{Tc@sdZddlZddlTddlTddlZddlTddlTddlTddlZddlZddl Z ddl Z ddl Z ddl Z defdYZ dfdYZdfd YZdS( s python/ui/Superpose.py: CCP4MG Molecular Graphics Program Copyright (C) 2001-2008 University of York, CCLRC Copyright (C) 2009-2010 University of York Copyright (C) 2012 STFC This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. iN(t*t Superposec BsPeZdKZidd6dd6dd6dd6dd6dd 6d d 6d d 6dd6dd6dd6dd6ddgd6dd6dd6dd6dd6Zdddd d!gZdd"d#d$d%gZid&Zd'Zd(Z d)Z d*Z d+Z d,Z d-Zd.Zd/Zd0Zd1Zdd2Zd3Zd4Zddd5Zid6Zdd7Zdd8Zddddd9Zgd:Zd;Zdd<Zddd=Zd>Zd?Z d@Z!dAZ"dBZ#dCZ$ddDZ%ddEdddddddddF Z&dGZ'ddHZ(dIZ)dJZ*RS(Ltssmtmethodttfixedtshow_equiv_molitshow_equivalentsitshow_distancest show_masks CA tclose_atoms_central_atomg@tclose_atoms_res_cutoffg?tclose_atoms_cutofftclose_atoms_initial_globaltmonomer_keep_matchestcatracetselected_atoms_modetCAtCBtselected_atoms_selectiontapply_interactive_alltblackt conn_colourtyellowtfixed_mask_colourtmagentatmoving_mask_colours main chains nucleic P,C1'sall equivalents user definedtmaintnucleictalltusercKs|t_i|_x-tjjD]\}}t|||q"Wtj|ddddgj|j s|j idd6n|j idd6|j dS(NRRtcloset interactiveRt submethod( RtinststsupModeltinitialisationtitemstsetattrt Applicationt__init__tcountRt setparamstinitiallise_status(tselftparamstkeywordstkeytvalue((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR(Hs  cCs|jxF|jjD]5\}}t|}|s|j|j|=qqWx'tddD]}|j|jqcW|jdS(Nt object_typetMolData( tset_default_fixedR#R%tdatatdeletet get_dataobjt add_MolDatatnametset_show_equiv_mol(R,tmodelR#tmolobj((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR+Ys   cCsddl}t|}| s.|jdkr2dS|jj|sft|||jd|j|R?RR*Rtclear_Connectivity2tupdate_Connectivity2RWt isinstancet StringTypetset_user_selected_atomststripRHRb( R,R-tkwR/R0R:R[R;R#RWtatnam((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR*sT     "       $cKs|jj|sdSdS(N(R#R>(R,tmasterR.((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRB?scKs\|jj|r0|j|j|j|=n|j|jgj|rX|jndS(N(R#R>R5RRR)R3(R,RsR.((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRAEs  cKs/|jj|jr+d|j|j_ndS(Ni(R#R>RRb(R,Rstmol1tmol2thideR.((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRCRscCsdS(N((R,t saved_list((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pythandle_saved_filesZsc Ks|jstjddSd}d}d}|jdkrxj|jjD]\}}||jkrN|jrN|jdkr|jddg}n |j }|ddkr|d}qd}}||dd}qNqNWn|jd kr{x|jjD]l\}}||jkr|jr|j }|ddkrU|d}qt|d}||dd}qqWn0|jd kr|jj |j d}|sdS|jrc|j} x|jjD]\}}||jkr|jr||j kr|j| n|j}|ddkr=|d}q\|d}||dd}qqWq|j}|ddkr|d}q|d}||dd}n||gS( NsNeed to select a fixed modeliiRRtgesamttOKs RR (RtMGGUItWarningMessageRR#R%tonR!tsuperpose_Gesamtt superpose_SSMtsuperpose_CloseRERRFRt get_matchest set_matchestsuperpose_Matched( R,RqtnMovedt output_texttrvR:R#trctmovingSupModelRI((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytapply`s\                cCsPd|_|r|g}n|jj}x|D]}|j|jq1WdS(NR(tgesamt_matchesR#RXtsuperpose_undo(R,RDtmollist((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytundos    cCsddl}|jj|s"dS|dkrB|j|jn<|dkra|j|j}n|j|jdt|dS(NiRtbesttmatch(R:R#R>Rt best_matchRRd(R,RDR0R:((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pythandle_change_matchs   cCs'|jj|sdS|j|jS(NR(R#R>tgetRMS(R,RD((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRscKsg}ddgj|jrx|jjD]\}}||jkr.