əxTc@ sddZddlmZddlZddlmZmZmZddl m Z ddlmZddl m Z ddl Z ddlZddlZdd d d gZd d d dgZdddddd dgZeedddd ddgZdZdZdZdefdYZdefdYZd ZeZd!efd"YZdS(#s This package is used to model elemental ions in crystal structures. It handles both identification and building of ions, but relies on the solvent module to flag candidate sites for screening. Notes ----- .. [1] Echols, N. et al. Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallogr. D. Biol. Crystallogr. 70, 1104–14 (2014). i(tdivisionN(t group_argstAutotslots_getstate_setstate(tSorry(R(texptMGtCAtZNtCLtFtBRtIODtMNtFEtCOtCUtNItPTtNAtKtCDtHGcC s|dkrdS|jdS(Nt.t,(tNonetsplit(tparam((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt_cif_param_as_lists cC s|dkrdSt|S(NR(Rtint(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt_cif_param_as_int!s cC s|dkrdSt|S(NR(Rtfloat(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt_cif_param_as_float%s tmetal_parameterscB s#eZdZdZdZRS(cC sd|jj|jfS(Ns%s%+d(telementtuppertcharge(tself((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt__str__*scC s|jS(sX Gets the charge of a parameter as an integer. Returns ------- int (R$(R%((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt charge_as_int-scC s_d}|jdkrd}n|jdkr6d}nd|jjt|j|f}|S(s* Makes a string showing the element and its associated charge. Note that this format is slightly different from the __str__ method, which puts the +/- between the element symbol and the charge number. Returns ------- str Examples -------- >>> from mmtbx.ions import metal_parameters >>> print metal_parameters(element="FE", charge=3) FE+3 >>> print metal_parameters(element="FE", charge=3).scattering_type() FE3+ >>> print metal_parameters(element="CL", charge=-1).scattering_type() CL1- tit+t-s%2s%1d%s(R$R"tstriptabs(R%t charge_symbolts((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytscattering_type7s  %(t__name__t __module__R&R'R/(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyR!)s  tparameter_servercB seZdZdddddgZdZdZdZd Zd Zdd Z d Z d Z dZ dZdZdZRS(sz Class for retrieving information from ion_parameters.cif Attributes ---------- params : iotbx.cif.model.block tparamst _metal_paramst_charge_paramst _resname_elemt_default_chargescC stjjtjjtdd}tjj|s=ttjj d|j }|d|_ i|_ i|_ i|_i|_dS(Nision_parameters.cift file_pathtions(tostpathtjoinRt__file__tisfiletAssertionErrortiotbxtciftreadertmodelR3R4R5R6R7(R%t params_patht cif_model((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt__init__^s     cC s||jdkS(s Checks if symbol is a supported element by this parameter server. Parameters ---------- symbol : str Returns ------- bool s_lib_valence.atom_symbol(R3(R%tsymbol((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytis_supported_elementis cC s||jdkS(s Checks if an element is a supported donor atom. Parameters ---------- symbol : str Returns ------- bool s_lib_valence.donor_symbol(R3(R%RG((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytis_supported_donorws c C sxt|jdD]\}}||jkrt|jd|}|jd|}t|jd|}||jkr||jkr||jkrt|jd|}|dfSqqW|j} |j} dS( s Gets the valence parameters (r_0 and b) used for calculating valences from bond distances. Parameters ---------- atom1 : mmtbx.ions.metal_parameters atom2 : mmtbx.ions.metal_parameters Returns ------- float or None r_0 in the equation exp((r - r_0) / b) float or None b in the equation exp((r - r_0) / b) Examples -------- >>> from mmtbx.ions import server, metal_parameters >>> zn_params = metal_parameters(element="ZN", charge=2) >>> n_params = metal_parameters(element="N", charge=-3) >>> print server.get_valence_params(zn_params, n_params) (1.77, 0.37) s_lib_valence.atom_symbols_lib_valence.atom_charges_lib_valence.donor_symbols_lib_valence.donor_charges_lib_valence.valuegGz?N(NN(t enumerateR3R"RR'RR( R%tatom1tatom2ti_elemRGti_chargeti_otherti_other_chargetvalencetcharge1tcharge2((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytget_valence_paramss   cC sy||jkr|j|S|j}xOt|dD]=\}}||kr4t|d|}||j|<|Sq4WdS(Ns_lib_charge.elements_lib_charge.chargei(R7R3RJR(R%R"tpRMtelemR$((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt_get_default_charges    cC s|jj}|dk r3|jj}n|j}|dkr||jkrg|j|}qgt|dD],\}}||krx||d|f^qx}t|dkrtd|n%t|dkrtd|n|dd}||j|>> from iotbx.pdb.hierarchy import atom >>> from mmtbx.ions import server >>> atom_dummy = atom() >>> atom_dummy.element = "N" >>> atom_dummy.charge = "-3" >>> print server.get_charge(atom_dummy) -3 >>> print server.get_charge("N") -3 RYiR(R"i( R_R`R+R#R^RR$RR'RbRYR"(R%RcR$RYR"((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt get_charges #  cC sv|j|}|j}t}xHt|dD]6\}}||kr2|jt|d|q2q2Wt|S(s Retrieves all charges that are expected to be associated with an atom or element within ion_parameters.cif. This list is manually updated based on the ligand IDs listed by the PDB. Parameters ---------- atom : iotbx.pdb.hierarchy.atom or str Returns ------- list of int Examples -------- >>> from mmtbx.ions import server >>> print server.get_charges("CU") [1, 2, 3] >>> print server.get_charges("ZN") [2] s_lib_charge.elements_lib_charge.charge(RdR3tsetRJtaddRtsorted(R%RcR"RUtchargesRMRV((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt get_chargess   "cC s|j}xtt|dD]b\}}||jkr||jkrR|j|S|d||kslttd|dt|d|dt|d|dt|d |d t|d |d t|d |dt|d|dt|d|dt|d|dt|d|dt|d|dt|d|dt|d| }||j|<|SqWdS(s Gets all metal parameters associated with an element. Parameters ---------- element : str Returns ------- mmtbx.ions.metal_parameters or None s_lib_elems.elements_lib_ligands.elementR"R$s_lib_elems.chargetvec_sum_cutoffs_lib_elems.vec_sum_cutofftcoord_num_lowers_lib_elems.coord_num_lowertcoord_num_uppers_lib_elems.coord_num_uppertmin_coordinating_non_waterss&_lib_elems.min_coordinating_non_waterst cvbs_lowers_lib_elems.cvbs_lowert cvbs_uppers_lib_elems.cvbs_uppert cvbs_expecteds_lib_elems.cvbs_expectedtallowed_coordinating_atomss'_lib_ligands.allowed_coordinating_atomstallowed_coordinating_residuess*_lib_ligands.allowed_coordinating_residuestallowed_geometriess_lib_ligands.allowed_geometriestallowed_backbone_atomss#_lib_ligands.allowed_backbone_atomsN( R3RJR#R4R?R!RR RR(R%R"RURMRGR3((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytget_metal_parameters3s@   cC s|j}|j|sdS|j||\}}|dkrtd|j|d|}|j||\}}|dkrdSnt|||S(sZ Calculates the single valence contribution of one ion donor pair, separated by distance. ion and donor should be AtomGuess objects. Parameters ---------- ion : mmtbx.ions.metal_parameters donor : mmtbx.ions.metal_parameters distance : float Returns ------- float Examples -------- >>> from mmtbx.ions import server, metal_parameters >>> ion = server.get_metal_parameters("ZN") >>> donor = metal_parameters(element="N", charge="-3") >>> valence = server.calculate_valence(ion, donor, 2.20) >>> print round(valence, 2) 0.31 iR$R"N(R"RIRTRR!ReR(R%tiontdonortdistanceR"tr_0tb((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytcalculate_valence`s    cC sg}x|D]}td|jd|j}t|j}|j||||j}|dkr|jdkr|j|j rqq |dkr |j|j||q q W|S(s  Calculates all of the valence contributions between ion and each atom of nearby_atoms, each element of which should be a tuple of an atom and a vector from the ion's location. Parameters ---------- ion : mmtbx.ions.metal_parameters nearby_atoms : list of mmtbx.ions.environment.atom_contact Returns ------- list of scitbx.matrix.rec List of vectors, whose magnitudes are equal to the valence contributions from each donor atom. Examples -------- >>> from libtbx import group_args >>> from iotbx.pdb.hierarchy import atom >>> from mmtbx.ions import server >>> from mmtbx.ions.environment import atom_contact >>> from scitbx.matrix import rec >>> ion = server.get_metal_parameters("ZN") >>> vector_1 = rec([2.0, 0, 0], [1, 3]) >>> vector_2 = rec([-2.0, 0, 0], [1, 3]) >>> vector_3 = rec([0, 2.0, 0], [1, 3]) >>> vector_4 = rec([0, 0, 2.0], [1, 3]) >>> atom_dummy = atom() >>> atom_dummy.element = "N" >>> atom_dummy.charge = "-3" >>> atom_dummy.occ = 1 >>> atom_dummy.parent = lambda: group_args(atoms=lambda: []) >>> donors = [atom_contact(atom_dummy, vector_1, None, None), ... atom_contact(atom_dummy, vector_2, None, None), ... atom_contact(atom_dummy, vector_3, None, None), ... atom_contact(atom_dummy, vector_4, None, None)] >>> vectors = server.calculate_valences(ion, donors) >>> bvs = sum(abs(i) for i in vectors) >>> print round(bvs, 2) 2.15 R"R$itHtCtAX(R}R~R( R!R"R$R,tvectorR|toccRItappend(R%Rwt nearby_atomstvectorstcontactRxRyRQ((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytcalculate_valencess+     N(R0R1t__doc__t __slots__RFRHRIRTRWRR^RdReRjRvR|R(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyR2Ss     '   )  - &cC s|d krtddn|tk rt|tsIt|trd|jddj}n7t|trt |dkr|djd}n|dgkrt SxO|D]D}|j