B bL@sLdZddlmZmZmZddlZddlmZddlZ ddl m Z ddl mZddlmZdd lmZdd lmZdd lmZdd lmZmZmZmZmZmZmZmZm Z m!Z!m"Z"m#Z#m$Z$m%Z%m&Z&m'Z'm(Z(dd l)m*Z*ddl+m,Z,m-Z-m.Z.ddl/m0Z0dgZ1e*d#ddZ2ddZ3ddZ4ddZ5ddZ6ddZ7ddZ8dd Z9d!d"Z:dS)$zf Convert an OpenMM Topology into a Structure instance, optionally filling in parameters from a System )absolute_importdivisionprint_functionN) defaultdict)unit) OpenMMWarning) load_file)!box_vectors_to_lengths_and_angles)Element) Structure)Angle AngleTypeAtomAtomTypeBondBondTypeCmapCmapTypeDihedral DihedralType ExtraPointImproper ImproperTypeNonbondedExceptionNonbondedExceptionType RBTorsionType UreyBradley) needs_openmm) integer_types iteritems string_types)range load_topologyTc Cs>ddlm}t}t}x|D]}|j} x|D]} | j} | j} x| D]} | j dkrlt | jd}nVyt | j}Wnt k r| j}YnXt|ts|nd}t| j j| j| j j|d}||| | | ||| <qPWq6Wq"Wx.|D]"\}}|jt||||qW|}|dk rvt|\}}|tj}|tj}|d|d|d|d|d|dg|_d}|dk rt|trt|d d }|j |_ |jdk r|jdk rd }|j|_n||_ |dk rd }||_|jdk rt!"|j|_|dkr |St|tr t|}t||j#s6t$d t%|j |&krdt$d t%|j |&ft'}|j(|j)|j*|j+|j,|j-|j.|j/f}|0r|s|1}t|\}}|tj}|tj}t!"|d|d|d|d|d|dg|_nd|_x4|2D]&}t||j3rF|j3|kr:t4||n t5||nt||j6r`t7||nt||j8rzt9||nt||j:rt;||nt||j<rt=||s&d |_>t?@d tAndt||jBrtC||nJt||jDrtE|||n.t||r qnd |_>t?@dtF|jGtA|HtF|qW|S)aL Creates a :class:`parmed.structure.Structure` instance from an OpenMM Topology, optionally filling in parameters from a System Parameters ---------- topology : :class:`simtk.openmm.app.Topology` The Topology instance with the list of atoms and bonds for this system system : :class:`simtk.openmm.System` or str, optional If provided, parameters from this System will be applied to the Structure. If a string is given, it will be interpreted as the file name of an XML-serialized System, and it will be deserialized into a System before used to supply parameters xyz : str or array of float Name of a file containing coordinate information or an array of coordinates. If file has unit cell information, it also uses that information unless ``box`` (below) is also specified box : array of 6 floats Unit cell dimensions condense_atom_types : bool, default=True If True, create unique atom types based on de-duplicating properties. If False, create one atom type for each atom in the system, even if its properties match an existing atom type. Returns ------- struct : :class:`Structure ` The structure from the provided topology Raises ------ OpenMMWarning if parameters are found that cannot be interpreted or processed by ParmEd TypeError if there are any mismatches between the provided topology and system (e.g., they have different numbers of atoms) IOError if system is a string and it is not an existing file Notes ----- Due to its flexibility with CustomForces, it is entirely possible that the functional form of the potential will be unknown to ParmEd. This function will try to use the energy expression to identify supported potential types that are implemented as CustomForce objects. In particular, quadratic improper torsions, when recognized, will be extracted. Other CustomForces, including