ƙxTc@ sdZddlmZddlZddlmZddlmZddl m Z ddl m Z ddl mZddlZdd lmZdd lmZdd lmZmZmZdd lmZdd lmZddlZddlZddlmZddlZddlmZddlm Z ddlm!Z!ddl"Z#ddl$Z$ddl%Z%ddl&Z&ddl'Z#dZ(ej)j*e(de+Z,ej)j*de(de+Z-de.fdYZ/dZ0e1dZ2dZ3e4dZ5e1e1e1dZ6dZ7e1e1e1dZ8dZ9dZ:d e&j;e+d!Z<d"fd#YZ=e1d$Z>d%Z?d&e!j@fd'YZAdS((s Common manipulations of (macromolecular) model files. This module is used as a standalone program, phenix.pdbtools, but some components are also used in phenix.refine, and it is also a dumping ground for individual related functions. i(tdivisionN(t rigid_body(tutils(tflex(tiotbx_option_parser(t show_string(tpdb(tcrystal(tSorrytnull_outt check_if_output_directory_exists(tcrystal_symmetry_from_any(tmonomer_library(tmodel_statistics(teasy_run(tcombine_unique_pdb_files(t runtime_utilssselection = None .type = atom_selection .help = Selection for atoms to be modified .short_caption = Modify atom selection .input_size=400 .style = bold noauto adp .help = Scope of options to modify ADP of selected atoms .multiple = True .short_caption=Modify ADPs .style = auto_align menu_item parent_submenu:model_modifications noauto { atom_selection = None .type = atom_selection .help = Selection for atoms to be modified. \ Overrides parent-level selection. .short_caption = Modify ADPs for selection .input_size=400 .style = bold randomize = False .type = bool .help = Randomize ADP within a certain range .short_caption=Randomize ADPs set_b_iso = None .type = float .help = Set ADP of atoms to set_b_iso .short_caption=Set isotropic B to .input_size = 64 convert_to_isotropic = False .type = bool .help = Convert atoms to isotropic convert_to_anisotropic = False .type = bool .help = Convert atoms to anisotropic shift_b_iso = None .type = float .help = Add shift_b_iso value to ADP .short_caption=Increase B_iso by scale_adp = None .type = float .help = Multiply ADP by scale_adp .short_caption=ADP scale factor } sites .help = Scope of options to modify coordinates of selected atoms .multiple = True .short_caption=Modify coordinates .style = auto_align noauto menu_item parent_submenu:model_modifications { atom_selection = None .type = atom_selection .help = Selection for atoms to be modified. \ Overrides parent-level selection. .input_size=400 .short_caption = Modify sites for selection .style = bold shake = None .type = float .help = Randomize coordinates with mean error value equal to shake .short_caption = Randomize coordinates (mean value) switch_rotamers = max_distant min_distant exact_match fix_outliers .type=choice(multi=False) translate = 0 0 0 .type = floats(size=3) .optional = False .help = Translational shift (x,y,z) rotate = 0 0 0 .type = floats(size=3) .optional = False .help = Rotational shift (x,y,z) euler_angle_convention = *xyz zyz .type = choice .help = Euler angles convention to be used for rotation } occupancies .help = Scope of options to modify occupancies of selected atoms .multiple = True .short_caption=Modify occupancies .style = noauto menu_item parent_submenu:model_modifications { atom_selection = None .type = atom_selection .help = Selection for atoms to be modified. \ Overrides parent-level selection. .input_size=400 .short_caption = Modify sites for selection .style = bold randomize = False .type = bool .help = Randomize occupancies within a certain range .short_caption = Randomize occupancies set = None .type = float .help = Set all or selected occupancies to given value .short_caption=Set occupancies to .input_size = 64 normalize = False .type = bool .help = Reset the sum of occupancies for each residue to 1.0. Note that this will be performed before any atoms are removed. .short_caption = Reset total occupancy to 1 } rotate_about_axis .style = box auto_align { axis = None .type = str angle = None .type = float atom_selection = None .type = str } change_of_basis = None .type = str .short_caption = Change of basis operator .help = Apply change-of-basis operator (e.g. reindexing operator) to the coordinates and symmetry. Example: 'a,c,b'. renumber_residues = False .type = bool .help = Re-number residues increment_resseq = None .type = int .help = Increment residue number .short_caption = Increment residue numbers by truncate_to_polyala = False .type = bool .help = Truncate a model to poly-Ala. .short_caption = Truncate to poly-Ala .style = noauto remove_alt_confs = False .type = bool .help = Deletes atoms whose altloc identifier is not blank or 'A', and resets the occupancies of the remaining atoms to 1.0. .short_caption = Remove alternate conformers .style = noauto always_keep_one_conformer = False .type = bool .help = Modifies behavior of remove_alt_confs so that residues with no conformer labeled blank or A are not deleted. Silent if remove_alt_confs is False. set_chemical_element_simple_if_necessary = None .type = bool .short_caption = Guess element field if necessary .help = Make a simple guess about what the chemical element is (based on atom name and the way how it is formatted) and write it into output file. set_seg_id_to_chain_id = False .type = bool .short_caption = Set segID to chain ID .help = Sets the segID field to the chain ID (padded with spaces). .style = noauto clear_seg_id = False .type = bool .short_caption = Clear segID field .help = Erases the segID field. .style = noauto convert_semet_to_met = False .type = bool .short_caption = Convert SeMet residues to Met .style = noauto rename_chain_id .help = Rename chains .short_caption = Rename chain ID .style = box { old_id = None .type = str .input_size = 50 .short_caption = Old ID new_id = None .type = str .input_size = 50 .short_caption = New ID } set_charge .short_caption = Set atomic charge .style = box auto_align { charge_selection = None .type = atom_selection .short_caption = Atom selection charge = None .type = int(value_max=7,value_min=-3) } output .help = Write out file with modified model (file name is defined in write_modified) .style = noauto { file_name=None .type=path .input_size=400 .short_caption = Output model file .help = Default is the original file name with the file extension replaced by "_modified.pdb". .style = bold new_file file_type:pdb format = *pdb mmcif .type = choice .help = Choose the output format of coordinate file (PDB or mmCIF) } remove_first_n_atoms_fraction = None .short_caption = Remove first N atoms (fraction) .type = float random_seed = None .type = int .help = Random seed tprocess_includessuse_neutron_distances = False .type = bool .help = Use neutron X-H distances (which are longer than X-ray ones) modify .short_caption = Modify starting model .style = menu_item scrolled auto_align { remove = None .type = atom_selection .help = Selection for the atoms to be removed .short_caption=Remove atom selection .input_size=400 .style = bold noauto keep = None .type = atom_selection .help = Select atoms to keep .short_caption=Keep only atom selection .input_size=400 .style = bold noauto put_into_box_with_buffer = None .type = float .help = Move molecule into center of