|jr.t|r.t|j}t|j}i|jd6|jd6|j j d6}|j j r|j j |dq n|j j rc|j j |dR(R,tstatusR((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR:sicCs7g}x*|jD]}|j|jd|qW|S(NR(RIR\RZ(R,Rt match_infoR((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRGsc Cs|sg|_nx|D]}t}|rc|jdd}|jdd|d<||dRER}RRbR(R,R-Rq((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR*qs  cCs t|jS(N(RHRI(R,((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyt nofMatches}scCs|jS(N(R(R,((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRscCsDit|dd6t|dd6t|dd6t|dd6S(NRRRRtrms(RY(R,((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytgetmatchesinfoscCs1||jkrd|_n||_d|_dS(Ni(RRb(R,R((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRcs  cCs1||jkrd|_n||_d|_dS(Ni(R Rb(R,R ((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRPs  icCsCg}x6|jD]+}|j|}|r|j|qqW|S(si Extract any selection on either this model (=2) or the fixed model (=1) that is not matched (RIt getUnmatchedR\(R,R:t unmatchedRR((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytextract_unmatcheds cCs|jj}|jj}ddl}d}xH|D]@}dddgj|drh||dd }q1d d d d gj|dr|d|dd|dd}q1dgj|dr1|dks|dkr|dkr||dd }qq|dkrP|d}x|D]}||d}qW|dd!d|dd}qq|d|d|dd}q1q1Wt|dkr|ddkr|dd!}n|S(s Convert a list of unmatched groups into a parseable selection command This method is independent of the MolData object iNRtatomtresiduetmonomeriis or Rtsidetbasetbackbones{ s and s } or trangeRRs { /1/*/*,*/Riisor (RRRtstringR)RH(R,tunmatched_listRRR6tseleR-tatm((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytget_unmatched_selection_commands*    %$    %"cCst|jjd|dd}|d r|dr|jsL|jnt|jdsbdS|jjj||r|jj|nd|j_ |jj ddd|j_ n|jr|jj ddndS(Ntcommandttestiit SelHandlet visibility( R4Rtparse_selectionR tcreate_MolDispRYR=t setCommandRgRbtset_visibilitytreapply_selection(R,R;RfR((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytdraw_unmatcheds!   cCsddgj|jjr@|jr|jjddqnp|jsV|jn|jjj|j|r|jj|nd|j_ |jjddd|j_ dS(NRRR>ii( R)RRpR RBR@R=RARgRbRC(R,Rf((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyt draw_masks   cCs{|j r| rdS|j|jjj|jd}|jr|jjdkr|j d}|j |}|j |d|jj |r |j d}|j |}|r|j |d|jj qq qn|jd|jj |rn|jd|jj qnn^|jrn|jjdd|jj|rn|jrn|jjdd|jjqnnd|_dS(NR iRfiR>i(Rbt draw_matchedRR#RERRFR RR.R:RDRRRER RBRN(R,tforceRR7R;((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRNs0  "  c Csx|jj}|jjj|jjj|dkrT|jrT|jjtddl }ddl }ddl }t j |jj}|j|}|jjr|j}n |j}|j|jj|jj||j|j j||jjtjd}|jjjt|dt|dt|d|d|dn|jjtj|jdS( Niit atom_labeltfamilytweighttslanttsizet underline(RtGetNofConnectionsR R`t clear_primst DeleteTextRRRRRRtMGCOLOURtRGBRRt DoubleVectorRtLABELLEDCENTREt NOTLABELLEDtDrawSimpleConnectiont connectedtDASHLINEt line_widtht FONTMANAGERtgetFontt SetTextFonttstrtrebuildRtrebuildGLDisplayObject( R,tnconnRRRtcoltcolvt label_modetfont((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRFs$$   &" icCsg}|dkr3|t|jkr3|g}ntt|j}xV|D]N}|j|j|jd|j|j|j|j|j|jfgqOW|S(Nis%-8s %-12s %-12s(RHRIR5R\R}ReR$R#(R,tiMatchtmenutrngtii((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytget_match_menu5s!  LcCsg}|j|jkr!d}nd}xett|jD]N}|j|jd|}x,|D]$}|j||d|dgqcWq=W|S(s@ Return a menu of the unmatched items in the match list iiR:i(R8RR5RHRItgetUnmatchedMenuR\(R,R;RfR:Rhtmenu_item_listt menu_item((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRBs  &cCsg}|j|jkr!d}nd}x`tt|jD]I}|j|jd|dd}x!