormatType)!box_vectors_to_lengths_and_angles!box_lengths_and_angles_to_vectorsreduce_box_vectors) AtomicNumelement_by_nameMass) Structure)Atom ExtraPoint)unit)genopen) add_metaclass string_typesc@s eZdZdZddZddZdS)_AtomLineParserz" Parses atom lines from GRO files cCsd|_d|_d|_dS)Nr)_digits_pdeci_ndeci)selfr8lib/python3.7/site-packages/parmed/gromacs/gromacsgro.py__init__sz_AtomLineParser.__init__c s8tdd}dd}dd}t|}t|}t|}tdd}|dkrnt||d} nt||||d} jdkrd d_ d j d _ j j _fd d t d D\| _ | _ | _djd jr.fdd t d D\| _| _| _| ||fS)a7 Reads a line Parameters ---------- line : str A line with an atom record from a GRO file Returns ------- atom, resname, resnum : Atom, str, int The Atom instance, residue name, and residue number containing the atom N r)namenumber) atomic_numberr"r#mass.c3s:|]2}td|jd|djdVqdS)r!r'rN)floatr).0i)linerrr ;sz'_AtomLineParser.read..c3s6|].}t|j|jdVqdS)rN)r(r)r)r*)r+rwbegwendrrr,Bs)intstripr r rrrrindexrrrangexxxyxzvxvyvz) rr+resnumresnameZatomnameelemr$r%Zatnumatomr)r+rr.r/rreads.    z_AtomLineParser.readN)__name__ __module__ __qualname____doc__rr>rrrrrsrc@s8eZdZdZeddZed ddZed dd Zd S) GromacsGroFilez% Parses and writes Gromacs GRO files c Cstt|}|yt|Wntk r@dSX|}ynt|dd|ddsrdS|ddsdSt|ddddt|D}|d |d d}xVtd d D]H}|d d d||d }|d d d||}t|||qWd }|d d d||d }|d d d||}|||rxXtd d D]J}|d d d||d }|d d d||}t|||qjWWntk rdSXd SQRXdS)aJ Identifies the file as a GROMACS GRO file Parameters ---------- filename : str Name of the file to check if it is a Gromacs GRO file Returns ------- is_fmt : bool If it is identified as a Gromacs GRO file, return True. False otherwise FNrrr r!cSsg|]\}}|dkr|qS)r&r)r)r*xrrr gsz,GromacsGroFile.id_format..r'rT) rrreadliner0r1 ValueError enumerater3r()filenamefr+ZpdeciZndecir*r.r/rrr id_formatLs>zGromacsGroFile.id_formatFc CsBt}t|tr t|d}d}n|}d}z|yt|}Wn tk rhtd|YnXt }xt |D]Z\}}||krPy| |\} } } Wn$tt fk rtd|YnX| | | | qzW|}|d|krtd|d|f|rydd |D} Wn"tk rDtd |YnXt| d kr| d d | dd | dd dddg|_nt| dkrt| d | d | dgtj| d| d| dgtj| d| d| dgtj\} }| tj\}}}|tj\}}}||||||g|_Wd|r.|X|s>||S)a" Parses a Gromacs GRO file Parameters ---------- filename : str or file-like Name of the file or the GRO file object skip_bonds : bool, optional If True, skip trying to assign bonds. This can save substantial time when parsing large files with non-standard residue names. However, no bonds are assigned. This is OK if, for instance, the GRO file is being parsed simply for its coordinates. This will also reduce the accuracy of assigned atomic numbers for typical ions. Default is False. Returns ------- struct : :class:`Structure` The Structure instance instantiated with *just* residues and atoms populated (with coordinates) rTFzCould not parse %s as GRO filez.Could not parse the atom record of GRO file %sr'z(Truncated GRO file. Found %d of %d atomscSsg|] }t|qSr)r()r)rDrrrrEsz(GromacsGroFile.parse..z,Could not understand box line of GRO file %sr-rrgV@ rFrrGN)r isinstancerrrHr0r1rIrrrJr> IndexErrorZadd_atomsplitlenboxr uZ nanometersZ value_in_unitZ angstromsZdegreescloseZ assign_bonds)rKZ skip_bondsstructZfileobj own_handleZnatomZ line_parserr*r+r=r;r:rWZlengZangabcZalphaZbetaZgammarrrparse{s`   " zGromacsGroFile.parser-c sDdd}d}t|tr&t|d}d}nt|ds8td|d|d t|jtd d |jD}|d krd \}} | } t dd | D} t |j} xPt | D]fdd| Dd} t }d}x| jD]}|d7}x|jD]}x| D]}|j|jkr|j|jkr|jj|jjkr|dk rX|j|jdkrXt||jdkrXq| d7} ||| d|d||||||}| |PqWtd|qWqWqWnBx@|jD]6}|jjdd}|jdd} ||| ||||qW|jdk rtt|j\}}}tdd|jddDr`|d|dd|dd|ddfnh|d|dd|dd|dd|dd|dd|dd|dd|dd|ddf |dn^|s2|jr2|j}|jdd|jdddd}|d|d|d|df|d|r@|dS)a Write a Gromacs Topology File from a Structure Parameters ---------- struct : :class:`Structure` The structure to write to a Gromacs GRO file (must have coordinates) dest : str or file-like The name of a file or a file object to write the Gromacs topology to precision : int, optional The number of decimal places to print in the coordinates. Default 3 nobox : bool, optional If the system does not have a periodic box defined, and this option is True, no box will be written. If False, the periodic box will be defined to enclose the solute with 0.5 nm clearance on all sides. If periodic box dimensions *are* defined, this variable has no effect. combine : 'all', None, or list of iterables, optional Equivalent to the combine argument of the GromacsTopologyFile.write method. If None, system atom order may be changed to meet the need for contiguously bonded groups of atoms to be part of a single moleculetype. All other values leave the atom order unchanged. Default is None. c Ss d|}d||f}d||df}|d||jjdd|jdd|f|||jdd||||jdd||||jdd||r|||jdd||||jdd||||jdd||ddS)Nrz%%%d.%dfr'z %5d%-5s%5s%5dr ) writeresiduer"r4r5r6r7r8r9) r=atidresidhas_velsdest precisionZvarwidthZcrdfmtZvelfmtrrr_write_atom_lines z.GromacsGroFile.write.._write_atom_lineFwTraz,dest must be a file name or file-like objectz*GROningen MAchine for Chemical Simulation z%5d css|]}t|dVqdS)r7N)hasattr)r)r\rrrr,sz'GromacsGroFile.write..all)rrcss|]}t|dVqdS)r'N)rV)r)molrrrr,scs g|]}|dkr|dqS)r'rr)r)rl)molidrrrE sz(GromacsGroFile.write..rNr'izCould not find %scSsg|]}t|dtkqS)Z)absr)r)rDrrrrE;sr-z%10.5f%10.5f%10.5frrOz6%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5fr`)Zaxisg?)rSrrrj TypeErrorrarVZatomsrkrUsumlistr3setZresiduestyper"rbidx intersectionZ bond_partnersaddremove RuntimeErrorrWr r Z coordinatesmaxminrY)rZrfrgZnoboxZcombinerhr[rerdrcZ split_structZn_molsZ unused_atomsZmoleculeZ new_moleculeZlast_found_atomrbr=Z original_atomr\r]r^ZcrdsZdiffr)rmrrasx                ..:    zGromacsGroFile.writeN)F)r-FF)r?r@rArB staticmethodrMr_rarrrrrCGs  / SrCN)%rBZ __future__rrr contextlibrZparmed.constantsrZparmed.exceptionsrZparmed.formats.registryrZparmed.geometryr r r Zparmed.periodic_tabler r rZparmed.structurerZparmed.topologyobjectsrrZparmedrrXZparmed.utils.iorZparmed.utils.sixrrobjectrrCrrrrs       2