ó Ë™xTc@ s2ddlmZddlmZddlmZmZmZmZddl Z ddl m Z ddl m Z mZddlmZddlmZmZdd lmZdd lmZdd lmZe jd „Zd „Zd„Zdddddd„Z dedd„Z!dd„Z"dd„Z#dS(iÿÿÿÿ(tdivision(t defaultdict(tcostpitsintsqrtN(tcrystal(tsasakitchemical_elements(tcommon_residue_names_water(tnull_outtxfrange(tserver(tflex(tgaussian_fit_1d_analyticalc C sñttjƒƒ}x1tjdD]"}|tkr |j|ƒq q Wd}|jƒ}xŒ|jƒD]~}xu|j ƒD]g}x^|j ƒD]P}xG|j ƒD]9}|j j ƒ|krž|jƒ} g} x³| D]«} | jj ƒ} | dkrüd} n*| dkrd} ntj| ƒjƒ} | j| jƒƒ|j | _d| _d | _d | _d | _| jd | | _qÒWd |_ xJt| | ƒD]6\} }|d|| jƒ| jfIJ|d7}qšWqžqžWq‹WqxWqeW||fS(sQ Convert any elemental ions in the PDB hierarchy to water, resetting the occupancy and scaling the B-factor. The atom segids will be set to the old resname. NOTE: this does not change the corresponding scatterer in the xray structure, but a new xray structure can be obtained by calling hierarchy.extract_xray_structure(crystal_symmetry). Parameters ---------- pdb_hierarchy : iotbx.pdb.hierarchy.root log : file, optional Returns ------- iotbx.pdb.hierarchy.root New pdb hierarchy with its ions anonymized int Number of atoms that were anonymized. s_lib_charge.resnameitHtDitHEis O tOtgð?i tHOHs%s --> %s, B-iso = %.2f(RR(R(tsetRtproper_upper_listR tparamstWATER_RES_NAMEStaddt deep_copytmodelstchainstresidue_groupst atom_groupstresnametstriptatomstelementRttablet atomic_numbertappendtid_strtsegidtnametcharget occupancytbtzip(t pdb_hierarchytlogt ion_resnamesRt n_convertedtmodeltchaint residue_groupt atom_groupR!tid_strstatomtelemR$R&((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pytanonymize_ionssB               !cC sr|jƒ|jƒjƒks$t‚|jƒt|dd„dtƒ}tjg|D]}|j^qVƒ}|S(sN Creates a list of atoms in pdb_atoms, sorted first by their atomic number, then by occupancy, and finally, by isotropic b-factor. Parameters ---------- pdb_atoms : iotbx.pdb.hierarchy.af_shared_atom xray_structure : cctbx.xray.structure.structure Returns ------- flex.size_t of int i_seqs of sorted atoms tkeycS s1tj|jjƒjƒƒjƒ|j|jfS(N(RR#R"R tupperR$toccR+(tx((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pytZstreverse( tsizet scattererstAssertionErrort reset_i_seqtsortedtTrueR tsize_tti_seq(t pdb_atomstxray_structuret atoms_sortedR6tsele((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pytsort_atoms_permutationGs$   %c C sÌtjƒ}g}x³|jƒD]¥}xœ|jƒD]Ž}x…|jƒD]w}xn|jƒD]`}|jjƒ|krX|jƒ}t |ƒdks—t ‚x|D]}|j |ƒqžWqXqXWqEWq2WqW|S(s± Collects a list of all ions in pdb_hierarchy. Parameters ---------- pdb_hierarchy : iotbx.pdb.hierarchy.root Returns ------- list of iotbx.pdb.hierarchy.atom i( RRRRRRRR R!tlenRAR%( R-telementstionsR1R2R3R4R!R6((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pyt collect_ionsas   $g@s segid IONc%C s |dkrtƒ}n|jƒ}|} t|ƒdkrm| ddjg|D]} d| ^qOƒ7} nCt|ƒdkr°| ddjg|D]} d| ^q’ƒ7} n|j| ƒjƒ} t| ƒdkrággfS|jƒ} | jƒ| j | ƒ} |j d|dƒ}|j ƒ}| j ƒ}|j d|ƒ}|j|d |jƒƒtjd |d |ƒ}|jƒ}|jƒjƒ}g}x'tt| ƒƒD]}|jgƒq®WxÀ|D]¸}|j|krð|j|ksÌ|j|kr|j|krqÌn|j|kr9|j|j}}n|j|j}}|||}t|jƒ}||}||j|ƒqÌWg}g}xjt|ƒD]\\}} | |}!t| ƒdkró|d |!jƒIJ|j|!jƒƒq¡g}"xL| D]D}||}#|!jjƒ|#jjƒkr|"j|#jƒƒqqWt|"ƒd krÖ|j|!jƒƒt|"ƒd krµ|d|!jƒIJx=|"D]}$|d|$IJqšWqý|d|!jƒ|"dfIJq¡|d |!jƒIJ|j|!jƒƒq¡W||fS(s Compares two pdb structures to determine the number of ions that appear in the reference structure and are either matched or missing in the other structure. Parameters ---------- hierarchy : iotbx.pdb.hierarchy.root reference_hierarchy : iotbx.pdb.hierarchy.root reference_xrs : ... distance_cutoff : float, optional log : file, optional ignore_element : iterable, optional only_elements : iterable, optional sel_str_base : str, optional Returns ------- int Number