B âêõb®2ã@sÈdZddlmZmZmZddlmZddlZddl m Z ddl m Z ddl mZdd lmZdd lmZmZdd lmZdd lmZd ZdZdeZee ƒGdd„deƒƒZee ƒGdd„deƒƒZdS)a Provides a class for parsing CHARMM-style coordinate files, namely CHARMM .crd (coordinate) files and CHARMM .rst (restart) file. Uses CharmmFile class in _charmmfile.py for reading files Author: Jason Deckman Contributors: Jason Swails Date: June 19, 2015 é)Úprint_functionÚdivisionÚabsolute_import)ÚclosingNé)Úio)ÚFileFormatType)Ú CharmmError)Úunit)Ú add_metaclassÚ string_types)Úrange)ÚVec3égRO8à©?éc@s\eZdZdZedd„ƒZdd„Zedd„ƒZedd „ƒZ ed d „ƒZ d d „Z edd„ƒZ dS)Ú CharmmCrdFilea¥ Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc. Parameters ---------- fname : str Name of the restart file to parse Attributes ---------- natom : int Number of atoms in the system resname : list of str List of all residue names in the system coordinates : np.ndarray with shape (1, natom, 3) Atomic coordinates in a numpy array positions : natom x 3 distance Quantity 2-D list of all coordinates with the appropriate distance unit attached. Has the format [ [x1, y1, z1], [x2, y2, z2], ... ] c CsJtt |¡ƒ0}| ¡}x |r:t| ¡ƒdkr:| ¡}qWd}x<|r|| ¡}t| ¡ƒdkrdd}qB|ddkrvd}qBd}qBWx |ržt| ¡ƒdkrž| ¡}q€Wy€t| ¡dƒ}xjtt |dƒƒD]X}| ¡ ¡}t|dƒt|dƒt |dƒt |dƒt |d ƒt |d ƒqÂWWnt t fk r:dSXdSQRXd S) a Identifies the file type as a CHARMM coordinate file Parameters ---------- filename : str Name of the file to check format for Returns ------- is_fmt : bool True if it is a CHARMM coordinate file rTFÚ*éréééé N) rrÚgenopenÚreadlineÚlenÚstripÚintÚsplitr ÚminÚfloatÚ IndexErrorÚ ValueError)ÚfilenameÚfÚlineÚintitleÚnatomÚrow©r(ú7lib/python3.7/site-packages/parmed/charmm/charmmcrds.pyÚ id_format2s6         zCharmmCrdFile.id_formatcCsJg|_g|_g|_g|_g|_g|_g|_g|_g|_d|_ |  |¡dS)Nr) ÚatomnoÚresnoÚresnameÚresidÚatnameÚcoordsÚtitleÚsegidÚ weightingr&Ú_parse)ÚselfÚfnamer(r(r)Ú__init__aszCharmmCrdFile.__init__cCsdd„|jdDƒtjS)zZ Atomic coordinates with units attached to them with the shape (natom, 3) cSsg|] }t|Ž‘qSr()r)Ú.0Úxyzr(r(r)ú tsz+CharmmCrdFile.positions..r)Ú coordinatesÚuÚ angstroms)r5r(r(r)Ú positionsoszCharmmCrdFile.positionscCs|jS)N)r0)r5r(r(r)r;vszCharmmCrdFile.coordinatescCsdS)Nr()r5r(r(r)ÚboxzszCharmmCrdFile.boxc Cstt |d¡ƒê}| ¡ ¡}xt|ƒdkr<| ¡ ¡}q"Wd}xH|rŠ|j |¡| ¡ ¡}t|ƒdkrrd}qD|ddkr„d}qDd}qDWxt|ƒdkr¨| ¡ ¡}qŽWy t|  ¡dƒ|_ xÖt |j ƒD]È}| ¡  ¡}|j  t|dƒ¡|j  t|dƒ¡|j |d¡|j |d¡|j t|d ƒ¡|j t|d ƒ¡|j t|d ƒ¡|j |d ¡|j |d ¡|j t|dƒ¡qÌWd|j t|jƒks¶tdƒ‚Wn"ttfk rÚtdƒ‚YnXt |j¡ d|j df¡|_WdQRXdS)NÚrrTFrrrrrrréérz# atom mismatchz$Error parsing CHARMM coordinate fileéÿÿÿÿ)rrrrrrr1Úappendrrr&r r+r,r-r/r0rr2r.r3ÚAssertionErrorr!r r ÚnpÚarrayÚreshape)r5r6Úcrdfiler$r%r'r(r(r)r4~sB      "zCharmmCrdFile._parsecCsðt|tƒrt |d¡}d}nd}| d¡| d¡| dt|jƒ¡|jdjdkr\dnd|jdj}xrt |jƒD]d\}}|j }|j   ¡pœ|j   ¡pœd }| d |d|j j||j j|j|j|j|j||j jdf ¡qxW|rì| ¡d S) aO Writes a CHARMM coordinate file from a structure Parameters ---------- struct : :class:`parmed.structure.Structure` The input structure to write the CHARMM coordinate file from dest : str or file-like object The file name or file object to write the coordinate file to ÚwTFz9* GENERATED BY PARMED (HTTPS://GITHUB.COM/PARMED/PARMED) z* z %10d EXT rrZSYSz=%10d%10d %-8s %-8s%20.10f%20.10f%20.10f %-8s %-8s%20.10f N)Ú isinstancer rrÚwriterZatomsZresiduesZnumberÚ enumerateZresiduer2rÚchainÚnameZxxZxyZxzÚclose)ZstructÚdestZ own_handleÚaddÚiZatomZresr2r(r(r)rL¨s"    $zCharmmCrdFile.writeN) Ú__name__Ú __module__Ú __qualname__Ú__doc__Ú staticmethodr*r7Úpropertyr>r;r?r4rLr(r(r(r)rs /   *rc@s†eZdZdZedd„ƒZdd„Zedd„ƒZedd „ƒZ ed d „ƒZ ed d „ƒZ edd„ƒZ edd„ƒZ dd„Zddd„Zdd„ZdS)Ú CharmmRstFileaq Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name 'fname' into class attributes Parameters ---------- fname : str Name of the restart file to parse Attributes ---------- natom : int Number of atoms in the system resname : list of str Names of all residues in the system coordinates : np.ndarray shape(1, natom, 3) List of all coordinates in the format [x1, y1, z1, x2, y2, z2, ...] coordinatesold : np.ndarray shape(1, natom, 3) List of all old coordinates in the format [x1, y1, z1, x2, y2, z2, ...] velocities : np.ndarray shape(1, natom, 3) List of all velocities in the format [x1, y1, z1, x2, y2, z2, ...] positions : natom x 3 distance Quantity 2-D list of all coordinates with the appropriate distance unit attached. Has the format [ [x1, y1, z1], [x2, y2, z2], ... ] positionsold : natom x 3 distance Quantity 2-D list of all old coordinates with the appropriate distance unit attached. Has the format [ [x1, y1, z1], [x2, y2, z2], ... ] c Cs,tt |¡ƒ}| ¡}WdQRX| d¡S)a Identifies the file type as a CHARMM restart file Parameters ---------- filename : str Name of the file to check format for Returns ------- is_fmt : bool True if it is a CHARMM restart file NZREST)rrrrÚ startswith)r"r#r$r(r(r)r*æszCharmmRstFile.id_formatcCs\g|_g|_g|_g|_g|_g|_d|_d|_d|_d|_ d|_ d|_ d|_ |  |¡dS)Nr)Úheaderr1ZenrgstatÚ coordsoldr0ÚvelsZ ff_versionr&ÚnprivÚnstepÚnsavcÚnsavvÚjhstrtr4)r5r6r(r(r)r7øszCharmmRstFile.__init__cCs|jS)N)r0)r5r(r(r)r; szCharmmRstFile.coordinatescCs|jS)N)r])r5r(r(r)ÚcoordinatesoldszCharmmRstFile.coordinatesoldcCsdd„|jdDƒtjS)z Atomic positions with units cSsg|] }t|Ž‘qSr()r)r8r9r(r(r)r:sz+CharmmRstFile.positions..r)r0r<r=)r5r(r(r)r>szCharmmRstFile.positionscCsdd„|jdDƒtjS)z! Old atomic positions with units cSsg|] }t|Ž‘qSr()r)r8r9r(r(r)r:sz.CharmmRstFile.positionsold..r)r]r<r=)r5r(r(r)Ú positionsoldszCharmmRstFile.positionsoldcCs|jS)z, Atomic velocities in Angstroms/picoseconds )r^)r5r(r(r)Ú velocitiesszCharmmRstFile.velocitiescCsdS)Nr()r5r(r(r)r?!szCharmmRstFile.boxc CsPtt |d¡ƒ4}d}x||r”| ¡}t|ƒs6tdƒ‚| ¡}| ¡}t|ƒdkr‚|ddksj|ddkrpd}q’|j  | ¡¡q|j  | ¡¡qWxút t|jƒƒD]è}t|j| ¡ƒdkr¦|j| ¡ ¡}|ddd…d ksú|ddd …d kr¦yp|j|d  ¡ ¡}t |dƒ|_ t |d ƒ|_ t |d ƒ|_t |dƒ|_t |dƒ|_t |dƒ|_PWq¦ttfk rŒtdƒ‚Yq¦Xq¦W| |d¡| ||j¡t |j¡ d|j df¡|_| |d¡| ||j¡t |j¡ d|j df¡|_|jt9_| |d¡| ||j¡t |j¡ d|j df¡|_WdQRXdS)Nr@TzPremature end of filerZENERGIESz !ENERGIESFrZNATOMrz!NATOMrrrrzProblem parsing CHARMM restartz!XOLDrCz!VXz!X)rrrrrr rrr\rDr rr&r_r`rarbrcr!r ÚscanÚ_get_formatted_crdsr]rFrGrHr^Ú ONE_TIMESCALEr0)r5r6rIZ readingHeaderr$Zwordsr'r(r(r)r4%sL (   zCharmmRstFile._parsercCshd}|r| d¡xP|rb| ¡}|s,tdƒ‚t| ¡ƒdkr| ¡ ¡ddt|ƒ…|krd}qWdS)NTrzPremature end of fileF)Úseekrr rrr)r5ZhandleÚstrr@Zscanningr$r(r(r)rgUs  zCharmmRstFile.scancCsžx˜t|jƒD]Š}| ¡}|s$tdƒ‚t|ƒdtkrrerfr?r4rgrhr(r(r(r)rZÇs       0 rZ)rWZ __future__rrrÚ contextlibrZnumpyrFZutilsrZformats.registryrÚ exceptionsr Úr r<Z utils.sixr r Zutils.six.movesr Zvec3rrnZ TIMESCALEriÚobjectrrZr(r(r(r)Ú s$       -