xTc@ sdZddlmZddlmZddlmZddlmZddl m Z ddl m Z ddl m Z dd lmZdd lZdd lZdd lZd efd YZeed Zd S(s This code is a portion of simple_ncs_from_pdb.py (tct 2006-12-12) moved into cctbx (Aug-2014) to make the core functionality available without phenix dependencies The original file is at phenix\phenix\command_line\simple_ncs_from_pdb.py The original functionality and interface is maintained via simple_ncs_from_pdb.py ***************************************************************************** Purpose: Figure out the ncs relations from the chains in a pdb object Major assumption: residue numbers are consistent among chains Approach: Use residue numbers to align the residue names, identify pairs of chains that can match. Choose groupings of chains that maximize the smallest number of matching residues between each member of a group and the first (reference) member of the group. Within a pair of chains, allow some segments to match and others not. Each pair of segments must have a length >= min_length and percent identity >=min_percent. A pair of segments may not end in a mismatch. An overall pair of chains must have an rmsd of CA atoms of <= rmsd_max. If find_invariant_domain is specified then once all chains that can be matched with the above algorithm are identified, all remaining chains are matched, allowing the break-up of chains into invariant domains. The invariant domains each get a separate NCS group. If residue numbers are not the same for corresponding chains, but they are simply offset by a constant for each chain, this will be recognized and the chains will be aligned. i(tdivision(t find_domain(tflex(tadopt_init_args(t superpose(tmatrix(tSorry(tncsNt ncs_from_pdbcB seZdZeejdddgeegddddddd d d Zd Zd Z dZ dZ dZ ddddeeedZ dZdZdZd4d4dZdZdZdZdZdZdZd Zd!Zd"Zd#Zd$Zd%Zd&Zd'Z d(Z!d)Z"d*Z#d+Z$d,Z%d-Z&d.Z'd/Z(dd0ed1Z)d2Z*d3Z+RS(5s/ find ncs relation in a biomolecules structure igffffff?g?g?g@g?iiig?cC s&i|_d|_t|tdS(s8 Setup common variables When two chains match but starts at a different residue number, use offset_dict to indicate that difference. For example Chains A and B match, but chain A first residue number is 1 and B first residue number is 10, so offset_dict[AB] = 9 if njump is not 1, then we are only going to take residues with numbers such that mod(resno,njump)=0 so if njump=10 then we take residue 0,10,20,30,40 and put them in position 1,2,3,4,5 Args: verbose (bool): print out during ncs processing log: indicate where to log output njump (int): residue sampling factor, reduces the number of residues used min_length (int): minimum number of matching residues in a segment for recursive call min_percent (float): min percent identity of matching residues suggested_ncs_groups (list): require_equal_start_match (bool): require that all matching segments start at the same relative residue number for all members of an NCS group, trimming the matching region as necessary. This is same, but not otherwise maximize_size_of_groups (bool): request that the scoring be set up to maximize the number of members in NCS groups (maximize_size_of_groups=True) or that scoring is set up to maximize the length of the matching segments in the NCS group (maximize_size_of_groups=False) required_chains (list): min_fraction_domain (float):domain must be this fraction of a chain initial_rms (float): Guess of RMS among chains match_radius (float): Keep atoms that are within match_radius of NCS-related atoms similarity_threshold (float): Threshold for similarity between segments min_contig_length (int): segments < min_contig_length rejected smooth_length (int): two segments separated by smooth_length or less get connected max_rmsd_domain (int): max rmsd of domains min_fraction_represented (float): Minimum fraction of residues represented by NCS to keep. If less...skip ncs entirely iN(t offset_dictttotal_residuesRtlocals(tselftverbosetlogtnjumpt min_lengtht min_percenttsuggested_ncs_groupstrequire_equal_start_matchtmaximize_size_of_groupstrequired_chainstmin_fraction_domaint initial_rmst match_radiustsimilarity_thresholdtmin_contig_lengtht smooth_lengthtmax_rmsd_domaintmin_fraction_represented((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyt__init__4s;  c' C sg}g}g}d}d}x5|jD]'}|d7}|dkrMq+nx|jD]} | j|kruqZn| j} | |krd} |jrZ|j| I| IJqZqZn|jr|jdI| IJnd} x1| jD]#} | d7} | dkr qnd}d}d}xi| jD][}|j}|d7}|j|rYq(n||krn|}n||kr(|}q(q(W|jrd} |j| I|I|IJng}||}||j d}x!t |D]}|j d qWg}x | jD]}|j}|j|r1q n||krCq n|j ||j |j}|r t}x<|jD].}|jdks|jd kr{t}Pq{q{W|r|d7}|||j }|||<|jr|jd I|jI|IJqqq q WqW||j|j krZ|j ||j | |j |qZqZWq+Wi}t|||}t|}xt |D]}||\}}} xt |dD]}!||!\}"}#}$|j||| |"|#|$\}%}&|%d kr8d}%|jrm|jd I|%I|I|#I||#IJqmn5|jrm|jd I|%I|I|#I||#IJn|%||&siRMRORQRSRTN(tsortedR)R'R2Rt get_overlap(R RMRNRORQRRRSttemptreverse_offsetRUt best_overlapt best_offsettoffset_aRTtoverlap((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR3s'+ !cC s.d}|}d}d} xtt|D]} | |j||} || } | |||j} | dkr| t|kr|| }nd}| dkr+|dkr+| |kr|d7}q| d7} q+q+Wdt|ttd|| |jkr dS||j|jkr&|SdSdS(s Args: chain1 (list): Residue single character list start1 (int): number of first residue in chain 1 chain2 (list): Residue single character list start2 (int): number of first residue in chain 2 offset (int): Returns: n_match iigY@N(R'R2RR)tfloattmaxRR(R RMRORQRSRTtoffset1toffset2tn_matcht mismatchesRGtresnotres1RPtres2((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR[s(     0cC sK|jdkrtStdtjd|j||jdkrGtSdS(s@ skip unless resno (residue number) falls on n * self.njump ig?idiN(RR,tinttmathtfmodR/(R Rh((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR&$s0c C s|jjdd}t|dkrG|dd=krG|d}nt|dkrv|dd>krv|d}nc|d?krxTtdddddgd d d d d gD]"\}}||kr|}PqqWndddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,g}d(d*d-d.d/d0d1d)d2d3d4d5d6d7d8d9d:d;d<d+d1d(d)d*d+d,g}xft||D]U\}}tjtj|ddtjtj|ddkrtj|SqWd@S(As return one char for DNA/RNA/Protein 070508 catch +G or DG and call both of them G: 2010-12-01 also Ar == A (ribo) call it A Args: residue_name (str): 3 letters residue code Returns: (str): One letter residue code t tiitdt+itrtadetcyttguatthyturitatctgtttutGLYtALAtSERtVALtILEtLEUtMETtCYStPHEtTYRtLYStARGtTRPtHIStGLUtASPtGLNtASNtPROtTHRtMSEtGtCtAtTtUtStVtItLtMtFtYtKtRtWtHtEtDtQtNtP(RpRq(Rr(RsRtRuRvRwN(tlowertreplaceR2R1tstringR)( R t residue_nametedited_residue_nametonetthreetaa_namest aa_lettersR.tletter((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR*+s> " "  "            !igY@g@ic 9C s8g} t|||} t|}x>t|D]0}| |\}}}| rh|j|| rhq1nxt||D]}| |\}}}|jr|jdI|I|IJn|j||||||d|d|d| \}}|rx||g}|j|}|j|r"qxn|}||g}|j ||||||\}}}} }!