ڙxTc@ s?ddlmZddlmZddlmZmZddlmZm Z m Z m Z ddl Zddl mZddlZdZdd Zd Zd Zd8d9d:d;d<d=gZeegeD]\ZZeef^qZdZdZdZddZddZdZdZdZ dZ!d Z"d!Z#d"Z$d#Z%de'de'dd$Z(de'dd%d>d(Z)d)d*Z*d+Z+d,Z,dde-ej.d-Z/ej0j1d.Z2d/e fd0YZ3dde e'ej.d1Z4d2Z5dddd3Z6d4e fd5YZ7d6e8fd7YZ9dS(?i(tdivision(tmake_sub_header(tSorrytnull_out(t group_argstAutotslots_getstate_setstatet+slots_getstate_setstate_default_initializerN(tsqrtcC sddlm}|j}|j}|jjd sDtx|jjD]p}xg|j D]Y}|j }t |dks|dj j dkrj|j|jjqjqjWqWW|S(Ni(tflexiit(tscitbx.array_familyR tatomstsize_tt extract_i_seqtall_eqtAssertionErrort only_modeltchainstresidue_groupst atom_groupstlentaltloctstriptextend(t pdb_hierarchyR R t selectiontchaint residue_groupR((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytmulti_conformer_selections   +$g@cC sddlm}d}g}|g}x|t|kr||}|j}d}} |dkrw||d} n|t|dkr||d}n|d7}| dk r| j} d} } xF| jdjD].} | jjdkr|| j } PqqWxF|jdjD].} | jjdkr*|| j } Pq*q*W|| dksd| | gkst | | |kr|g}|j |q(qn|j |q(W|S(sd Split a protein chain into continuous peptide fragments (as lists of residue_group objects). i(tcoliitCtNN( t scitbx.matrixRRt resseq_as_inttNoneRR tnameRtxyztabstappend(tresiduestchain_break_distanceRtktcurrent_fragmentt fragmentstrestresseqtnext_restprev_rest prev_resseqtc_atomtn_atomtatom((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytfragment_single_conformer_chains@            cC s%t|jdkr$|j}nt|jdkrH|j}n|d|ddksx|d|ddkr|dS|d|dko|dknr|d|ddS|d|dko|dknr|d|ddSt|d|dd|d|ddSdS(s Compute the gap or overlap between two selections (order-independent). Returns 0 if the selections are directly adjacent, or the number of residues overlapped (as a negative number) or missing between the selections (positive). tbooliiiN(ttypet__name__t iselectiontmax(tsel1tsel2((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytget_selection_gap@s0((cC sddlm}|j}d}|j|}xN|jjjD]4}|j|j}|dkrJ|d7}qJqJW|S(s] Count the number of rotamer outliers from a selection of residues in a PDB hierarchy. i(t rotamer_evalitOUTLIERi( t mmtbx.rotamerR>t RotamerEvaltselectRt only_chainRtevaluate_residuetonly_atom_group(t hierarchyRR>trt n_outlierst sub_hierarchytrgt rotamer_flag((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytscore_rotamersTs  tOD1tOD2tOE1tOE2tND2tNE2tCD1tCD2tCE1tCE2cC sddlm}t|t|koDt|koDdknsOtd}}d}}d}xt|||D]s\} } } | jjdkrq|nt|| || } || d7}| |kr| }n|d7}q|W|dkstt ||}|dj j dkrAt d |d|Sd}} xt|||D]x\} } } | jjdkrq^n| j j}| j}tj|d}|dk rxt|||D]\}}}|j}|j|jkr|j|jkr|j j|krt|| ||} || d7}| | krm| } nPqqWttj}ttj} Pq^t|| || } || d7}| | kr^| } q^q^Wt ||}t d t||dt|| S(s Calculate RMSD and maximum distance for a pair of coordinate arrays, taking into account the symmetric or pseudo-symmetric nature of many sidechains. i(RitHiitASPtGLUtASNtGLNtPHEtTYRtrmsdtmax_devN(RXRYRZR[R\R](R!RRRR#tziptelementRR&RtparenttresnameRR$t fetch_labelstsymmetric_atom_names_dicttgettresidtchain_idtfloattsystmaxinttmin(tsites1tsites2R Rt rmsd_no_flipt rmsd_fliptmean_sqtmax_deviation_no_fliptn_sitestsite1tsite2R4tdistancetmax_deviation_flipt atom_nametlabelstsymmetric_namet site1_flipt site2_flipt atom_flipt labels_flip((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytcoord_stats_with_flipsns\?  "   "  "     c C sddlm}|j}|j}g}x|jD]}|jjdkr\q;nt}xi|jD][}|j|jkro| stt }|j ||j |j |j |j qoqoWq;Wt |||S(Ni(R RWtD(RWR( R R t vec3_doubleR RaRtFalseR$RtTrueR'R%R( tresidue1tresidue2R RmRnR tatom1tfoundtatom2((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytcoord_stats_for_atom_groupss     c C sg}xP|D]H}x?