of ions in reference_hierarchy that were also found in hierarchy. int Number of ions in reference_hierarchy that were not found in hierarchy. is and (%s)s or s element %ss and not (%s)tbuffer_thicknessgš™™™™™¹?t sites_carttmin_distance_sym_equivt asu_mappingstdistance_cutoffsNo match for %sisMultiple matches for %s:s %ssIon %s matches %sN(tNoneR tatom_selection_cacheRLtjoint selectiont iselectionR!RBtselectRSt unit_cellt extract_xyzt fractionalizetprocess_sites_fracRRRtneighbors_fast_pair_generatorR@R?trangeR%RFtj_seqRtdist_sqt enumerateR&R"R:(%t hierarchytreference_hierarchyt reference_xrsRTR.tignore_elementst only_elementst sel_str_baset sel_cachetsel_strtetion_iselRGRNRSR[RQt sites_fractpair_generatortreference_atomstn_xraytion_ref_i_seqstktpairtion_seqtref_seqt site_fractdxyzRatmatchedtmissingRFt ref_i_seqstiontref_ionstref_atomtref_ion((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pyt compare_ions{s‚    % %                  gš™™™™™É?ic C sô|g}dg}xÕt|||ƒD]Á}x¸tt t|ƒD]£}xštt t|ƒD]…}|t|ƒt|ƒ|d} |t|ƒt|ƒ|d} |t|ƒ|d} |j| | | fƒ|j|ƒqYWq?Wq%W||fS(s Generates a list of points and their associated radius in steps around a sphere. Parameters ---------- point : tuple of float, float, float X, Y, Z, coordinates to center the sampling around. radius : float Max radius around the center to sample. radius_step : float, optional Steps along the radius to use when sampling. angle_step : float, optional Steps around each radii distance to use when sampling. Amount is in radians. Returns ------- list of tuple of float, float, float List of points to be sampled. list of float List of radii corresponding to each point. iii(R RRRR%( tpointtradiust radius_stept angle_steptpointstradiusestrtthetatphiR<tytz((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pyt_get_points_within_radiusÜs  ""gš™™™™™ù?cC sët||ƒ\}}g|D]}|j|j|ƒƒ^q}tjƒtjƒ}} xFt||ƒD]5\} } | dkri|j| ƒ| j| ƒqiqiWytd|d| ƒ} Wntk rÖ} | GHdSX| j | j fSdS(s– Fit a gaussian function to the map around a site. Samples points in concentric spheres up to radius away from the site. f(x) = a * exp(-b * x ** 2) Parameters ---------- unit_cell : uctbx.unit_cell site_cart : tuple of float, float, float The site's cartesian coordinates to sample the density around. real_map : scitbx.array_family.flex Real space map of the electron density in the unit cell. radius : float, optional The max radius to use for sampling. Returns ------- float Height of gaussian curve. float Spread of guassian curve. See Also -------- scitbx.math.gaussian_fit_1d_analytical iR<RŠgN(gg( RŒttricubic_interpolationR]R tdoubleR,R%Rt RuntimeErrortaR+(R[t site_carttreal_mapR‚R…R†tit map_heightsR<RŠtradtheighttfitterr((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pyt fit_gaussians(  g@cC s’g}ttƒ}xy|D]q}|jƒ|kr|jjƒ}xG|D]}||krGPqGqGW|j}||cd7<|j|ƒqqW|S(s] Count the number of residues of each type involved in the coordination sphere. This may yield additional clues to the identity of ions, e.g. only Zn will have 4 Cys residues. Parameters ---------- nearby_atoms : list of mmtbx.ions.environment.atom_contact distance_cutoff : float, optional Returns ------- dict of str, int i(RtinttdistanceR6tparentRR%(t nearby_atomsRTtunique_residuestresidue_countstcontactRœtresidueR((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pytcount_coordinating_residues6s     ((($t __future__Rt collectionsRtmathRRRRtsystcctbxRt cctbx.eltbxRRt iotbx.pdbR Rt libtbx.utilsR R t mmtbx.ionsR tscitbx.array_familyR t scitbx.mathRtstdoutR8RKRORUR€RŒR™R¢(((s>/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/utils.pyts&" 7    _& 3