B ba@sdZddlmZmZmZddlZddlmZddlmZddl m Z ddl m Z m Z dd lmZmZmZmZmZdd lmZmZdd lmZGd d d eZddZddZdS)z This module contains classes for parsing and processing CHARMM parameter, topology, and stream files. It only extracts atom properties from the topology files and extracts all parameters from the parameter files Author: Jason M. Swails )absolute_importdivisionprint_functionN) OrderedDict)copy) permutations)ParameterErrorParameterWarning)AtomType DihedralTypeDihedralTypeList NoUreyBradleyUnassignedAtomType) iteritems itervalues)rangec@sfeZdZdZddZddZedddZdd d Ze d d Z e d dZ e j ddZ ddZdS) ParameterSeta Stores a parameter set defining a force field Attributes ---------- atom_types : dict(str:AtomType) Dictionary mapping the names of the atom types to the corresponding AtomType instances atom_types_int : dict(int:AtomType) Dictionary mapping the serial indexes of the atom types to the corresponding AtomType instances atom_types_tuple : dict((str,int):AtomType) Dictionary mapping the (name,number) tuple of the atom types to the corresponding AtomType instances bond_types : dict((str,str):AtomType) Dictionary mapping the 2-element tuple of the names of the two atom types involved in the bond to the BondType instances angle_types : dict((str,str,str):AngleType) Dictionary mapping the 3-element tuple of the names of the three atom types involved in the angle to the AngleType instances urey_bradley_types : dict((str,str,str):BondType) Dictionary mapping the 3-element tuple of the names of the three atom types involved in the angle to the BondType instances of the Urey-Bradley terms dihedral_types : dict((str,str,str,str):list(DihedralType)) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the dihedral to the DihedralType instances. Since each torsion term can be a multiterm expansion, each item corresponding to a key in this dict is a list of `DihedralType`s for each term in the expansion improper_types : dict((str,str,str,str):ImproperType) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the improper torsion to the ImproperType instances improper_periodic_types : dict((str,str,str,str):DihedralType) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the improper torsion (modeled as a Fourier series) to the DihedralType instances. Note, the central atom should always be put in the *third* position of the key rb_torsion_types : dict((str,str,str,str):RBTorsionType) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the Ryckaert-Bellemans torsion to the RBTorsionType instances cmap_types : dict((str,str,str,str,str,str,str,str):CmapType) Dictionary mapping the 5-element tuple of the names of the five atom types involved in the correction map to the CmapType instances nbfix_types : dict((str,str):(float,float)) Dictionary mapping the 2-element tuple of the names of the two atom types whose LJ terms are modified to the tuple of the (epsilon,rmin) terms for that off-diagonal term pair_types : dict((str,str):NonbondedExceptionType) Dictionary mapping the 2-element tuple of atom type names for which explicit exclusion rules should be applied parametersets : list(str) List of parameter set names processed in the current ParameterSet residues : dict(str:ResidueTemplate|ResidueTemplateContainer) A library of ResidueTemplate objects mapped to the residue name defined in the force field library files cCst|_|_t|_t|_t|_t|_t|_t|_t|_ t|_ t|_ t|_ t|_ t|_g|_d|_t|_t|_d|_|_t|_dS)Nlorentzg?)r atom_typesZatom_types_stratom_types_intatom_types_tuple bond_types angle_typesurey_bradley_typesdihedral_typesimproper_typesimproper_periodic_typesrb_torsion_types cmap_types nbfix_types pair_typesZ parametersets_combining_ruleresiduespatchesZ default_sceeZ default_scnb_improper_key_map)selfr'0lib/python3.7/site-packages/parmed/parameters.py__init__Ks& zParameterSet.