the CustomNonbondedForce used to implement NBFIX (off-diagonal L-J modifications) and the 12-6-4 potential, will not be processed and will result in an unknown functional form. If an OpenMM Atom.id attribute is populated by a non-integer, it will be used to name the corresponding ParmEd AtomType object. rN)name) atomic_numberr$masstyperFT)Z skip_bondszSsystem must be an OpenMM System object or serialized XML of an OpenMM System objectz?Topology and System have different numbers of atoms (%d vs. %d)z-Unknown functional form of CustomTorsionForcezUnsupported Force type %s)IZ simtk.openmmZopenmmr dictZchainsidZresiduesr$indexatomselementrint ValueError isinstancerrr&r'Zadd_atombondsappendrZgetPeriodicBoxVectorsr value_in_unitu angstromsZdegreesboxr!r Z coordinatesnpZasarrayZSystem TypeErrorlengetNumParticlessetZCMMotionRemoverZAndersenThermostatZMonteCarloBarostatZMonteCarloAnisotropicBarostatZMonteCarloMembraneBarostatZCustomExternalForceZ GBSAOBCForceZ CustomGBForceZusesPeriodicBoundaryConditionsZgetDefaultPeriodicBoxVectorsZ getForcesZHarmonicBondForce_process_urey_bradley _process_bondZHarmonicAngleForce_process_angleZPeriodicTorsionForce_process_dihedralZRBTorsionForce_process_rbtorsionZCustomTorsionForce_process_improperunknown_functionalwarningswarnrZCMAPTorsionForce _process_cmapZNonbondedForce_process_nonbondedr(__name__add)ZtopologysystemZxyzr7condense_atom_typesZmmstructZatommapcchainrZresidueZresidaatomZaidZatypeZa1a2ZvectorsZlengZangZ loaded_boxZprocessed_forcesZignored_forcesforcerT6lib/python3.7/site-packages/parmed/openmm/topsystem.pyr#s8       *               2         c Cst}xt|D]}||\}}}}|j||j|}} |j|jf} | |kr^|| } n"t|d|} | || <|j| | |j krx |j D]} | | krPqWt d| | _ q|j t || | dqW|jdS)z' Adds bond parameters to the structure g?z4aj in ai.bond_partners, but couldn't find that bond!)r(N)r*r" getNumBondsgetBondParametersr-_valuerZ bond_typesr3 bond_partnersr2 RuntimeErrorr(rclaim) rLrStypemapiiijreqkaiajkeyZ bond_typeZbondrTrTrUr>s$     r>c Cst}xt|D]}||\}}}}}|j|jf} |j||j||j|} } } | |krl|| } n"t|d|} | || <|j| |j t | | | | dqW|j dS)z( Adds angle parameters to the structure g?)r(N) r*r"Z getNumAnglesZgetAngleParametersrXr-rZ angle_typesr3anglesr r[)rLrSr\r]r^r_raZtheteqZfrc_krdrbrcakZ angle_typerTrTrUr?s "  r?c Cs|jstdtt}xt|D]}||\}}}}|j||j|}} |j |j f} |jr|| j krtd|j | j ft| |kr|| } n"t |d|} | || <|j | |jt|| | dq&W|j dS)z/ Adds Urey-Bradley parameters to the structure zAdding what seems to be Urey-Bradley terms before Angles. This is unexpected, but the parameters will all be present in one form or another.zAdding what seems to be Urey-Bradley terms, but atoms %d and %d do not appear to be angled to each other. Parameters will all be present, but may not be in expected places.g?)r(N)rerDrErr*r"rVrWr-rXZangle_partnersidxrZurey_bradley_typesr3Z urey_bradleysrr[) rLrSr\r]r^r_r`rarbrcrdZ urey_typerTrTrUr=s&    r=c Cst}xt|D]}||\}}}}}} } |j||j|} } |j||j|} }|| j| jf}||kr|||}n t| || }|||<|j|| | j ko| | j ko|| j k}|j t | | | |||dqW|j dS)z) Adds periodic torsions to