xTc@ s*ddlmZddlmZddlmZddlmZddlm Z ddl m Z m Z ddlZddlZde fd YZd e fd YZd e fd YZdefdYZdZdZdZdZdefdYZdefdYZdS(i(tdivision(tbackbone(tflex(tcol(t format_value(tAutotslots_getstate_setstateNtresidue_group_proxycB s;eZdZddddgZdZdZdZRS(s;Pickle-able stand-in for iotbx.pdb.hierarchy.residue_group.tresseqticodet _atom_groupst_id_strcC sa|j|_|j|_|j|_g|_x*|jD]}|jjt|q=WdS(N(RR tid_strR R t atom_groupstappendtatom_group_proxy(tselft residue_grouptag((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyt__init__s    cC s|jS(N(R (R((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR scC s|jS(N(R (R((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR s(t__name__t __module__t__doc__t __slots__RR R (((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRs   RcB s/eZdZdddgZdZdZRS(s8Pickle-able stand-in for iotbx.pdb.hierarchy.atom_group.tresnametaltloct_atomscC s1|j|_|j|_t|j|_dS(N(RRt atoms_proxytatomsR(Rt atom_group((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR#s  cC s|jS(N(R(R((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR(s(RRRRRR(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR s RcB s;eZdZdgZdZdZdZdZRS(sh Pickle-able stand-in for af::shared array, using the atom_with_labels objects as elements. RcC s&g|D]}|j^q|_dS(N(t fetch_labelsR(RRta((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR1scC s |j|S(N(R(Rtidx((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyt __getitem__4scC s&tjg|jD]}|j^qS(N(RtdoubleRtocc(RR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyt extract_occ7scC s&tjg|jD]}|j^qS(N(RR"Rtb(RR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyt extract_b:s(RRRRRR!R$R&(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR+s     tdisordered_segmentcB seZdZdZdZdejdZddZe e ddZ d Z d Z d Z e d Zd ZdZdZddZeddZddZddZdZddZddZdZdZRS(se A group of one or more adjacent residues presumed to form continuous alternate conformations. cC s>g|_i|_i|_i|_g|_|j|dS(N(tresidue_groupstoutlierstrotamerst ramachandrantbackrubstappend_residue_group(RR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRBs      cC sO|jdkr#|jdjSd|jdj|jdjfSdS(Niis %s --> %si(t n_residuesR(R (R((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyt__str__Jstc C s|jdkr@||d|jdj|jfIJnD||d|j|jdj|jdj|jfIJxt|jD]\}}||d|jIJx|jD] }d}}x?|jj|jgD]"}|j |j kr|}PqqWx?|j j|jgD]"}|j |j kr3|}Pq3q3W||dd|j |j t j |jjtd t|d dtd t|d dt|d dfIJqWt|j|dkr$x2|j|D] } | jd |d|dqWn|j|j} t| dkrZ||dIJnx5| D]-} ||dt| jt| fIJqaWqWdS(Nis&Segment: 1 residue (%s), %d conformersis/Segment: %d residues (%s --> %s), %d conformersis residue_group=%ss s7atom_group=%1s %3s occ=%.2f phi=%-6s psi=%-6s rot=%-7ss%.1ftphitpsit rotamer_nametouttprefixs MolProbity outliers:s %s: %s(R.R(R tn_confst enumerateR tNoneR+tgetRR*RRtmeanRR$tfvtgetattrtlenR,tshowR)ttypeRtstr( RR5R4ti_restrgRtramatrotatotbackrubR)toutlier((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR>QsF $ ! "" ! icC s`|jd}d}xF|jD]8}|jjdkr ||krK|S|d7}q q WdS(NiiR0i(R(R RtstripR8(RtindexRBti_groupR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytget_previous_conformerws  g@cC s|j}t|dks$tt|t|jdjkrV|sVtSnd}x[|D]S}|jdkrc|j}|jd|} | d kr|stPn|d7}| j|jkrtS| j} | dj |dj kr|stSnd \} } x*| D]"} | j dkr| j } PqqWx*|D]"} | j dkrE| j } PqEqEW| d ks| d krtSt t | t | }||krtSqcqcWtS( s Determine whether a residue_group object is part of the same continuous disordered segment. The precise meaning of this can be adjusted depending on user preferences; by default a continuous segment must have the same number of conformers for each residue, and occupancies must be constrained for each conformation. The latter assumption will probably be violated most often. iiiR0RIis C s N N(NN(R R=tAssertionErrorR(tFalseRRRKR8R#tnametxyztabsRtTrue(Rtothertignore_inconsistent_occupancyt ignore_inconsistent_n_conformerst*max_peptide_bond_distance_within_conformert other_groupsRJRt other_atomst prev_groupt prev_atomstcurr_ntprev_ctatomtdist((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytis_part_of_segmentsF %             cC s<|jjt|tjd|}|jj|dS(NR(R(RRRt find_backrubsR,(RRBt rg_backrubs((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR-scC sg}xy|jD]n}tg|jD]}|jj^q&}t|dkr|j|jtt |fqqW|S(sG Find any residue groups with heterogeneous chemical identity. i( R(tsetR RtupperR=RR tsortedtlist(Rt disorderedRBRtresnames((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytdetect_sequence_disorders .,cC s t|jS(N(R=R((R((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR.scC sd}x|jD]}}xt|jD]f}|jjdkr#|r{x>|jD]#}|jdkrQ|d7}PqQqQWn |d7}Pq#q#WqW|S(sK Count the number of residues where not all atoms have alternates. iR0s CA i(R(R RRHRRN(Rtjoin_at_calphat n_partialRRR\((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytn_partial_splitss    cC sg}x]|jD]R}|jdx<|jD].