|D]}|j||gqiWq=W|S(sB Return a menu of the unfinished ranges in the match list iiR:tstart(R8RR5RHRIRjR\(R,R;RfR:RhRkRl((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRUs  cCsxltdt|jD]R}|j|dkrddddgj|j|dd!rd|j|:  O    - $4*)$*)'    $T$  c Cs(td}ddddddgj|dd !rXdd d d d d dddg }nd gj|dd !rdd d d d ddddg }nX|dd !d krdddd d ddddg }n!dd d d d d d d dg }x%tddD]}|||||j jd|_|j j|_|j jd|_d |j j|j jf|_|jd |jj|jd|_dd gSd dl} | j| jd d | j} |jj| t d|j | gSdS(NisError with fixed modelsError - possibly model deleted?is%Error selecting mask for moving models$Error selecting mask for fixed modelisSuperpose status (0=success)s%.2f/%iR=Rii(!RR4RRRR#tCMGAlignRt GetTransformRRRRRRRRtGetMatchNumbertGetNumberofSSEMatchesRRtGetRMSDRNRRRRbRtQuatRt getInvMatrixRtssm_error_message( R,RRRRtRuRRt new_MGAligntcurrent_transformRRtrotmat((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRsF         %    $cCsddl}t|j}t|j}d|jd|jdt|d}|tkrx|d|jd}n|tkr|d|jd}nj|tkr|d|jd}nF|t kr|d|jd}n"t t gj |r|d }nd G|GH|S( Nis Superposing s onto s FAILED error code=s s5No secondary structure elements in the selection for s+No matching secondary structures found for s3Can not superpose the apparently matching SSEs for s}Failed to create graphs. Possibly model does not have secondary structure. Possibly program error. Contact ccp4mg@ccp4.ac.uk sSuperpose error:( R:R4RRR8R]tSPSN_noVerticestSPSN_noVertices2t SPSN_noHitst SPSN_noSPSNt SPSN_noGrapht SPSN_noGraph2R)(R,RR:RRR((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRs  *      cCs5ddl}|jjdkr-d}d}n|jjdkrNd}d}np|jjdkrod}d }nO|jjd krd}d }}n*|jjd krd }|jj}nt|j}|sddgS|jj}|rtj d|d|j }nd }t jj ||j dd |jd |jd ||d d t |dkr|jj ||j ||jnt} t} tj|j|| } | j} | dkr|jj|dd|d|j gSt|j} | jj} t}tj| j|| }| j}|ratj d|d| j }nd }| jj | |j dd |jd |jd ||d d t |dkr| jj | |j ||jntj| j| | }| j}|dkr;|jj|| jj| dd|dtj gS|| kr|jj|| jj| dd|j dt| d| j dt|gS| jj||| }| jj||| }d||f|_| jd|jj|jd|_|jj|| jj| dd gS(NiRsCA,N,O,Ct amino_acidRRRs P,C1',C1*t nucleic_acidRRRRsError with fixed modelR/Riiiis$Less than three residues containing s selected for s1Different number of residues selected for models s has s s%.2f/%iR=( RRRRR4RRRRtget_names_stringRt fixed_olobjRRtANY_RESRtSKEY_ANDRRRtGetAtomSelIndexR0RRRR]tTransformToSuperposeAtomstAtomicRMSDistanceRRRR(R,t fixed_selHndt moving_selHndRt central_atomtres_typet fixed_molobjtfixedHndt fx_amino_acidt selindexpt fixed_atomt fixed_natt moving_molobjt movingHndt moving_atomt moving_natt mv_amino_acidRR*((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyt superpose_LSQs      !% "      !% "   5  c Csddl}t|j}t|j}| s8| rBddgS|j}|dkrkdd|jgS|jj|jj}|dkrdd|jgS|jj |jj |j ||j ||jj |jj |jjd}|dkrddgS|dkrddgS|jjd |jj}|jj}d ||f|_|jd |jj|jd|_d |_dd gS( NisFixed model not definediisError selecting atoms for sError serching for close atomsis!Less than three close atoms foundis%.2f/%iR=R(RR4RRRRRR#RRRRR R R RRRNRRRRRb( R,RRRR1R0RR*R=((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRCs6      $       cCs|j|jjdkr)ddgS|jjd|jj}d||jjf|_|jj|jt |jj dddgS( NiisLess than three matched atomsis%.2f/%iR=iR( RlRRNRRRRRRR4R(R,R*((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRes  cCs^|jj|_|jr'|j}nd}t|jjd|}|dsZ|dSdS(NRR;iii(RRpR4RR?(R,R8R((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRws   cCst|j}|jdkr=t|jjdkr=dS|j}|dkrYdSddl}t}|j j }|j j ||j ||j t}tj|j ||}|j}|j j||S(Niii(R4Rt nmr_modelsRHtmodel_symmetrytget_symmetry_modelsRRRRRRt STYPE_MODELRt newPPCModelRtGetModelSelIndexR0R(R,R;RRR7t model_selHndtpModelstnModels((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRs       cCsddl}t|j}|js|jd|d|jdd|j|_|jjdd|jj|jjdd d gj|j s|jj |j |jj j d d d dqndS(NiRR8t _superposetmaster_applicationt style_modetPYRAMIDSRRRhR;tone_atomtoptand( R:R4RR Rt set_styleRgRR)Rt set_selectionR=tmergeSelection(R,R:R;((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR@s  cCst|j}t|j}|s/d|jS|jjdkrUd|jd}nd|jd|jd}|d|jd|jj|jjd}|jr|d t |jd }n|j rA|jj d krA|d