box. %s move_waters_last = False .type = bool .short_caption = Move waters to end of model .help = Transfer waters to the end of the model. Addresses some limitations of water picking in phenix.refine. } input { pdb { include scope mmtbx.utils.pdb_params } monomer_library { include scope mmtbx.utils.cif_params } crystal_symmetry .help = Unit cell and space group parameters .short_caption = Crystal symmetry .style = hidden { unit_cell=None .type=unit_cell .style = noauto space_group=None .type=space_group .style = noauto } } model_statistics = None .type = bool .style = hidden stop_for_unknowns = True .type = bool .short_caption = Stop for residues missing geometry restraints include scope mmtbx.monomer_library.pdb_interpretation.grand_master_phil_str include scope libtbx.phil.interface.tracking_params tmodifycB seZddZdZdZdZdZdZdZ dZ dZ d Z d Z d Zd Zd ZdZdZdZdZRS(c C s||_|j|_|jdkr3tj|_n||_||_||_t|_ d|_ d|_ t|_ |jj dk rtj|jj tj|jj ny|jj}Wn*tk rntk rd}nXy|jj}Wn*tk rntk r&d}nX|jdk r|d|jIJddlm}|j|j}|jj||_|jjj|jj|dIJ|jjjd|ddt |_ n|dk rtj!dt"j#d td |d |gd |d |_ n|dk retj!dt"j#d td |d |gd |d |_ n|j dk r|j dk rt$dt%|t%|fn|j dk r|j dkst&tj!d|j j'|_ ntj!dt"j#d td |d |jj(gd |d |_)|j*|j+|j,|j-|j.y|j/Wn$tk rntk rnXdS(Ns&Applying change-of-basis operator '%s'i(tsgtbxs New symmetry:tftprefixs tflagst iselectiontall_chain_proxiestselection_stringstxray_structureisfAmbiguous selection: 'keep' and 'remove' keywords cannot be used simultaneously: keep=%s remove=%s(0tlogt pdb_hierarchytNonetsyststdoutRRtparamstFalset_occupancies_modifiedtremove_selectiontkeep_selectiontxray_structure_was_replacedt random_seedtrandomtseedRtset_random_seedtremovetKeyboardInterruptt Exceptiontkeeptchange_of_basistcctbxRtchange_of_basis_opt change_basistatomstset_xyzt sites_carttcrystal_symmetryt show_summarytTruetsmart_selectionRtget_atom_selectionsRRtAssertionErrorRt selectiont top_selectiont&_process_remove_first_n_atoms_fractiont_rotate_about_axist _process_adpt_process_sitest_process_occupanciest _put_in_box( tselfRR RRtparams_remove_selectiontparams_keep_selectionRtcb_op((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyt__init__2s                                   cC s|jjdk r|jj}t|j|jj}tj|t j tj|j|t }|j dk r||j j @}ntjd||_ ndS(NR(R tremove_first_n_atoms_fractionRRt scattererstinttsizeRtboolR!t concatenateR7R#RR8(RCRItn_removetsel((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyR=vscC sJ|jjdk rF|jjd|jj}|jj|jndS(Nt buffer_size(R tput_into_box_with_bufferRRt1orthorhombic_unit_cell_around_centered_scattererstreplace_scatterersRI(RCtresult((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRBs cC s!|jd||jfIJdS(Ns%s: selected atoms: %s(Rtformat_summary(RCttextR;((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyt _print_actions c C sx|jjD]}|jdkr.|j}n@tjdtjdt d|j d|jgd|j d}|j r|j d|n|jr|jd|n|jd|d|j|jd|d |j|jd|d |j|jr |jd|q q WdS( NRRRRRiR;tb_isotfactortshift(R tadptatom_selectionRR<RR8RR9R!RRtconvert_to_isotropict_convert_to_isotropictconvert_to_anisotropict_convert_to_anisotropict _set_b_isot set_b_isot _scale_adpt scale_adpt _shift_b_isot shift_b_isot randomizet_randomize_adp(RCR[R;((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyR?s$        cC s0|jddd||jjd|jdS(NRVsConverting to isotropic ADPR;(RWRR]tindices(RCR;((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyR^s cC s0|jddd||jjd|jdS(NRVsConverting to anisotropic ADPR;(RWRR_R(RCR;((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyR`s cC sI|dk rE|jdd|d||jjd|d|jndS(NRVs Setting