__init__cCst|}x$t|jD]\}}t||j|<qWx$t|jD]\}}t||j|<q\}}||j kr0qt|}||j |<||j tt|<qWxLt|j D]>\}}||j kr~qft|}||j |<||j tt|<qfWxLt|j D]>\}}||j kr̐qt|}||j |<||j tt|<qWx6t|j D](\}}||j krqt||j |<qWxLt|jD]>\}}||jkrRq:t|}||j|<||jtt|<q:WxLt|jD]>\}}||jkrqt|}||j|<||jtt|<qWxLt|jD]>\}}||jkrqt|}||j|<||jtt|<qWx&t|jD]\}}t||j|<q$Wx&t|jD]\}}t||j|<qLWt|j|_|j|_|S)N)typerrrrrrtuplereversedr!rrrrrrrr#r$r%combining_rule)r&otherkeyitemtypr'r'r(__copy__as                   zParameterSet.__copy__Tc Cs&|}t}x|jD]}|jtdfkr`t|jd|j|j}||j |j |j |j ||j |j<qt|j}||j t|<|jdk r||jt|<||jt|t|f<qW|r&xp|jD]f}|jjrt|jj}xH|D]@}|jj|\} } } } ||jf|jkr q| | f|j|j|f<qWqWx|jD]} | jdkrBq.| jj| jjf}||jkr|s.|j|| jkr.td|q.t| j}| jj| jjf}||j|<||jtt|<q.Wx|j D]}|jdkrސq|jj|jj|j!jf}||j"kr(|s|j"||jkrtd|qt|j}|jj|jj|j!jf}||j"|<||j"tt|<|j#dkr|jj|jj|j!jf}t$|j%|<t$|j%tt|<qWx|j&D]~}|jdkrȐq|j'r0xZt(|D]N}||j)kr|s|j)||jkrtd|qt|j}||j)|<qWq|jj|jj|j!j|j*jf}||j+kr||r|st,|jt-r|j+||jkrtd|n>t,|jt.rx.|j+|D]}||jkrPqWtd|qq||j+krt,|jt-r6d||<d|tt|<t|j}||j+|<||j+tt|<n`x|j+|D]6}|j/|jj/krB|st||jkrttd|PqBWt|j}|j+|0|nt,|jt-rd||<d|tt|<t|j}||j+|<||j+tt|<nJd||<d|tt|<t-}|0t|j||j+|<||j+tt|<qWx|j1D]v}|jdkrRq>|jj|jj|j!j|j*jf}||j2kr|s>|j2||jkr>td |q>t|j|j2|<q>Wx|j3D]}|jdkrԐq|jj|jj|j!j|j*j|jj|j!j|j*j|j4jf}||j5krZ|s|j|j5|krtd |d |d |d |d|dfqt|j}||j5|<||j5tt|<qWt6|j%d k}x|j7D]|}|jdks|jt$krqt8|}|dkrҐq|r||j%krt9:dt;t|j}||j%|<||j%tt|<qW|s^t6|j%d kr^x*|j"D] }||j%krNq:t$|j%|<q:Wx|js|j?s|j@s|jAs|j>s|jBr"tCd|S)a Extracts known parameters from a Structure instance Parameters ---------- struct : :class:`parmed.structure.Structure` The parametrized ``Structure`` instance from which to extract parameters into a ParameterSet allow_unequal_duplicates : bool, optional If True, if two or more unequal parameter types are defined by the same atom types, the last one encountered will be assigned. If False, an exception will be raised. Default is True Returns ------- params : :class:`ParameterSet` The parameter set with all parameters defined in the Structure Notes ----- The parameters here are copies of the ones in the Structure, so modifying the generated ParameterSet will have no effect on ``struct``. Furthermore, the *first* occurrence of each parameter will be used. If future ones differ, they will be silently ignored, since this is expected behavior in some instances (like with Gromacs topologies in the ff99sb-ildn force field) unless ``allow_unequal_duplicates`` is set to ``False`` Dihedrals are a little trickier. They can be multi-term, which can be represented either as a *single* entry in dihedrals with a type of DihedralTypeList or multiple entries in dihedrals with a DihedralType parameter type. In this case, the parameter is constructed from either the first DihedralTypeList found or the first DihedralType of each periodicity found if no matching DihedralTypeList is found. Raises ------ :class:`parmed.exceptions.ParameterError` if allow_unequal_duplicates is False and 2+ unequal parameters are defined between the same atom types. `NotImplementedError` if any AMOEBA potential terms are defined in the input structure Nz,Unequal bond types defined between %s and %sz2Unequal angle types defined between %s, %s, and %sz9Unequal dihedral types defined between %s, %s, %s, and %sTz9Unequal dihedral types defined bewteen %s, %s, %s, and %sFz9Unequal improper types defined between %s, %s, %s, and %sz9Unequal CMAP types defined between %s, %s, %s, %s, and %srrz2Angle corresponding to Urey-Bradley type not foundz,Unequal pair types defined between %s and %sz@Cannot extract parameters from an Amoeba-parametrized system yet)DdictZatoms atom_typerr r*ZmassZ atomic_numberZ set_lj_paramsepsilonrminZ epsilon_14Zrmin_14rrstrZnumberrintrZ has_NBFIXZnbfixlistkeysr Zbondsatom1atom2rr r+r,Zanglesatom3rZfunctrrZ dihedralsimproper_find_improper_keysratom4r isinstancer r ZperappendZ impropersrZcmapsZatom5rlenZ urey_bradleys_find_ureybrad_keywarningswarnr Zadjustsr!Ztrigonal_anglesZout_of_plane_bendsZtorsion_torsionsZ stretch_bendsZ pi_torsionsNotImplementedError)clsZstructZallow_unequal_duplicatesZparamsZfound_dihed_type_listatomr8Z other_atomsZ other_atomr:r9Zrmin14Z epsilon14Zbondr/r1ZangleZdihedralZdttrBZcmapZurey_brads_preassignedureyZadjustr'r'r(from_structuresB,                                        &              zParameterSet.from_structurecCsh||j||j||j|r@||j||j||j||j||j|S)aW This function goes through each of the parameter type dicts and eliminates duplicate types. After calling this function, every unique bond, angle, dihedral, improper, or cmap type will pair with EVERY key in the type mapping dictionaries that points to the equivalent type Parameters ---------- do_dihedrals : bool=True Dihedrals can take the longest time to compress since testing their equality takes the longest (this is complicated by the existence of multi-term torsions). This flag will allow you to *skip* condensing the dihedral parameter types (for large parameter sets, this can cut the compression time in half) Returns ------- self The instance that is being condensed Notes ----- The return value allows you to condense the types at construction time. Example ------- >>> params = ParameterSet().condense() >>> params ) _condense_typesrrrrrrrr)r&Z do_dihedralsr'r'r(condense|s        zParameterSet.condensecCsrt|}x`tt|dD]L}||}x>t|dt|D](}||}||||kr>||||<q>WqWdS)z Loops through the given dict and condenses all types. Parameter --------- typedict : dict Type dictionary to condense rN)r=r>rrG)ZtypedictZkeylistiZkey1jZkey2r'r'r(rQs zParameterSet._condense_typescCs|jS)N)r")r&r'r'r(r-szParameterSet.combining_rulecCs|dkrtd||_dS)N)rZ geometricz/combining_rule must be "lorentz" or "geometric") ValueErrorr")r&valuer'r'r(r-scCsddlm}m}xvt|jD]h}t||rVxX|D] }x|D]}|j|j|_q:Wq0Wqt||sht dx|D]}|j|j|_qnWqWdS)z. Assign atom types to atom names in templates r)ResidueTemplateContainerResidueTemplatez Wrong type!N) Zparmed.modellerrWrXrr#rErr*r8AssertionError)r&rWrXZresidueZresrMr'r'r(typeify_templatess    zParameterSet.typeify_templatesN)T)T)__name__ __module__ __qualname____doc__r)r2 classmethodrPrR staticmethodrQpropertyr-setterrZr'r'r'r(rs4< _ +  rcCs\|j|j}}t|jt|j@}tdd|DdkrDtdt|jt |dj|jfS)z Finds a key for a given Urey-Bradley by finding the middle atom in an angle. Raises a ParameterWarning if no middle atom found cSsh|] }|jqSr')r*).0ar'r'r( sz%_find_ureybrad_key..rz-Urey-Bradley %r shares multiple central atomsr) r?r@set bond_partnersrGrIrJr r*r=)rOZa1Za2Zshared_bond_partnersr'r'r(rHs  rHc#s|jstd|j|j|j|jh}xp|D]hxb|D]}|kr@q2|jkr2Pq2Wx:tfdd|DD] }|d|dj|dfVqhWdSq(Wx@t|jj|jj|jjgD]"}|d|d|jj|dfVqWdS)z? Finds the central atom (i.e., that bonded to everything else) z%Should not be called on non-improper!csg|]}|k r|jqSr')r*)rcrd)rMr'r( sz'_find_improper_keys..rrr4N) rBrYr?r@rArDrgrr*)ZdihZ all_atomsZoatomr/r')rMr(rCs     rC)r^Z __future__rrrrI collectionsrr itertoolsr exceptionsr r Ztopologyobjectsr r r rrZ utils.sixrrZutils.six.movesrobjectrrHrCr'r'r'r(s    >