ó ¢™xTc@ sddlmZddlmZddlmZddlZdefd„ƒYZddd d d d gZd efd„ƒYZ defd„ƒYZ defd„ƒYZ de fd„ƒYZ e d„Zde efd„ƒYZdefd„ƒYZdefd„ƒYZdZdS(iÿÿÿÿ(tdivision(tslots_getstate_setstate(t format_valueNtentitycB sÝeZdZddddgZdZgZd„Zed„ƒZdd „Z d „Z d d „Z d „Z dd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„ZRS(s8 Base class for all validation results. This includes a boolean outlier flag, the information used to zoom in the Phenix GUI (optional, but strongly recommended), and some kind of numerical score (also optional, but strongly recommended - although some analyses may require multiple distinct scores). tatom_selectiontxyztoutliertscores%scK sfx/|jƒD]!}||jks t|ƒ‚q Wx-|jD]"}t|||j|dƒƒq<WdS(N(tkeyst __slots__tAssertionErrortsetattrtgettNone(tselftkwdstname((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt__init__scC s tƒ‚dS(s/ Format for header in result listings. N(tNotImplementedError(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytheadersR cC st|j|jd|ƒS(Ntreplace_none_with(Rt score_formatR(RR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt format_score$scC s|jS(N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt is_outlier(stcC s tƒ‚dS(N(R(Rtprefix((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt as_string+scC s |jƒS(N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt__str__.scC s tƒ‚dS(s“ Returns a formatted (probably fixed-width) string describing the molecular entity being validation, independent of the analysis type. N(R(Rt ignore_altloc((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytid_str1scC s|jƒjƒS(N(Rt__hash__(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR8scC s tƒ‚dS(sN Optional; returns old format used by some tools in mmtbx.validation. N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytas_list;scC s tƒ‚dS(sL Returns a list of formatted table cells for display by MolProbity. N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytas_table_row_molprobityAscC s tƒ‚dS(sH Returns a list of formatted table cells for display by Phenix. N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytas_table_row_phenixGscC s tƒ‚dS(s> Returns a kinemage string for displaying an outlier. N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt as_kinemageMscC s tƒ‚dS(N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt format_oldSscC s tƒ‚dS(sâ Compare two validation results to determine whether they correspond to the same molecular entity and analysis type. This is intended to be used for analysis of a structure before-and-after refinement (etc.). N(R(Rtother((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt__eq__VscC st|j|jƒS(N(tcmpR(RR$((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt__cmp__^scC s tƒ‚dS(N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytis_single_residue_objectascC sdS(sE Returns PDB atom selection string for the atom(s) involved. N(R (R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytas_selection_stringdscC s|jƒ|jgS(s] Returns data needed to zoom/recenter the graphics programs from the Phenix GUI. (R)R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt zoom_infojsN(t__name__t __module__t__doc__R Rtmolprobity_table_labelsRt staticmethodRRRRRR RRRR R!R"R#R%R'R(R)R*(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRs2                 tchain_idtresseqticodetresnametaltloctsegidtresiduecB s»eZdZejedgZd„Zd„Zed„Z d„Z e d„ƒZ ed„Z d„Zed „Zd „Zd „Zd „Zd „Zd„Zd„Zdd„ZRS(sÉ Base class for validation information about a single residue, which depending on context could mean either any one of the residue_group, atom_group, or residue objects from the PDB hierarchy. t occupancycC s.x'tD]}t||t||ƒƒqWdS(N(t__residue_attr__R tgetattr(RR$tattr((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt_copy_constructors cC s?x8|jD]-}t||ƒdk s |dks t‚q WdS(NR5(R8R9R R (RR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytassert_all_attributes_defined…scC sxd|j|j|jf}|s6|d|j7}n |d7}|d|j7}|jdk rt|d|j7}n|S(Ns %2s%4s%1ss%1st s%3ss segid='%4s'(R0R1R2R4R3R5R (RRtbase((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR‰s cC s,ddlm}|jt|jƒ|jƒS(Niÿÿÿÿ(t hybrid_36(t iotbx.pdbR?t hy36decodetlenR1(RR?