|jD]1}|jj|jkr |j|q q Wq Wd}t|dkrxft|D]U\}}xFt||dD]0\}} |j| } | |kr| }qqWq~Wn|S(Nii(R R$RR'Rt enumerateRv( RRxR t atom_groupR4tdxyz_maxti_atmRtj_atomRtdxyz((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pyt$max_distance_between_atom_conformerss ! g?cC st|d}||kS(NR (R(Rtmax_acceptable_distanceRv((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytrequires_nterm_splitscC st|d}||kS(NR(R(RRRv((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytrequires_cterm_splitstNEW1tNEW2tOLDs segid OLDs segid NEW1s segid NEW2ssegid NEW1 or segid NEW2s%segid NEW1 or segid NEW2 or segid OLDc sddkrtndIJdIJ|j}|j|jd|dkrs|jjt}n't|t r|jj|}nfd}d}x|j j D]} | j } xt | D]q\} } | j} | j}t| dkr| djj}|j|jtsQqn| dkr| | d}|j}||dkrt|jdkr|st| r|||d7}qqn| t| dkrX| | d}|j}||dkrUt|jdkrU|s8t| rR|||d7}qRqUqXqqWqW|S(s Given a model with some residues in alternate conformations, split the adjacent residues to allow for backbone movement. R s Splitting adjacent residues...ic srd|jIJnd}dk rJtdtd}n|j}d|_x*|jD]}d||_t|_ qlW|j }d|_x/|jD]!}||_t |_ d|_ qW|j |dS( Ns %sg?g?g?tAg?tBi(tid_strR#R:RlRERR tocct SEGID_MAINtsegidt detached_copytSEGID_NEW_SPLITttmptappend_atom_group(Rtnew_occt main_confR4talt_conf(tlogt new_occupancytverbose(s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pyt split_residues"          iiN(R#RR t reset_i_seqt reset_tmptatom_selection_cacheRtSELECTION_NEW_REBUILTt isinstancetstrRRRRRR"RRRBRRRR(RRtsplit_all_adjacentRRRt pdb_atomsRtn_splitRRti_resRRR.tlast_group_i_seqst prev_groupR1t next_groupt next_resseq((RRRs]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytspread_alternatessL              (  ( g?ig@cC sd|kodkns"t|j}|jj}|j|||j||j} |d k r| j|} n|j | dt |j dddt } | j d|} | j j} |j dddt } | j d|}|j j}|d k rAd d l}|jj| | |n|rtd |d | d |}td | d | d |} n|j |dt || fS(s Generate an mFo-DFc map with a selection of atoms at reduced occupancy. Will write the map coefficients (along with 2mFo-DFc map) to an MTZ file if desired. Reflections flagged for calculating R-free will always be omitted. ig?t update_f_calctmap_typesmFo-DFctexclude_free_r_reflectionstresolution_factors2mFo-DFciNtmap_datatxray_structureR9(RRt scattererstextract_occupanciest set_selectedtset_occupanciestdeep_copy_scatterersR#RBtupdate_xray_structureRtmap_coefficientstfft_maptapply_sigma_scalingtreal_map_unpaddedtiotbx.map_toolst map_toolstwrite_map_coeffstnegate_surrounding_sites(tfmodelRtselection_deletetnegate_surroundingt map_file_nametpartial_occupancyRtxrsRtxrs_tmpt fofc_coeffstfofc_ffttfofc_mapttwo_fofc_coeffst two_fofc_fftt two_fofc_maptiotbx((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytget_partial_omit_maps@"           g?c C s^ddl}|jjjd|ddd|}|jjjd|d|d|d |}|S( s= Makes the target map negative around an atom selection. iNRtselection_within_radiusiR9Rtnegate_selectiont atom_radius(tmmtbx.refinement.real_spacet refinementt real_spacetselection_around_to_negatet6negate_map_around_selected_atoms_except_selected_atoms(RRR9tradiustmmtbxRt target_map((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pyRJs   s discard_outliers = *rama *rota *cbeta *geo *map .type = choice(multi=True) min_model_map_cc = 0.85 .type = float use_difference_map = True .type = bool sampling_radius = 2.5 .type = float ignore_stub_residues = False .type = bool cC s|j}t}|jr0d|kr0t}n|jrQd|krQt}n|jrrd|krrt}n|jrd|krt}n|jrd|krt}n|jd|j