}|jjdkr0|dcd7        8cC sq|jd|}g}x6|D].}t|dkr|jt|qqWt|dkrmt|SdS(NRi(RR=RRpR8(RRtpaired_distancest paired_maxR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytmax_distance_between_conformers6s  cC s|jd|}d}x}|D]u}t|dkr=qntjtg|D]}|d^qMt|}|dks||kr|}qqW|S(NRii(RR8R=tmathtsqrttsum(RRRtrmsd_maxRtdxyztrmsd((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytmax_rmsd_between_conformers@s 6 cC sx|jD]}g|j|jRKRMR^R-RgR.RjR6RqR{R8RRR~RRRRRRR(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR'=s2  &  -        ,   cC s]xV|jD]H}|jjdkr x*|jD]}|jdkr5tSq5Wq q WtS(NR0s CA (R RRHRRNRQRM(RRR\((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytis_joined_at_calphas cC s-g}x|jD]}d}}xb|jD]T}|jjdkr]t|j}q0|jjdkr0t|j}q0q0Wd||gkr|j||qqWt|dkr)g}d}xL|t|dkr|j||j ||ddt |d7}qWt |SdS(s Calculate angles between carbonyl oxygen (C=O) bonds in each pair of atom groups, and return the maximum value (or None if fewer than two such bonds are found). RRiiitdegN( R R8RRNRHRRORR=tangleRQRp(Rt c_o_vectorsRtc_xyzto_xyzR\tanglesR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRs$ ( cC sOxH|jD]:}|j}|jjdkr |jdkr tSq WtS(s Detect cases where the only alternate conformation is for the amide hydrogen, presumably because the previous residue was split and Reduce was used to add hydrogens. These residues are ignored in our analyses. R0s H (RRRRHRNRMRQ(RR\tlabels((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pytonly_amide_hydrogen_splits  $cC s~t|jdkr!d}nYxV|jjD]B}|jr4|j}t||krvt|}qvq4q4W|S(s4 Count the number of conformers in a structure. ii(R=tmodelst only_modeltchainst is_proteint conformers(t pdb_hierarchyR6tchaintconfs((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyt get_nconfss   tprocess_residue_groupscB s/eZdeejdZdejdZRS(c C sg|_|j|_d|_d|_i|_i|_|jsKtd}xe|j D]W}|jd7_|j }|dj }||jkrd|j|(RR5R4R((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR>s N(RRR8RMRRRR>(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRs+tprocess_pdb_hierarchycB sSeZeejdZedZddZ ddZ eje dZ RS(c C sCg|_d|_d|_g|_|jj|_|jj|_|j j|_ d}|dk rr|j }nx|j jD]}|jr*|d|jIJtd|d|d|d|}|jj||j|j7_|j|j7_x;|jD]}|jj|jqWq|d|jIJqWdS(Nis processing chain '%s'RRRSRs! skipping non-protein chain '%s'(RRRtsequence_disordertramalyzeRtn_rama_outlierstrotalyzetn_rota_outlierstcbetadevRR8tas_multi_criterion_viewRRRRRRtextendRg( RRt validationRSRRRt chain_infoR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRs.        cc s1x*|jD]}x|jD] }|VqWq WdS(N(RR(RRR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRscC sad}}xJ|jD]?}|jd|}|dksD||kr|}|}qqW||fS(NR(R8RR(RRRt segment_maxRR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRs  cC sad}}xJ|jD]?}|jd|}|dksD||kr|}|}qqW||fS(NR(R8RR(RRtdist_maxRRR]((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR s  c C s|dIJ|dt|jIJ|d|jIJ|d|jtg|jD]}t|j^qLfIJt|jdkr|dt|jIJx2|jD]$\}}d|dj|fGHqWnd}}}g} xZ|jD]O} || j7}|| j 7}|| j d t 7}| j | j qW|d |IJ|dkrk|d |IJn|dkr|d |IJnt| dkr|d IJx+| D] \} } |d| | fIJqWn|j\} }|jdt \}}| dk st|dIJ|d| |fIJ|dk rO|d||fIJn|j\}}|jdt \}}|dk st|dIJ|d||fIJ|dk r|d||fIJn|rx.|jD]}|jd|qWn |dIJ|dIJdS(NR0sOverall: %d protein chain(s)s %d residuess$ %d disorered in %d segmentsis%d heterogeneous residues:s %s (%s)t,Rhs-%d disordered residues have multiple rotamerss1%d disordered residues have a single C-alpha atoms-%d disordered residues have C-beta deviationss%d apparent peptide flips:s %s (angle=%.1f)RsMax. RMSD between conformers:s %6.3f (%s) [all non-H atoms]s %6.3f (%s) [backbone only]s!Max. distance between conformers:R4s/Run with --verbose to show per-residue results.(R=RRRRRRtjoinRRRjRQRRRR8RLRR>(RR4tverbosetctrg_idRfRt n_cbeta_devRjt peptide_flipsRtresidue_id_strRRRt rmsd_mc_maxtsegment_mc_maxRt dist_mc_maxR((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyR>)sf  /                N( RRRMRRRtpropertyRR8RRRQR>(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyRs  (t __future__Rtmmtbx.disorderRtscitbx.array_familyRt scitbx.matrixRtlibtbx.str_utilsRR;tlibtbxRRRRRRRtobjectR'RRRRRR(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/disorder/analyze_model.pyts$   D   5