((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt resseq_as_int”scC sd|j|jfS(Ns%4s%1s(R1R2(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytresid˜scC s|jd|ƒS(NR(R(RR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt residue_idœscC s d|j|j|jfjƒS(Ns%s%s%s(R0R1R2tstrip(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt simple_idŸscC sSt|dƒr1|jd|ƒ|jd|ƒkS|jd|ƒ|jd|ƒkS(NRER(thasattrRER(RR$R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytis_same_residue£s cC sF|j|jkoE|j|jkoE|j|jkoE|j|jkS(N(R0R1R2R5(RR$((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytis_same_residue_groupªscC s&d|j|j|j|j|jfS(Ns%1s%3s%2s%4s%1s(R4R3R0R1R2(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytatom_group_id_str°scC sd|j|j|jfS(Ns %2s%4s%1s(R0R1R2(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytresidue_group_id_str´scC s@t|ƒt|ƒks*tt|ƒƒ‚|jƒ|jƒkS(N(ttypeR R(RR$((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR%·s*cC stS(N(tTrue(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR(»scC s d|j|j|j|jfS(Ns:(chain '%s' and resid '%s' and resname %s and altloc '%s')(R0RDR3R4(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytatom_selection_string¾scC sp|dkr|jƒ}n|j|jƒƒ}t|ƒdksHt‚|jƒj|ƒjƒj ƒ|_ dS(Ni( R tatom_selection_cachet selectionRORBR tatomstselectt extract_xyztmeanR(Rt pdb_hierarchyRPtsel((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytset_coordinates_from_hierarchyÂs  N(R+R,R-RR R8R;R<tFalseRRCtpropertyRDRERGRIRJRKRLR%R(ROR RX(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR6zs"            RRcB sZeZdZdgZejeZd„Zd„Zd„Zd„Z d„Z d„Z RS(s€ Base class for validation results involving a specific set of atoms, such as covalent geometry restraints, clashes, etc. t atoms_infocC s t|jƒS(N(RBR[(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytn_atomsÔscC sFt|ƒt|ƒks*tt|ƒƒ‚t|jƒt|jƒkS(N(RMR tsortedR[(RR$((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR%×s*cC stS(N(RY(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR(ÛscC scd}xV|jD]K}|jjƒdkr|dkrC|j}q[|j|ks[t‚qqW|S(NR(R[R4RFR (Rtconsensus_altloctatom((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt get_altlocÞs  cC sg|jD]}|j^q S(N(R[R(Rta((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt sites_cartèscC s;|dkrtSx$|jD]}|j|krtSqWtS(N(R RNR[R0RY(RR0Ra((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt is_in_chainës  ( R+R,R-t__atoms_attr__RR R\R%R(R`RbRc(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRRÊs      t atom_basecB sieZdZddddddgZeeZd„Zd„Zd „Ze d „Z d „Z d „Z RS( s« Container for metadata for a single atom, in the context of validation results involving multiple atoms. Intended to be used as-is inside various atoms classes. RtelementRtsymopR7tb_isocK s-|jddƒ}|dk r(|d=nx/|jƒD]!}||jks5t|ƒ‚q5Wx-|jD]"}t|||j|dƒƒqdW|dk r)|jƒ}|j|_|j|_|j |_ |j |_ |j |_ |j |_ |j |_ |j|_|j|_|j|_|j|_ndS(Ntpdb_atom(R R RR R R t fetch_labelsR0R1R2R3R4R5RRtoccR7tbRhRf(RRRiRtlabels((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRs(               cC st|jƒ|jƒƒS(N(R&R(RR$((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR'scC s7t|tƒs!tt|ƒƒ‚|jƒ|jƒkS(N(t isinstanceReR RMR(RR$((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR%s!cC sd|j|j|jf}|s6|d|j7}n |d7}|d|j|jf7}|jdk r}|d|j7}n|S(Ns %2s%4s%1ss%1sR=s%3s %4ss segid='%4s'(R0R1R2R4R3RR5R (RRR>((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR!s cC sd|j|j|jfS(Ns %2s%4s%1s(R0R1R2(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRL,scC