ó Ë™xTc@ s\dZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z ddlmZdd lmZd Zeeƒ\ZZZZZZZZZZZZZ Z!d d d dddddddddddgZ"defd„ƒYZ#defd„ƒYZ$defd„ƒYZ%dd e&d!„Z'd"„Z(d#„Z)d$S(%sg Deals with examing the atoms around a site and recognizing distinct and useful chemical environments. iÿÿÿÿ(tdivision(tions(tcommon_residue_names_get_class(tsasaki(tcol(tSorry(tslots_getstate_setstate(tCounterisCoordinating carboxy groupsCoordinating amide groupsCoordinating backbone atomsCoordinating water moleculesCoordinating sulfate groupsCoordinating phosphate groupsCoordinating disulfide groupsCoordinating primary nitrogensCoordinating secondary nitrogensCoordinating tertiary nitrogensCoordinating chloridesCoordinating oxygensCoordinating nitrogensCoordinating sulfurtScatteringEnvironmentc B sPeZdZddddddddd d d g Zd d d d d d d „ZRS(s— Container for information summarizing a site's scattering environment. Attributes ---------- d_min : float wavelengeth : float fp : float fpp : float b_iso : float b_mean_hoh : float occ : float fo_density : tuple of float, float fofo_density : tuple of float, float anom_density : tuple of float, float pai : float Principal axes of inertia at site, currently unused. td_mint wavelengthtfptfpptb_isot b_mean_hohtocct fo_densityt fofc_densityt anom_densitytpaic C sÅ||gjdƒdks!t‚||gjdƒdksBt‚||gjdƒdksct‚|j|} |jjƒjƒ|_|j|_|j|ƒ|j |ƒ|_ |_ |j j | jƒ} |dk ræ||_n!tjj|j | j|ƒ|_|dk r||_n|j| ƒdf|_|dk rO||_n0|dk rv|j| ƒdf|_n d|_|j|ƒ|_|j|_| j|_|j|ƒjƒ|_dS(Nii(NN(tcounttNonetAssertionErrort pdb_atomstfmodeltf_obsR R tget_fptget_fppR R t unit_cellt fractionalizetxyzRRtutilst fit_gaussianRteight_point_interpolationRt get_b_isoR RRtprincipal_axes_of_inertiatcenter_of_massR( tselfti_seqtmanagertfo_maptfofc_maptanom_mapRRRtatomt site_frac((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt__init__Gs0 !!!  %           N(t__name__t __module__t__doc__t __slots__RR-(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyR2st atom_contactcB sªeZdZdddddddgZd„Zd „Zd „Zed „Zd „Z d „Z e d„ƒZ d„Z d„Zed„Zd„Zd„Zd„ZRS(sp Container for information about an interacting atom. Most of the methods are simply wrappers for frequently called operations on the atom object, but symmetry-aware. Attributes ---------- atom : iotbx.pdb.hierarchy.atom charge : int element : str rt_mx : cctbx.sgtbx.rt_mx site_cart : tuple of float, float, float vector : scitbx.matrix.rec R+tvectort site_carttrt_mxtis_carboxy_terminustelementtchargecC sg|jƒ|_t|ƒ|_||_||_||_tjj |ƒ|_ tjj |ƒ|_ dS(N( t fetch_labelsR+t_is_carboxy_terminusR6R3R4R5Rtservert get_elementR7t get_chargeR8(R%R+R3R4R5((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyR-s   cC s t|jƒS(sn Actual distance from target atom. Returns ------- float Distance, in angstroms. (tabsR3(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pytdistance™s cC st|j|jƒS(sÄ Distance from another coordinating atom. Parameters ---------- other : mmtbx.ions.environment.atom_contact Returns ------- float Distance, in angstroms. (R>R3(R%tother((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt distance_from¤s cC sF|jjƒ r5| r5|jjƒdt|jƒS|jjƒSdS(s Creates a string from the atom's id string and the symmetry operator associated with that site. Parameters ---------- suppress_rt_mx : bool, optional Don't include symmetry operator information in the string. Returns ------- str t N(R5t is_unit_mxR+tid_strtstr(R%tsuppress_rt_mx((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyRD³scC s|jjjƒS(s^ Retrieves the coordinating atom's name (i.e. "OX1") Returns ------- str (R+tnametstrip(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt atom_nameÆscC s|jjƒjjƒjƒS(sw Retrieves the residue name associated with te coordinating atom (i.e. "ARG") Returns ------- str (R+R9tresnameRHtupper(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyRJÐscC s |jjS(sP Occupancy of the coordinating atom. Returns ------- float (R+R(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyRÚs cC s |jjS(s^ Retrieves the sequence ID of the coordinating atom. Returns ------- int (R+R&(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt atom_i_seqåscC s|jjƒjjƒS(s| Retrieves the alternate conformation label, if any, of the coordinating atom. Returns ------- str (R+R9taltlocRH(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyRMïs cC s^|jjƒ}|j|jƒ|jj}|jjƒsA|rE|S|dt|jƒSdS(sÜ Unique identifier for an atom, ignoring the altloc but taking the symmetry operator (if any) into account. Parameters ---------- suppress_rt_mx : bool, optional Returns ------- str RBN(R+R9tchain_idtresidRGR5RCRE(R%RFtlabelstbase_id((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pytatom_id_no_altlocús cC s|jƒ|jƒkS(sÒ Equality operator, taking symmetry into account but ignoring the altloc identifier. Parameters ---------- other : mmtbx.ions.environment.atom_contact Returns ------- bool (RR(R%R@((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt__eq__s cC s |jƒS(N(R?