j t krtdd |djt fqqWnt S( s2 Checks if elements are supported by ion identitication process. Parameters ---------- elements : list of str Returns ------- bool Raises ------ libtbx.utils.Sorry Examples -------- >>> from mmtbx.ions import check_supported >>> check_supported(["CA", "ZN", "FE"]) True s7No elements specified for ion picking - must be either s4'Auto' or a comma-separated list of element symbols.Rt iitXsBIdentification of ions with element symbol '%s' is not supported! sChoices are: %sN(RRRR_R`tunicodetreplaceRtlistRXtTrueR+R#t SUPPORTEDR<(telementsRV((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytcheck_supporteds    ! 'tatom_type_flagscB seZdZd:d;d<d=d>d?d@dAdBdCdDdEdFdGdHdIdJdKdLdMdNdOdPdQdRdSgZgeD]\ZZe^qgd5gZd6Zd7Ze j d8d9Z RS(Ts Simple container for information about the identity of an atom via a set of enumerated boolean flags. The responsibility for toggling these flags based on analysis of the site is left to external code. Parameters ---------- name: element symbol or HOH Examples -------- >>> flags = atom_type_flags("HOH") >>> if (fofc_map_value > 3.0) : ... flags.high_fofc = True t low_b_isosAbnormally low B-factorthigh_occsAbnormally high occupancyt high_fofcs mFo-DFc peakt high_two_fofcs"Abnormally high 2mFo-DFc map valuet high_anomsAnomalous map peakthigh_fdpsAbnormally high refined f''t high_b_isosAbnormally high B-factortlow_occsAbnormally low occupancyt low_two_fofcsLow 2mFo-DFc map valuetlow_fofcs mFo-DFc holetlow_anomsPoor anomalous map valuetlow_fdpsAbnormally low refined f''tbad_geoms Unexpected coordination geometryt missing_geoms%No recognizable coordination geometryt bad_vectorssBad coordination vectorst bad_valencesBad bond valence sumttoo_few_non_waterss$Too few non-water coordinating atomst too_few_coordsToo few coordinating atomsttoo_many_coordsToo many coordinating atomst like_coords Coordinating atom of same chargetbad_coord_atoms'Disallowed or unusual coordinating atomtbad_coord_residues*Disallowed or unusual coordinating residuetvery_bad_valencesVery bad bond valence sumt bad_halidesPoor halide sitet coord_geoms>Appears to be coordinating another site with distinct geometryt close_contacts&Unusually close contact to oxygen atomtnamecC s5||_x%|jd D]}t||tqWdS(Ni(RRtsetattrtFalse(R%Rtattr((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyRFs cC sg}xt|jd D]\}}t||r|dkr`|jd|j|dqd|kowdknr|jd|j|dq|j|j|dqqW|S(s Retrieve a list of strings describing the issues that have been identified. These will have '+++' or '---' appended if they indicate that the actual element is heavier or lighter than the current refined scatterer type. iis%s (+++)ii s%s (---)(RJRtgetattrRtflag_names_and_labels(R%tcaptionsti_attrR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytget_flag_captions!s  R(cC s|j}t|dkr/||dIJn||d|jIJt}}xJ|D]B}||d|IJd|krt}qUd|krUt}qUqUW|s|r||dIJndS( sC Print out a list of all issues that have been identified. is(No problems detected.)s-The following problems were detected with %s:s %ss---s+++s>(+++ indicates a heavier element, --- indicates a lighter one)N(RRXRRR(R%touttprefixRt have_plust have_minustcaption((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pytshow2s        (RsAbnormally low B-factor(RsAbnormally high occupancy(Rs mFo-DFc peak(Rs"Abnormally high 2mFo-DFc map value(RsAnomalous map peak(RsAbnormally high refined f''(RsAbnormally high B-factor(RsAbnormally low occupancy(RsLow 2mFo-DFc map value(Rs mFo-DFc hole(RsPoor anomalous map value(RsAbnormally low refined f''(Rs Unexpected coordination geometry(Rs%No recognizable coordination geometry(RsBad coordination vectors(RsBad bond valence sum(Rs$Too few non-water coordinating atoms(RsToo few coordinating atoms(RsToo many coordinating atoms(Rs Coordinating atom of same charge(Rs'Disallowed or unusual coordinating atom(Rs*Disallowed or unusual coordinating residue(RsVery bad bond valence sum(RsPoor halide site(Rs>Appears to be coordinating another site with distinct geometry(Rs&Unusually close contact to oxygen atom( R0R1RRtfltlabelRRFRtsyststdoutR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyRs@ &  (Rt __future__Rt iotbx.cifR@tlibtbxRRRt libtbx.utilsRtmathRttimeR:Rt DEFAULT_IONStHALIDEStTRANSITION_METALSRRRR R!R2RtservertobjectR(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/__init__.pyt s,        *n )