| sZt|dkr}q]| r|d|kr|jrZd|d|df}"|j|"IJqZq]|rA|d|krA|d|krA|jd I|IdI|dIJd t t |dd }"|j|"d IJq]| j ||||gqxqxWq1W|jr|jd I| IJn|}#t }$g}%g}&xC|$rd}'d}(d})d}*xS|#D]K}+|j|+|#| \},}}|,|(kr|,}(|+}'|}*|})qqW|(dkr|jrJ|jdI|)I|(I|*IJn|%j |)|&j |*g}-x*|#D]"}.|.|)krq|-j |.qqqqW|-}#|jr|jdI|#IJqq|jr|jdIJnt}$qW| r.|jr.|#r.|jr|jdI|%I|&IJng}/g}0g}1xYt|||D]E\}2}3}4|3|#krB|/j |2|0j |3|1j |4qBqBW|j||/|0|1d|jd|jdddddt \}5}6|5r.|j||5|6|/|0|1\}7}8|7r+|jdI|7I|8IJ|%|7|&|8fSq.n|%|&fS(s Args: hierarchy (object) chains (list of lists): list of the residue sequence list (one letter characters) of each chain chain_ids (list of str): list of chains IDs starting_residue_numbers (list): list of chains first residue numbers min_length (int): minimum number of matching residues in a segment for recursive call min_percent (float): min percent identity of matching residues max_rmsd (float): max rmsd of domains max_rmsd_user (int): max rmsd of chains suggested by user (i.e., if called from phenix.refine with suggested ncs groups) called_by_self (bool): exact_match_only (bool): quick (bool): Returns: groups list_of_residue_range_list s Comparing RRtexact_match_onlyiis Alignment s rejected with rmsd =sNOTE: User-suggested alignment sSet max_rmsd_user=gH.?s to keep its MATCH LIST: iayisBest new group:sCurrent remaining idss No new groupssCurrent groups: tmax_rmsdg~.At max_rmsd_useritcalled_by_selfsInvariant groups found:N(R1R2R't have_enoughR Rtmatches_approxtare_in_suggested_ncs_groupst%are_in_different_suggested_ncs_groupstget_rmsdtstrRkR(R/R)tget_score_and_groupR,tfind_invariant_domainst find_groupsRRtfind_invariant_groups(9R R4R!R6R7RRRRRRtquickt match_listRKt data_lengthRGRMt chain_id1RORPRQt chain_id2RStmatchestkeep_range_listtgrouptin_suggested_ncs_groupst residue_rangetresidue_range_listt rmsd_listtr_listt trans_listt center_listtresidues_in_common_listR<t remaining_idststill_finding_groupstgroupstlist_of_residue_range_listtbest_idt best_scoret best_grouptbest_residue_range_listttrial_idtscoretnew_remaining_idsR"tremaining_chainstremaining_chain_idst"remaining_starting_residue_numbersR:R;tstarting_residue_numbertadditional_groupst%additional_list_of_residue_range_listtinvariant_groupst$invariant_list_of_residue_range_list((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRZs!      $                        c> C sg}g}| s| r$||fSxxt||D]g\} } |jrq|jdI| I|j| | IJn| d} |j| |||\} } | d}d$}d$}g}g}g}g}g}xt| | D]\}}| |krqn|jr&|jdI| I|IdIJn|j||||\}}| sR| rtdt| dt|dt|n|j| | ||||| |}|sqn|jr|jdI|IJnd}|j d j t | |g}|j | |||\}}|j ||||\}} |jr_|jd I|I|IJnt |jtt| t|j}!|d$krqn|!t|krt|}!nt|d krqnt|| d |jd |jd|jd|!}"g}#g}$x|"jD]}%g}&g}'|%dj}(x;|(D]3})|)|$krE|'j|)|&j||)qEqEW|$|'7}$|#j|j|j|j|&qW|jr|jdI| I|IJng}*g}+xt|#|"jD]\}&}%|& s|% r/|jr|jdIJqqn|jr||jdI|&IJ|jdI|%dIJ|jdI|%d IJn|%d|jkr|jr|jdIJqqn|*j|&|+j|%qW|+ s|* r|jr|jdIJqqn|jr|jdIJng},g}-xqt|*|+D]`\}&}%|jrY|jdI|&IJng}.x| D]}/|.j|&qfW|j| |||||.