the structure )improperr(N) r*r"getNumTorsionsgetTorsionParametersr-rXrZdihedral_typesr3rYZ dihedralsrr[)rLrSr\r]r^r_ralZperZphaseZphi_krbrcrfalrd dihed_typerhrTrTrUr@s     r@c Cs2t}xt|D]}||\ }}}}}} } } } } |j||j|}}|j||j|}}y$|j| j| j| j| j| jf}d}Wn*tk r|| | | | | f}tj}YnX||kr||}n>t ||| || || || || |}|||<|j ||j t |||||dqW|j dS)z3 Adds Ryckaert-Bellemans torsions to the structure r))r(N)r*r"rirjr-rXAttributeErrorr5kilojoules_per_molerZrb_torsion_typesr3Z rb_torsionsrr[)rLrSr\r]r^r_rarkZc0Zc1Zc2Zc3Zc4Zc5rbrcrfrlrdfrmrTrTrUrAs$  * rAc Cs$|dd}d|kr*|d|d}|dkr6dS|drFd}nd }t}xt|D]}||\}}}} \} } |j||j|} } |j||j| }}| | f}||kr||}n8t | |t j t j d | t j }|||<|j ||jt| | |||d q^W|j d S) a@ Processes a CustomTorsionForce and looks at the energy expression to see if it's a quadratic improper torsion. Then adds the parameters if applicable Returns ------- is_improper : bool Returns True if the energy expression is recognized as a quadratic improper, and False otherwise  r%;N)z0.5*k*(theta-theta0)^2zk*(theta-theta0)^2zk*dtheta_torus^2z0.5*k*dtheta_torus^2Fz0.5g?r)r)r(T)ZgetEnergyFunctionreplacer, startswithr*r"rirjr-rr5Zkilojoule_per_moleZradianZimproper_typesr3Z impropersrr[)rLrSZeqnZfacr\r]r^r_rarkZpsi_kZpsi_eqrbrcrfrlrdZimp_typerTrTrUrB2s.      rBc CsXg}xft|D]V}||\}}t|r:t||}nt||tj}|||jj |_d|_ qWxt| D]}| |\ }}}} } } } } }|| ks| | ks| | krtdtqz|j||j||j| }}}|j| |j|}}||}d|_ |jt||||||dqzWx"|D]}|j r,|j|q,W|jdS)z Adds CMAPs to the structure Fz5Non-continuous CMAP torsions detected. Not supported.T)r(N)r"Z getNumMapsZgetMapParametersr5Z is_quantityrror3gridTZ switch_rangeZusedrirjrDrErr-Zcmapsr cmap_typesr[)rLrSrwr]sizerutypZmapidxZijZikZilZjiZjjZjkZjlrbrcrfrlZamZ cmap_typerTrTrUrF\s0    "  rFc Cs`t}tt}|t|jks(tdxt|D]}|j|}||\}}} |j dkrd|j nt |j } | |j | j f} | |kr|r|| } nD|j dkr|| d7<d| || f} t | d|j|j || <} |tj|_|tjdd} | tj} | | | | |_| j|_ q6Wtt}tt}xr|jD]h}x`|jD]V}||k rb|||x6|jD],}||kr|qj||k rj|||qjWqFWq:Wx t|D]}||\}}}}} |tjd}|tj}| tj} |j||j|}}|dkrL|dks,| dkrL||||||qy||j|j}Wn0tk r|dkrt d |d}YnXt!|d| |}|j"#t$|||d |j%#|qW|j%&d }x$|j%D]}|j'dk r|j'}PqWx"|j%D]}|j'dkr||_'qWx8t(|D],\}}|||r,d |_)t*+d t,Pq,WdS)z, Adds nonbonded parameters to the structure zAtom # mismatchr%r)z%s%dNgÚ?rrz(Can't scale charge product 0 to match %s)r(g?Tz.Detected incomplete exceptions. Not supported.)-r*rr/r;r:r-AssertionErrorr"ZgetParticleParametersr(r r&rXrr'r4r5Zelementary_chargeZcharger6Zkilocalories_per_moleZ set_lj_params atom_typer$r<rYrIZgetNumExceptionsZgetExceptionParametersZangstromZkilocalorie_per_moleZeroDivisionErrorr0rZadjustsr3rZ adjust_typesr[chgscaler rCrDrEr)rLrSrKr\Zelement_typemapr^rQZchgZsigZepsZ atype_namerdr{ZrminZexplicit_exceptionsZbond_graph_exceptionsrRZa3r]r_qrbrcr}ZnbtypeZfirst_scaling_factorZ adjust_type exceptionsrTrTrUrG{s                            rG)NNNT);__doc__Z __future__rrrrD collectionsrZnumpyr8r%rr5rrZformatsr Zgeometryr Zperiodic_tabler Z structurer Ztopologyobjectsr rrrrrrrrrrrrrrrrZutils.decoratorsrZ utils.sixrr r!Zutils.six.movesr"__all__r#r>r?r=r@rArBrFrGrTrTrTrUs4       L   '*