rd|krt}n|S(Ntrotatramatcbetatgeotclashtcc_mintmap( tdiscard_outliersRtis_rotamer_outlierRtis_ramachandran_outliertis_cbeta_outliertis_geometry_outliertis_clash_outliertis_map_outliertmin_model_map_cc(t validationtparamstfilterstoutlier((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytis_validation_outlieris         c! C sddlm}ddlm}ddl} ddlm} ddlm} ddl m } |dkr| j |j jjt}n|jj|jd|d |d |d t} |r| jd |n| j}|dkr tjjtj}n| jjj}| jd |\}}g}|j}td d |x9|j j!D]%}|j"sqhnx |j#D]}|j$}|j%}|jj&}|j'|}|j(tsqnt)|dkr|d|IJqn|d}| |j*}|dkr@|d|IJqn|j+d|d|dt}t)|dkr| j,|r|j- rq|d|t)|fIJqn|j.|}t/||}|r|dt0|IJqn|j1rv| j2|}| j3d|d|d|d|j d|j4} | j5dkrv| j6dkrv|r|d|IJqqqvn|j7|j8qWqhWt)|dkrt9dn|dIJ|d t)|IJ| j:|d |d!d"|dIJ|S(#s Pick residues suitable for building alternate conformations - by default, this means no MolProbity/geometry outliers, good fit to map, no missing atoms, and no pre-existing alternates, but with significant difference density nearby. i(t molprobity(R>N(tbuilding(tcommon_residue_names_get_class(R RRtgeometry_restraints_managert outliers_onlytouts#Identifying candidates for buildingis %s is already multi-conformeritcommon_amino_acids %s: non-standard residuetresiduet mon_lib_srvtignore_hydrogenss% %s: missing or incomplete sidechains %sRRtatom_selectionRRs no difference density for %ss*No residues passed the filtering criteria.R s8Alternate conformations will be tried for %d residue(s):tprefixs (;tmmtbx.validationRR@R>tmmtbx.monomer_library.serverRRt iotbx.pdbRR R R#R6RRtsizeRR RRtshowtas_multi_criterion_viewtlibtbxtphiltparsetfilter_params_strtextracttmonomer_librarytservertget_difference_mapsRRRRt is_proteinRRRRRBRRRcteval_residue_completenesstis_stub_residuetignore_stub_residuestget_residue_group_dataRRtuse_difference_maptget_non_hydrogen_atom_indicestlocal_density_qualitytsampling_radiust$number_of_atoms_below_fofc_map_levelt+fraction_of_nearby_grid_points_above_cutoffR'RERtshow_chain_resseq_ranges(!RRRRRRRRR>RRRR tfull_validationtmulti_criterionRRRR(RRRRRti_seqst residue_selRt res_classt missing_atomsRt is_outliert i_seqs_no_hdt map_stats((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytfilter_before_build{s  $                     sO min_occupancy = 0.1 .type = float min_distance_over_u = 1.0 .type = float t disorder_infoc B sPeZdddddddddd d g Zed Zejd d d ZRS(tn_confstsitest atom_namesRtu_isostu_starstmax_rmsdtmax_distance_over_ut dxyz_savet u_iso_savetatom_name_savecC sddlm}ddlm}ddlm}g|_g|_g|_g|_ |j |_ |j }i}x|j D]} | j j} t| dkr| j| drtd| j nxh| j D]Z} | jjdkr |r qn| j|kr+g|| j||_||_||_|jj||j|_dS(N(RRtprocessed_pdb_filet__dict__RgR R(RLRRRtkwds((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pyRYs    cC shddlm}|jd|jd|jjd|jd|d|d|jjjd t }|S( Ni(RRRRRRtd_minR( RRtbox_build_refine_baseRRRRtf_obsRR(RLRRRtbox((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pytmake_boxs     (R8R]t__doc__RYR(((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pyRs (RMRN(RORP(RMRQ(RORR(RSRT(RURVg?(:t __future__Rtlibtbx.str_utilsRt libtbx.utilsRRR RRRRt libtbx.philtmathRRjRR5R=RLtsymmetric_atom_namestdicttn1tn2ReRRRRRtSEGID_NEW_REBUILTRRt SELECTION_OLDRtSELECTION_NEW_SPLITt SELECTION_NEWtSELECTION_MODIFIEDR#RRRRRRRR_R(R R t rejoin_philR)R}tfinalize_phil_strRRtobjectR(((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/building/alternate_conformations/__init__.pyts|"   &   ) 6     B *  \  bd