\}0}1}2}3}4|jr|jdI|&IdI|0IJn|0 st|0dkrg},Pnd}5d}6x9t|0d|4dD] \}7}8|5|77}5|6|87}6qW|5tt|0d}5|6tt|0d}6|,j|5|-j|6q.Wd}9d$}:|,r'd};x1t|,|-D] \}7}8|9|77}9|;|87};qW|9tt|,}9|;tt|,};td|j|9|;}:n|jrL|jdI|9I|:IJn|:d$k r|d$ksp|:|kr|:}|9}|+}|*}|"}|-}<|,}qqW|d$k r4|d$k r4|jr*|jd I| Id!I|I|:IJ|jd"IJx3t||<D]\}7}8|j|7I|8IJqWn|jrI|jd#|jnxO|D]D}#|j| g}=x| D]})|=j|#qpW|j|=qPWq4q4W||fS(%s for each group in additional groups, see if there is some way to break it down into invariant sub-groups. Return list of these and new residue ranges... Returns: invariant_groups,invariant_list_of_residue_range_list s&Looking for invariant domains for ...:isUsing s to find domains...s Chain id Rns. are not both present in remaining chain_ids: sresidues in commonRos Centers: iRRt overlap_threst minimum_sizes Domains in sDomain completely removed...sDomain: sRMSD: isN: s&RMSD too large...rejecting this domainsNo domains from this pairs=Evaluating rmsd for all chain pairs using these final matchess domain...srmsd_list for t:igisrmsd for this match: sBest rmsd for group s: s"Rmsd and residues used by domain: toutN( R1R Rt add_offsetst get_chainR)RRtget_residues_in_commonR tjoinRZt get_xyz_listRkRRbR2RRRRRRtas_1dR(t remove_smallt connect_ranget list_to_rangeRRRctshow(>R R4RRRRRRRRRRNRMROtresidue_range1t best_rmsdRt best_matchestbest_domain_listt best_domainstbest_overall_rmsd_listtbest_number_of_residues_usedRRtresidue_range2RQRSt residue_listRdRetcenter1t xyz_list1tcenter2t xyz_list2tmin_sizetdomainst domain_listt used_listtmatchtdomain_residuest keep_listtiselectRGtfinal_domain_listt final_matchestoverall_rmsd_listtnumber_of_residues_used_listtlist_of_domain_residuesR"RRRRRt overall_rmsdtmean_residues_usedtrmsdtrest test_rmsdRttest_mean_lengtht!best_number_of_residues_used_listt%list_of_residue_ranges_for_this_group((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRs@        "   " )                    "$    $  %      c C s}ggg}}}xYt|||D]E\}} } | |kr'|j||j| |j| q'q'W|||gS(N(R1R(( R R!R6R7tused_idst new_chainst new_chain_idstnew_starting_residue_numbersR:R"tstart((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pytremove_used_chainss"   cC sBx;|D]3}x*|D]"}||kr|j|qqWqW|S(N(R((R RRRR"((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pytadd_idss    cC sd}x5|jD]'}x|jD]}||7}q&WqW|dk r|dkrt|t|}||jkrtStSntS(s count up how many residues are represented in the NCS and return True if not a fraction self.min_fraction_represented iN(t ncs_groupsRR)RbRR/R,(R t ncs_objectR ttotal_representedt ncs_grouptcommontfraction((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyttoo_few_residues_representedscC sg}g}d}xt|D]l}|dks;||dkrQ|}|j|q|r|j|dd!|d|g}|}qqW|r|j|dd!|dg}n|S(s@ [1,2,3,6,7] -> [[1,3],[6,7]] print >>self.log,"LIST",list iiiN(R)R((R tlistt range_listt work_listti_prevRG((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRs    cC sFx9t|||D]%\}}}||kr||fSqWgdfS(Ni(R1(R RNRRtremaining_starting_res_numbersR:R"R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRs   cC sv|j|j}g}xY|D]Q}|d|dd|kra|jrn|jdI|IJqnq|j|qW|S(sT remove all ranges that are smaller than self.min_contig_length//self.njump iisRejecting short range (RRR RR((R R!t contig_lengthtnew_range_listtrange((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRs  cC s|j|j}g}g}x]|D]U}|s8|}q#|d|d|dkre|d|d1 ID: raise an exception as we cannot be sure that it is handled correctly. assume that all residue numbers go up sequentially! In this routine there are no offsets. iis;This version of simple_ncs_from_pdb requires any input NCS sE specifications to have only one chain in each reference or selections& ('chain A or chain B' is not allowed)N(NN(R4tsizetpdb_inpR-tAssertionErrorR1RkttmpR R/R!R#R)R$t is_selectedR,R"R(R%R2R(R R8R6tid_listRR4R0RJR@R9tfirst_in_modelR:tfirst_in_chainR=R>tfirst_in_conformert last_residueRBRht first_residue((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR2EsX '%          " cC s(x!