(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt__abs__scC s |jƒS(N(RD(R%((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt__str__ s(R.R/R0R1R-R?RAtFalseRDRIRJtpropertyRRLRMRRRSRTRU(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyR2s        tChemicalEnvironmentcB sAeZdZdddddgZd„Zd d„Zd„ZRS( sY Container for information summarizing a site's chemical environment. Attributes ---------- atom : iotbx.pdb.hierarchy.atom contacts : list of mmtbx.ions.environment.atom_contact contacts_no_alts : list of mmtbx.ions.environment.atom_contact chemistry : collections.Counter of int, int geometry : list of tuples of str, float R+tcontactstcontacts_no_altst chemistrytgeometrycC sý|j|jƒ|_||_g|_x˜t|ƒD]Š\}}|jdkrVq5nt}xG||dD]7}t|j|jƒrk|j |j krkt }PqkqkW|r5|jj |ƒq5q5W|j |j|ƒ|_ tjj|jdtƒ|_dS(s˜ Parameters ---------- i_seq : int contacts : list of mmtbx.ions.environment.atom_contact manager : mmtbx.ions.identify.manager tHtDitminimizer_methodN(R]R^(RR9R+RYRZt enumerateR7tTruet_same_atom_different_altlocR5RVtappendt_get_chemical_environmentR[RR\tfind_coordination_geometry(R%R&RYR'tindextcontactt no_alt_loct other_contact((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyR-1s$   cC s¥|dkr!tjj|ƒ}ntjd|d|ƒ}tjj||jƒ}td„|Dƒƒ}|dkr•tt|t dƒƒƒ|}nd}||fS(sU Calculates the BVS and VECSUM for a given element / charge identity. Parameters ---------- element : str The element identity to calculate valences for. charge : int, optional The charge to calculate valences for. Returns ------- float Bond-valence sum (BVS). float Vector sum (VECSUM). Notes ----- .. [1] Müller, P., Köpke, S. & Sheldrick, G. M. Is the bond-valence method able to identify metal atoms in protein structures? Acta Crystallogr. D. Biol. Crystallogr. 59, 32–7 (2003). R7R8cs s|]}t|ƒVqdS(N(R>(t.0ti((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pys rsiN(iii( RRR;R=tmetal_parameterstcalculate_valencesRYtsumR>R(R%R7R8t ion_paramstvectorstbvstvecsum((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyt get_valenceVs  "c s“‡fd†}‡fd†}tƒ}xe|D]]}|j}|jj}g||ƒD]} tjjˆj| ƒ^qV} |||ƒƒ} |dkr¬|tcd7|dkr|tcd7}|ˆko?ˆj|ƒdko?ˆjƒ|jƒkVqdS(gffffffþ?N(RAR?(RjRi(Rg(sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pys BsR(R]R^N(R„R‚RRƒ(RƒRR(Rt sites_fract get_rt_mxtinversetitemsR7RKRHRbtmultiplyt orthogonalizeRR>RR2RCR?RcRRLtanyRf( R&txray_structureRt asu_mappingst asu_tableRttfar_distance_cutofftnear_distance_cutofftfilter_by_bondingRYRRŸR,tasu_dicttsite_it rt_mx_i_invtatom_iR|t j_sym_groupstsite_jtatom_jt j_sym_grouptj_sym_idR5tsite_jit site_ji_carttvec_itvec_jitfilteredt all_i_seqst bonded_j_seqsRi((RgsD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pytfind_nearby_atomsïsn                     cC s…d}t|ƒjdkr0|jƒjƒ}n't|ƒjdksKt‚|jƒ}x'|D]}|jjƒdkr^tSq^Wt S(sb Checks if an atom or residue is part of a carboxy terminus. Parameters ---------- pdb_object : iotbx.pdb.hierarchy.atom or iotbx.pdb.hierarchy.residue_group or iotbx.pdb.hierarchy.atom_group Returns ------- bool .. note:: Deprecated in favor ChemicalEnvironment._get_chemical_environment in the SVM code. R+t residue_groupt atom_grouptOXTN(R½R¾( RttypeR.tparenttatomsRRGRHRaRV(t pdb_objectRÂR+((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyR:Ys  c C s˜g||gD]}|jƒ^q \}}|jjƒ|jjƒ}}|j|j}}|jƒ|jƒ} } ||ko—||ko—| | kS(sÎ Determines whether atom1 and atom2 differ only by their alternate location. Parameters ---------- atom1 : iotbx.pdb.hierarchy.atom atom2 : iotbx.pdb.hierarchy.atom Returns ------- bool (R9RGRHRNRO( tatom1tatom2Rktlabel1tlabel2tname1tname2tchain1tchain2tres1tres2((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyRbts +N(*R0t __future__RtmmtbxRt iotbx.pdbRR‰t cctbx.eltbxRt scitbx.matrixRt libtbx.utilsRtlibtbxRt collectionsRtN_SUPPORTED_ENVIRONMENTStrangeR•R–R“RŠR‹RŒR’RŽRRR‡RˆRR‘tCHEM_ENV_LABELSRR2RXRaR¼R:Rb(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/environment.pyts@6 M¤Ó a