s&d|j|j|j|j|jfS(Ns%1s%3s%2s%4s%1s(R4R3R0R1R2(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRK/s( R+R,R-t __atom_attr__R8t__atom_slots__RR'R%RYRRLRK(((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyReós      t atom_infocB seZdZejdgZRS(s« Container for metadata for a single atom, in the context of validation results involving multiple atoms. Intended to be used as-is inside various atoms classes. Rg(R+R,R-ReRpR (((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRq3sc C s¼g}x¯t|ƒD]¡\}}||}|jƒ}|rG|j}n |j}td|jd|jd|d|jd|jd|j d|j d|j d |j ƒ } |j | ƒqW|S( NRRfR0R1R2R3R4R7R(t enumerateRjR5R0RqRRfR1R2R3R4RkRtappend( t pdb_atomst iselectiontuse_segids_in_place_of_chainidst proxy_atomstnti_seqR_RmR0tinfo((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytget_atoms_info;s&            R_cB s'eZdZejejZd„ZRS(s¿ Base class for validation results for a single atom. This is distinct from the atom_info class above, which is used to track individual atoms within a multi-atom validation result. cC stS(N(RN(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR([s(R+R,R-RR ReRpR((((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR_Sst validationcB seZdZddddgZdZdZgZgZd„Z d„Z e d„ƒZ d„Z d „Zd „Zd „Zejed „Zejd d„Zejdeed„Zed„Zd„Zd„Zeed„Zddd„Zddd„ZRS(s Container for a set of results from a single analysis (rotamers, clashes, etc.). This is responsible for the console display of these results and associated statistics. Individual modules will subclass this and override the unimplemented methods. t n_outlierstn_totaltresultst_cachecC s(d|_d|_g|_d|_dS(Ni(R}R~RR R€(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRks   cC sH|jdkrDt|jƒ|j}|dks7t‚|j|fSdS(Nigð?g(ig(R~tfloatR}R (Rtfraction((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytget_outliers_count_and_fractionqs  cC s|jƒ\}}|dS(NgY@(Rƒ(RR}t frac_outliers((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytpercent_outliersxscC s#t|dƒr|jStƒ‚dS(s  Return a flex.size_t object containing the i_seqs of atoms flagged as outliers (either individually or as part of an atom_group). This needs to be implemented in the underlying classes unless they include a pre-built _outlier_i_seqs attribute. t_outlier_i_seqsN(RHR†R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytoutlier_selection}scC s tƒ‚dS(N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytget_outliers_goalˆscC s tƒ‚dS(N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytget_result_class‹scC sdS(NR((R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt coot_todoŽscC si|r+|jdk st‚||jIJnx!|jD]}||jƒIJq5W|re|j|ƒndS(sj For backwards compatibility with output formats of older utilities (phenix.ramalyze et al.). N(t output_headerR R RR#t show_summary(Rtouttverbosetresult((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytshow_old_output‘sRcC s tƒ‚dS(N(R(RRR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyRŒžss cC szt|jƒdkr`|||jƒjƒIJx.|j|ƒD]}||t|ƒIJq?Wn|jd|d|ƒdS(NiRR(RBRR‰Rt iter_resultststrRŒ(RRRt outliers_onlyRŽR((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytshow¡s cc s3x,|jD]!}| s#|jƒr |Vq q WdS(N(RR(RR“R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR‘©scC sdS(N(R (R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyR"®scC s tƒ‚dS(sE Return results in a format suitable for unpickling in Coot. N(R(R((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pyt as_coot_data±scC s–g}x‰|j|ƒD]x}g}|r7|jƒ}n|jƒ}t|ƒt|jƒkort|jƒkns}t‚|j||ƒqW|S(s7 Format results for display in the Phenix GUI. (R‘R*R!RBtgui_list_headerst gui_formatsR Rs(RR“t include_zoomttableRtextratrow((sG/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/__init__.pytas_gui_table_data·s :cC sü||gjdƒdks!t‚|dk rxt|dƒrK|jƒ}qxt|dƒri|jƒ}qxt|ƒ}n|jdkrÌi|_x9t|j ƒD]%\}}|jƒ}||j|s& k P)@