B bo@sbdZddlmZddlmZddlmZddlm Z m Z m Z ej fddZ edej fd d ZdS) zL This package contains some useful functionality for common tasks in OpenMM )unit) needs_openmm) iteritems)rangezipmapcCst}t}t}x8t|D],}|drt||}|dd||<qWx(|D]}|} || || <qZWx8t |D],\} } |j dd| >d} | ||| <qW|j dd } | ||d<|S)a' This computes the energy of every force group in the given structure and computes the energy for each force group for the given Context. Note, the context must have positions already assigned. Parameters ---------- structure : Structure This should be the Structure object from which the System object in the Context was created context : mm.Context The OpenMM context set up for computing forces and energies nrg : energy unit, optional The unit to convert all energies into. Default is kcal/mol Returns ------- dict {str:float} A dictionary mapping the name of the force group (taken from the attribute names of the format XXX_FORCE_GROUP in the structure object) with the energy of that group in Z _FORCE_GROUPT) getEnergygroups)r Ztotal) dictdirendswithgetattrreplacelowerZ getSystem getForces getForceGrouprgetStategetPotentialEnergy value_in_unit) structurecontextnrgZ all_namesZforce_group_namesZenergy_componentsattrvalforceZgpgrpnamestateer!2lib/python3.7/site-packages/parmed/openmm/utils.pyenergy_decomposition s   r#Nc sJddlm}ddD}g}fddzxFtD]6\}}t||jrl||||| |q@W|dkr| | dn| | d|j ||j|jdk rԈj|jttfdd tSd} xJt|D]8\} } t| |jr4| || | d 7} | | qWXdS) a This function computes the energy contribution for all of the different force groups. Parameters ---------- structure : Structure The Structure with the coordinates for this system system : mm.System The OpenMM System object to get decomposed energies from platform : str The platform to use. Options are None (default), 'CPU', 'Reference', 'CUDA', and 'OpenCL'. None will pick default OpenMM platform for this installation and computer nrg : energy unit, optional The unit to convert all energies into. Default is kcal/mol Returns ------- energies : list of tuple Each entry is a tuple with the name of the force followed by its contribution rNcSsg|] }|qSr!)r).0fr!r!r" Rsz/energy_decomposition_system..cs0|jdd|>d}t|j|fS)NTr )r r )rtypeZgetForce__name__rr)rrst)rsystemr!r"_eneTsz)energy_decomposition_system.._enegMbP?cs |S)Nr!)x)r+conr!r"hz-energy_decomposition_system..r )Z simtk.openmmZopenmmr enumerate isinstanceZNonbondedForceappendZgetReciprocalSpaceForceGroupZsetReciprocalSpaceForceGroupZ setForceGroupZContextZVerletIntegratorZPlatformZgetPlatformByNameZ setPositionsZ positionsZboxZsetPeriodicBoxVectorsZ box_vectorslistrrZ getNumForcesr) rr*platformrZmmZ old_groupsZold_recip_groupir%idxrrr!)r+r-rr*r"energy_decomposition_system6s0       r7)__doc__ZparmedruZparmed.utils.decoratorsrZparmed.utils.sixrZparmed.utils.six.movesrrrZkilocalories_per_moler#r7r!r!r!r"s   -