|jD]}|jr tSq WtS(N(R-R?R/R,(R RBRJ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR@}s cC sJy|jjd|}Wn*tk r/ntk rEd}nX|S(NR(tall_chain_proxiesR0tKeyboardInterruptt ExceptionR)(R tsel_strR0((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR1s   c C sg}g}g}|s"||fSt|tdksV|j||}||fS|}x|D]}|dkr|rd}t|qqc|dkr|stdn|j||\}}qc|dkrc||krtdt|dt|n|j|qcqcW|rC|j||\}}ng} xc|D][}xR|D]J} | | krtdd t| d t|n| j| q]WqPW||fSd S( s! expect a phil object or text... tABCDt[s:Format for suggested_ncs_groups is "[ABCD][EFG]" or "ABCD"t]tABCDEFGHIJKLMNOPQRSTUVWXYZsThe chain ID 'sB' is not among the chain ids in this PDB file. Available chains: s8Each chain can be used only once in suggested_ncs_groupss Chain s is listed more than once in N(ttypeR;Rtfinish_suggested_groupRR(( R RR6RRR3t input_texttcharR<tlist_of_used_chainsR"((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pytget_suggested_groupssH             (cC sPt|dkr3tdt|ddn|j|g}||fS(Nis The group s# seems to have fewer than 2 memberss; Format for suggested_ncs_groups is "[ABCD][EFG]" or "ABCD"(R2RRR((R RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRPs  c C sd}g}g}xO|D]G\}}} } ||kr| |kr|j||j| qqWx|D]}\}}} } ||krk| |krk| |krk|j| |j| |dkr|}q||kr|}qqkqkW|jr |j||}n|jrA|dk rA|tjtt|}n|j rt } x'|D]} | |j krWt } PqWqWW| sd}g}g}qnt|dkrd}g}g}n|r|j |r|d7}n|||fS(sh score as the MINIMUM number of matches of anything to the trial_id if all the members of a user-specified group are present, add 10000 to score return residue ranges that are not necessarily the same for all members of a group... 090708: allow user to increase score for large groups with self.maximize_size_of_groups 021107: Solution: need to use only those with id1==trial_id to keep numbering consistent. Then we also need matches to include both directions. 021207 this didn't do it completely...we want to return offsets based not on trial_id but on the firstid in the list... the real problem is that here we use a seed (C) to pull out the set of chains (A C E G) and the offset matches C here. Then later we assume that the offset matched A. One solution might be to always use the quick option...using each set of chains identified with sequence. HERE JUST this is the best plan? 021207 better: make sure that trial_id is first in list! 090808 allow calling program to require a particular set of chains to always be present ii'N( R)R(Rt&require_matches_to_start_at_same_placeRRltsqrtRbR2RR,R/t&a_suggested_ncs_group_is_in_test_group( R RRRRRRRRNRRRtfoundR"((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRsH $      "     cC sOxH|jD]=}t}x$|D]}||krt}PqqW|r tSq WtS(sa Returns: (bool): True -> all of a suggested_ncs_group are contained in test_group (RR/R,(R t test_groupRtare_inR"((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRWs  c C sg}t|dkr"dgfSt|d}|dg}xt||D]\}}|dkrvt|}ng}|t| t|t|dg} x_t| |D]N\} } | dk