d t |j d t |j dt |jd|j j|j|jd}n|jrt|jj dkrtd ||jd }n|d|jj}|jjr|d|jj}n|S(NsFixed model not set for: Rs Superposing s1 (atoms close to those selected for fixed model) sMoving: s (s) sFixed: s RMS of selected atoms: s Rs Match number s of s (best result is number s) s Rys- Transformation applied to the moving model s-NOTE: The fixed model is also transformed by (R4RRRRRRR#RR]RR!RRRRRRRR(R,RRR((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRs$ - acCs1ddl}|j r5|jjdkr5ddgS|jjtd}|jj}xtd|D]}|jj|d}|jj|d} |rj| rj|d|jd|d d|jd| d d|jj |d }qjqjWd d d|j |j |jd} | d} x |D]} | d| d} q8W| d} | d} | |jdt |jj d} | |jdt |jj d} |jjtjkrd} nd} | d| d} | d|}|r'ddl} | jd|d|nd|gS(NiiisNo matches definedsdloop_ _vector.start_model_id _vector.start_atom _vector.end_model_id _vector.end_atom _vector.label it"s" "s" s" s" s/#Definition of vectors for display with CCP4mg s!# Matched atoms in Superposition s #Created on s s data_VECTORS s# s s loop_ _model.id _model.filename s s"label centre"s "no label"s loop_ _display_objects.line_colour _display_objects.line_style _display_objects.line_width _display_objects.label_mode _display_objects.label_colour "complement" "dashed" 2 s "complement" RR(RRRNRRR5t GetAtomIDRRtGetLabeltasctimet localtimeR4t getFilenameRRRRTR{tsaveFile(R,RRtcommentsRRtnVtiVtatom1tatom2theadRtlabmoR{((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pytexport_matchess:   S.   ((  N(8RRRFR(R5RaRMRQRSRRRRZR*R)RR+RcRPR.R:RDRERNRFRiRRRqRRRrRRRRRRkRlRuRxRRRR R~RRR?RRRRR@RRa(((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR?sj'             '     7$    8 8 , _ "     !R%cBseZidd6dd6dd6dd6dd6dd 6Ziddddddd Zd Zd Zd ZddZdZddZ dddZ ddddZ dddZ RS(R5ReiRiR}RR#R$RtcCsG||_||_||_||_||_||_|j|dS(N(ReRR}R#R$RtR*(R,R-ReRR#R$RtR}((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR( s      cCst|||dS(N(R&(R,R/R0((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRi*scCst||dS(NR(RY(R,R/((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRE-scCs|j|jks6|j|jks6|j|jkr:dS|j|jkrb|j|jkrbdS|j|jkr|j|jkrdSdSdS(Niii(ReRRtR#R$(R,tother((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR&0s6$$cCsii}x'tjD]}t||d||(R,R:Rmt conversionsR-Rk((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRjQs*)$ Rmc Cs|dkrd}nd}|j|j|}|j|j|}d}d}d} d} t|dkr|djj|djjkrddgS|dj|dj} nt|dkr/|djj|djjkrddgS|dj|dj} n| r^| r^| | krQddgSdd gSnf| rv| rvdd gS| rt|r|djj|dj|| }n|sdd gS|dkrt|j ||d} nt|j |d|} | d|_n| rt|r]|djj|dj|| }n|smdd gS|dkrt|j ||d} nt|j |d|} | d|_ndd gS( NRyiiiisBThe selected residues in the fixed model are not in the same chainsCThe selected residues in the moving model are not in the same chains6The selected ranges have different numbers of residuesRsNo range selected yetsLThe selected range in the fixed model can not be matched in the moving modelsLThe selected range in the moving model can not be matched in the fixed model( RR#R$RHtGetChaint GetChainIDRt GetResidueR4t getResidueID( R,ReRRt directionRRtpr1tpr2tirdif1tirdif2R((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRzysT  , !, !      .   .  c Cst|}ddl}|jd}|dkr7gS|jd}g}|dkr|j|}|ddkr|j|dqn|j|d|!}|j|d|d!||d} |ddkr|j|dn| ddkr|j| dn|S(NiRiRi(R4R6trfindRR\( R,R8RR;R6tpslashtpdashRRR((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyRs$    &( RRRcR(RiRER&RZR*R,RjRzR(((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyR%s       (7(t__doc__tsystmgappRtdataobjR'tglobal_definitionsRRRRRRRR?R%(((s@/opt/xtal/ccp4-6.5-linux32/lib/py2/ccp4mg/python/ui/Superpose.pyts.             8