B âêõbÉã@shdZddlmZddlmZddlmZmZddl Z Gdd„de ƒZ Gdd „d e ƒZ Gd d „d e ƒZdS) z© This module contains classes for reading and writing (single frame) NAMD binary files. The main functionality is currently aimed at manipulation rather than analysis. é)Údivision)Úunit)ÚunpackÚpackNc@sZeZdZdZdZgfdd„Zedd„ƒZedd„ƒZ d d „Z d d „Z ddd„Z dd„Z d S)Ú NamdBinFilea¿From the NAMD manual: NAMD uses a trivial double-precision binary file format for coordinates, velocities, and forces ... The file consists of the atom count as a 32-bit integer followed by all three position or velocity components for each atom as 64-bit double-precision floating point ... The main attributes are the number of atom entries (natom) and a (flat) numpy array of size 3*natom (values). The meaning of "values" is effectively arbitrary, but for convenience derived classes are provided which alias the values to more descriptive names (e.g. "coordinates"). See also -------- :class:`NamdBinCoor` and :class:`NamdBinVel` gð?cCst |tj¡|j|_dS)N)ÚnpÚasarrayÚfloat64Ú _SCALE_FACTORÚ_values)ÚselfÚvalues©rú7lib/python3.7/site-packages/parmed/namd/namdbinfiles.pyÚ__init__ szNamdBinFile.__init__cCst|jjdƒS)z#The current number of atom entries.é)Úintr Úsize)r rrrÚnatom#szNamdBinFile.natomcsLt|dƒ‰ttdˆ d¡ƒdƒ}‡fdd„td|ƒDƒ}ˆ ¡||ƒS)z7Return an object from the values in a NAMD binary file.ÚrbÚiércs g|]}tdˆ d¡ƒd‘qS)Údér)rÚread)Ú.0Ún)Úinfilerrú -sz$NamdBinFile.read..r)ÚopenrrrÚrangeÚclose)ÚclsÚfnameÚnatomsr r)rrr(s  zNamdBinFile.readcCsNt|dƒ}| td|jƒ¡x$|j|jD]}| td|ƒ¡q*W| ¡dS)z'Write the current attributes to a file.ÚwbrrN)rÚwriterrr r r!)r r#ZoutfileÚxrrrr&1s  zNamdBinFile.writecCsnt t |tj¡¡}t |jtj¡}d||<t d|j|jtj ¡}||j   |jdf¡|  ¡7}||_ dS)z7Delete entries corresponding to the given atom indices.FrN) rZ atleast_1drZint32ZonesrÚboolÚzerosrr r ÚreshapeÚflatten)r ÚindicesZ del_indicesÚmaskÚ newvaluesrrrÚdelatoms9s zNamdBinFile.delatomsNcCsj|dk r&t |¡}|jd|ks4t‚nt d|¡}d|}t |jd|…||j|d…f¡}||_dS)z’Insert space for natom entries beginning at start_index. If specified, give them the provided values, otherwise set them to zero. Nr)rrrÚAssertionErrorr)Z concatenater )r Ú start_indexr$r Zhinger.rrrÚ insertatomsBs  zNamdBinFile.insertatomscCs,|jd||d|…}| |||¡dS)z—Convenience function, same as insertatoms() but set 'values' to be the same as the previous natoms' values (i.e. make a copy of them). rN)r r2)r r1r$r rrrÚ copyatomsQszNamdBinFile.copyatoms)N)Ú__name__Ú __module__Ú __qualname__Ú__doc__r rÚpropertyrÚ classmethodrr&r/r2r3rrrrrs    rc@s*eZdZdZedd„ƒZejdd„ƒZdS)Ú NamdBinCoorz5 Class to read or write NAMD "bincoordinates" files. cCs|j d|jdf¡S)Néÿÿÿÿr)r r*r)r rrrÚ coordinates[szNamdBinCoor.coordinatescCs*t |¡r| tj¡}t |¡ ¡|_dS)N)ÚuÚ is_quantityÚ value_in_unitÚ angstromsrÚarrayr+r )r Úvaluerrrr<_s  N)r4r5r6r7r8r<Úsetterrrrrr:Ys r:c@s.eZdZdZdZedd„ƒZejdd„ƒZdS)Ú NamdBinVelz4 Class to read or write NAMD "binvelocities" files. g, Ô‹ot4@cCs|j d|jdf¡S)Nr;r)r r*r)r rrrÚ velocitiesjszNamdBinVel.velocitiescCs0t |¡r| tjtj¡}t |¡ ¡|_dS)N) r=r>r?r@Z picosecondrrAr+r )r rBrrrrEns N)r4r5r6r7r r8rErCrrrrrDes rD)r7Z __future__rZparmedrr=ZstructrrZnumpyrÚobjectrr:rDrrrrÚs  K