r| dks| d| kr| d} n|j| qW|}qOWxt||D]\}}g} |t| t|t|dg} xRt| |D]A\} } | dk rp| dk rp| d| krp| | dRHRBRCRIRJRlR ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRsr               1   cC sxx|jD]m}xd|D]\}||krxG|jD]9}||krKq3nx|D]}||krRtSqRWq3WqqWq WtS(s find a group that contains a member of test_group. If any other member is in another group, return True Returns: (bool): True when members of test_group is contained in > 1 suggested ncs group (RR/R,(R RYtgroup1R"tgroup2((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRs      cC s@x9t|||D]%\}}}||kr||fSqWdS(sJ get chain and starting residue number for chain with id chain_id N(NN(R1R)(R RR!R6R7R:R;R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRds" cC sOxH|jD]=}t}x$|D]}||krt}PqqW|r tSq WtS(s` Returns: (bool): True when all of test_group is contained in a suggested group (RR/R,(R RYRRZR"((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyRs  i_c C sdjt||g} | |jjkr@|j| } n|jdI| IJd} || } g} | sw| rd| fS|t|d|j}| t|d|j}|}|}| |kr| }n||kr|}n||j}||j}|jrD|jdI|IdI|IdI|I|IJng}xt|||j|jD]}||||j}||| |j}|r|r||kr|j t q|j t | rd| fSqg|j t qgWg}t }t|}d}xT|rd|j ||||\}}|d krJt }q|j |||7}qW|j|jr|jdI|IJnx=|D]5\}}| j ||j|||j|gqW|jr |jd I|Id I|IJ|jd I|IJn|| fS( s return number of residues matching total, and a list of residue ranges over which chain1 and chain2 match within the tolerance min_percent and each with minimum length of min_length NOTE: residue range is in terms of position in chain (relative to start, and if njump>1 then the residue numbers are in units of njump Returns: matching (int): number of matching residues keep_range_list (list): list of lists of the matching residues range, a list of ranges like [[1,3],[7-9]...] RosNO ID in matches_approx: iis(Finding matching segments in range from s to s for chains sList of segments: s Possible: s Matching: sResidue range used: N(RRZR RoRR2RR R'R(R/R,tfind_best_segmentR)tsort( R RMRORQRSRNRRRRRR"RTRqRtend1tend2RRxt start_njumpt end_njumptmatched_residuesRGRiRjtsegmentst still_lookingtpossibletmatchingt best_segmentt best_lengtht pos_starttpos_end((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR!sl        '#           ' c C st|dkrtSx|dD]}}t}x?|D]7\}}}}||dkr4||kr4t}q4q4W|s!|jr|jdI|I|IJntSq!W|jr|jdI|I|IJntS(s( are all ids matched to a set of id #1? iiismissing shave (R2R/R,R R( R R6RR"RXRRNRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyR}s   cC s|}x<|D]4\}}x%t||dD]}t||   V cC s| r| rtdn|r6| r6|j}ntdtdt}t}|jd|dg\}}}}}|jd|d|d|d|d d d d d ddddtdt \} } |j|| | |||\} } | r| } | }xt | |D]\}}|j ||||||\}}}}}|j ||}||g}|j d|d|d|d|d|d|qW|SdS(s0 Build and return ncs object from pdb hierarchy s;No input is provided. Please provide pdb_inp or hierarchy. t exclude_dt exclude_hR4R5R!R6R7RiRgffffff?Rg@Rg@RRt ncs_rota_matrRRt center_ortht trans_orthtchain_residue_idN( RR4RR/RRVRR,RR1RRtimport_ncs_group(R=R4Rt ncs_processR!R6R7R R tsequence_groupst#sequence_list_of_residue_range_listRRRRRRRRRRRtresidue_range_list_with_offsetsR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pytget_ncs_object_from_pdbsJ   '     (Rt __future__Rtmmtbx.invariant_domainRtcctbx.array_familyRtlibtbxRt scitbx.mathRRt libtbx.utilsRt mmtbx.ncs.ncsRRRlRtobjectRR)R(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_from_pdb.pyt#s$