ó ±™xTc @ syddlmZddlmZddlmZddlmZmZddl m Z ddl m Z ddl Z ddl mZmZddlZddlZd „ZeƒZeZd efd „ƒYZd efd „ƒYZdefd„ƒYZddddeeedd„Zdd„Zdd„Zde jfd„ƒYZ d„Z!e"dkrueej#dƒndS(iÿÿÿÿ(tdivision(tutils(tflex(t make_headert format_value(t runtime_utils(tSorryN(tadopt_init_argst group_argscC s#ddlm}|dtddƒS(Niÿÿÿÿ(t generate_master_phil_with_inputstenable_automatic_twin_detectiont phil_strings find_peaks .style = auto_align { include scope mmtbx.find_peaks.master_params } map_cutoff = 3.0 .type = float .short_caption = mFo-DFc map cutoff (sigma) anom_map_cutoff = 3.0 .type = float .short_caption = Anomalous map cutoff (sigma) include_peaks_near_model = False .type = bool .short_caption = Don't filter peaks by distance to model .help = By default, the program will only display peaks that map to points outside of the current model, ignoring those that overlap with atoms. Setting this option to True is equivalent to specifying a distance cutoff of zero for the filtering step. .style = OnChange:toggle_min_model_peak_dist wavelength = None .type = float .help = Optional parameter, if defined this will cause all atoms to be treated as anomalous scatterers using the standard Sasaki table to obtain theoretical fp and fpp values. Only really useful if the Phaser LLG map is being used for the anomalous map. filter_peaks_by_2fofc = None .type = float .short_caption = Filter peaks by 2mFo-DFc .help = If this is set, peaks outside 2mFo-DFc density at the cutoff will be discarded. (This does not apply to the analysis of solvent atoms.) Holes will not be changed. use_phaser_if_available = True .type = bool .short_caption = Use Phaser LLG map .help = If True, and Phaser is installed and configured, an anomalous LLG map will be used in place of the simple anomalous difference map. The wavelength should be specified for this to be maximally useful. write_pdb = True .type = bool .short_caption = Write peaks to PDB file write_maps = True .type = bool .short_caption = Save map coefficients output_file_prefix = peaks_holes .type = str include scope libtbx.phil.interface.tracking_params (tmmtbx.command_lineR tTrue(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pytget_master_phils0tpeaks_holes_containercB sneZdd dd d d d„Zejd„Zd„Zd„Zd„Z de e e d d„Z d„Z RS( g@c C s¿t|tƒƒ|jjdtƒ|jjƒ|jdk rU|jjdtƒn|jdk rt |jd„ƒ|_n|j dk r©t |j d„ƒ|_ nd|_ d|_ dS(NtreversecS st|j|jƒS(N(tcmpt peak_height(txty((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pytUscS st|j|jƒS(N(RR(RR((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyRXs( RtlocalstpeakstsortR tholest anom_peakstNonet water_peakstsortedtwater_anom_peakstpdb_filetmap_file( tselfRRt map_cutoffRtanom_map_cutoffRRtnon_water_anom_peaks((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyt__init__Js    cC s|jƒjd|ƒdS(Ntout(t get_summarytshow(R!R&((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyt show_summary\scC sd}|jdk r*t|jjƒ}nd}}|jdk rUt|jƒ}n|jdk rvt|jƒ}nd}}t|jjƒdkr°tj|jjƒ}nt|j jƒdkràtj |j jƒ}nd}t |ddƒdk rt|j ƒ}nt d|jj|jkjtƒd|jj|jdkjtƒd|jj|jdkjtƒd|j j|j kjtƒd |j j|j dkjtƒd |j j|j dkjtƒd |d |d |d|d|d|jd|jd|ƒS(sF Returns a simple object for harvesting statistics elsewhere. iR$t n_peaks_1t n_peaks_2it n_peaks_3it n_holes_1t n_holes_2t n_holes_3tpeak_maxthole_maxt n_anom_peakst n_water_peakstn_water_anom_peaksR"R#tn_non_water_anom_peaksN(RRtlentheightsRRRRtmaxRtmintgetattrR$tsummaryR"tcountR R#(R!R2R3R4R1R0R5((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyR'_s>  ""##  cC s+|dkst‚|jj|kjtƒS(Ni(tAssertionErrorRR7R<R (R!tcutoff((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pytn_peaks_above_cutoffƒscC s+|dkst‚|jj|kjtƒS(Ni(R=RR7R<R (R!R>((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pytn_holes_below_cutoff‡ss peaks.pdbc sy|dkrtj}nddl‰|jjdtƒˆjjj ƒ}ˆjjj ƒ}|j |ƒˆjjj ddƒ}|j |ƒ‡fd†} d} xRt|jj|jjƒD]5\} } | | | | ƒ} |j| ƒ| d7} q¾Wt|dƒ}|jd ƒ|jd |jƒ|rÅ|jd |j ƒˆjjj dd ƒ}|j |ƒd} xUt|jj|jjƒD]5\}} | | || ƒ} |j| ƒ| d7} q‰Wn|rq|jdk rq|jd |jƒˆjjj ddƒ}|j |ƒd} xUt|jj|jjƒD]5\} } | | | | ƒ} |j| ƒ| d7} q5Wn|r¥|jdk r¥|jd|jƒˆjjj ddƒ}|j |ƒxFt|jƒD]5\} } | | j| j| dƒ} |j| ƒqÏW|r¥|jdk r¥|jd|jƒˆjjj ddƒ}|j |ƒxIt|jƒD]5\} } | | j| j| dƒ} |j| ƒqfWq¥n|rAt|ddƒdk rA|jdƒˆjjj ddƒ}|j |ƒxIt|jƒD]5\} } | | j| j| dƒ} |j| ƒqWn|j|jƒƒ|j ƒ|d|IJ||_!dS(s Write out a PDB file with up to three chains: A for peaks, B for holes, C for anomalous peaks. Atoms are UNK, with the B-factor set to the height or depth of the peak or hole. iÿÿÿÿNRtidtAc sœˆjjjdt|ƒƒ}ˆjjjddƒ}|j|ƒˆjjjƒ}|j|ƒd|_d|_ ||_ ||_ d|_ ||_ |S(NtresseqtresnametUNKs UNKtXgð?(tpdbt hierarchyt residue_grouptstrt atom_grouptappend_atom_grouptatomt append_atomtnametelementtxyztbtocctserial(RQtpeakRTtrgtagta(tiotbx(sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyt create_atomžs        itws6REMARK Interesting sites from mmtbx.find_peaks_holes s5REMARK Chain A is difference map peaks (> %g sigma) s5REMARK Chain B is difference map holes (< %g sigma) tBs0REMARK Chain C is anomalous peaks (> %g sigma) tCs:REMARK Chain D is waters with mFo-DFc peaks (> %g sigma) tDs8REMARK Chain E is waters with anom. peaks (> %g sigma) tER$s<REMARK Chain F is non-water, non-HD atoms with anom. peaks tFsWrote %s("Rtsyststdouttiotbx.pdb.hierarchyRRR RGRHtroottmodelt append_modeltchaint append_chaintzipR7tsitestappend_residue_grouptopentwriteR"RRR#Rt enumerateRQRRR:R$t as_pdb_stringtcloseR(R!t file_namet include_holest include_anomt include_watertlogRdRet peaks_chainRZtkRURQRVtft holes_chaintholet anom_chaint waters_chaintwaters_chain_2t anom_chain_2((RYsQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyt save_pdb_file‹s†     (       (    (          cC sZg}|jdk r.|j|jdfƒn|jdk rV|j|jdfƒn|S(NsPeaks as PDB atomssMap coefficients(RRtappendR (R!t output_files((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pytget_output_file_infoås N( t__name__t __module__RR%RaRbR)R'R?R@R RR‚(((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyRIs   $   UR;cB seZejd„ZRS(cC s¿|dIJ|dIJ|j|jd|jdg}|j|j|jg}g}g}x?t||ƒD].\}}|jd|ƒ|jd|ƒqhW|jdƒ|jtd|jƒƒ|j|j |j g}x?t||ƒD].\}} |jd |ƒ|jd| ƒqèW|jd ƒ|jtd|j ƒƒ|j dk rz|jd |jƒ|jd|j ƒn|jdk r´|jd |jƒ|jd|jƒn|jdk rî|jd |jƒ|jd|jƒn|jdk r!|jdƒ|jd|jƒng|D]} | jƒd^q(}tg|D]} t| ƒ^qNƒ} d| } x;t||ƒD]*\} }| | }|d||fIJqƒW|dIJdS(NtsSUMMARY OF MAP PEAKS:g@g@smFo-DFc > %-4gs%6ds mFo-DFc maxs%6.2fsmFo-DFc < -%-4gs mFo-DFc minsanomalous > %-4gssuspicious H2O (mFo-DFC > %g)sanomalous H2O (anomalous > %g)sanomalous non-water atomst:s%%-%dss %s %s(R"R*R+R,RiR€RR0R-R.R/R1R2RR#R3R4R5tstripR8R6(R!R&tcutoffsRtlabelstvaluesR>tn_peaksRtn_holestlt label_lentformattlabeltvaluet formatted((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyR(îsH      #%  (RƒR„RaRbR((((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyR;íst water_peakcB s#eZdd„Zejd„ZRS(smFo-DFccC st|tƒƒdS(N(RR(R!tid_strRQRtmap_type((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyR%scC s$|d|j|j|jfIJdS(Ns %s map_type=%s peak=%g(R”R•R(R!R&((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyR(s (RƒR„R%RaRbR((((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/find_peaks_holes.pyR“s g@c -C s| dkrtj} n|dkr<tjƒjƒj}n|rQd|j_n|j ƒ} |j j ƒ} ddl m} ddl m} d}|dk rç|jƒjd|jd| jddd tƒ}|jƒ|jƒ}ntd d | ƒ| jd |dd d|d|d| ƒ}|jƒ|j| ƒ|jƒ}|dk rŒ|jd|d|ƒ}| dIJ| dt|jƒIJn| j|jƒ|_| dIJ| jƒtdd | ƒ| jd |dd d| d|d| ƒ}|jƒ|j| ƒ|jƒ}| j|jƒ|_| dIJ| jƒd}d}|j ƒj!ƒr—tdd | ƒd}|rÒt"j#j$dƒrÒ|j% rÒddl&}| dIJd}|j'j(d |d|d| ƒ}n| jd |d|d|d|d|d| ƒ}|jƒ|j| ƒ|jƒ}|dk rk|jd|d|ƒ| dIJ| dt|jƒIJn| j|jƒ|_| dIJ| jƒnd}|j)ƒ}|j j*ƒ}|j+dƒj,ƒ}ddg}t|ƒdkr¾d g}|g} |j ƒj!ƒr,|j-dƒ| j-|ƒnxt.|ƒD]~\}!}"d}#|"dkr„|dk r„|jd|jd| jƒ}#n0|jƒjd|jd| jd|"d tƒ}#|#jƒj/ƒ}$|"dkrÛ|$}ng}%xu|D]m}&| |&}'|$j0||&ƒ}(|(| |!krèt1d|'j2ƒd |'j3d!|(d|"ƒ})|%j-|)ƒqèqèWt|%ƒdkr9td"|"d | ƒx|%D]})|)j4d | ƒq†W| dIJ|%||!s:    5 ¤'  ² 7