all isotropic ADP = %.3fR;tvalue(RRWRRbR(RCR;RX((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRas    cC sI|dk rE|jdd|d||jjd|d|jndS(NRVs&Multiplying all ADP with factor = %.6gR;RY(RRWRRdR(RCR;RY((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRcs    cC sI|dk rE|jdd|d||jjd|d|jndS(NRVsAdding shift = %.2f to all ADPR;tb_shift(RRWRtshift_usRi(RCR;RZ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRes    cC s0|jddd||jjd|jdS(NRVsRandomizing ADPR;(RWRt shake_adpR(RCR;((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRhs c C sx|jjD]}|jdkr.|j}n@tjdtjdt d|j d|jgd|j d}|j d|d|j |jd|d |j|jd|d |jd |jd |jq WdS( NRRRRRiR;trms_differencetmodet translatetrotateteuler_angle_convention(R tsitesR\RR<RR8RR9R!RRt _shake_sitestshaket_switch_rotamerstswitch_rotamerst _rb_shiftRpRqRr(RCRsR;((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyR@s         cC s|dkrdS|jdd|d|tjjj}|jjj|jj t j d|jd|d|j |_|jj d|jjjdS(NRVsSwitching rotamers; mode = %sR;RRoR4(RRWtmmtbxR tserverRR2R3RR4RRwRtset_sites_cartt extract_xyz(RCR;Rot mon_lib_srv((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRvs      cC sI|dk rE|jdd|d||jjd|d|jndS(NRVsShaking sites (RMS = %.3f)R;Rn(RRWRtshake_sites_in_placeR(RCR;Rn((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRts    c C sg|D]}t|^q}g|D]}t|^q&}t|dkrctd|nt|dkrtd|n|ddks|ddks|ddks|ddks|ddks|ddkr|jddd||d kr:tjjd |dd |dd |d}n-tjjd |dd |dd |d}|jj d |j j d|d|j ndS(NisWrong value: translate= iiiRVsRigid body shiftR;tzyztphitpsitthetrotttrans( tfloattlenRRWtscitbxRt rb_mat_zyzt rb_mat_xyzRtapply_rigid_body_shifttrot_mattas_mat3Ri( RCR;RpRqRrtiRRtrot_obj((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRxs000          c  smfd}xWjjD]I}|jdkr=j}n@tjdtjdt dj d|jgdj d}|j rj dd d ||j jd |jn|jdk rj dd |jd ||j jd |jd |jn|jrj dd d ||tdjd |jdj djqqWdS(Nc s2jr dSjr%tdn t_dS(Ns,Can't modify occupancies (already modified).(R<R"RR7((RC(s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytcheck_if_already_modified s   RRRRRiRVsRandomizing occupanciesR;sSetting occupancies to: %8.3fRjs Resetting total occupancy to 1.0t hierarchyR(R t occupanciesR\RR<RR8RR9R!RRRgRWtshake_occupanciesRtsettset_occupanciest normalizetnormalize_occupanciesRR(RCRtoccR;((RCs</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRA sB                cC sD|jdk r@|jjdkr@|jjd|jddndS(NitouttlabelsAtoms to be kept: (R#Rt selected_sizeR6R(RC((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyt$report_number_of_atoms_to_be_removed5s   c C s|jj}|jj}|j|j|jgjddkrg}y1x*|jj D]}|j t |q[WWnjt k rt jdtd|jd|jd|jd}g|j|jD] }|^q}nXt|dkrtdt|jntjj|d }tjj|d}|jd |d |jd t} t jdtd|jd|jd|jd}|jtdkrtd t|jn| |j|} |jj|j|| ndS( NiRRRRis(Bad selection rotate_about_axis.axis: %sitpointtangletdegs/Empty selection rotate_about_axis.selection: %s(R trotate_about_axisRR4taxisR\RtcountRtsplittappendRR,RR9R!Rtselectt as_doubleRRtstrRtmatrixtcolt#rt_for_rotation_around_axis_throughR7R{t set_selected( RCtraapR4RtaRORtp1tp2traatsites_cart_rotated((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyR><s> '    ,     N(t__name__t __module__RRGR=RBRWR?R^R`RaRcReRhR@RvRtRxRARR>(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyR1s$ D             + cC s|d|jIJ|d|jIJd}xV|jD]H}x?|jD]1}|j|jkrH|j|_|d7}qHqHWq5W|dkr|dIJndS(Ns old_id= '%s's new_id= '%s'iisJWARNING: no chain id renamed: check input PDB file or renaming parameters.(told_idtnew_idtmodelstchainstid(RR Rtcountertmodeltchain((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytrename_chain_id^s  c C sdt|tst|d kr0tdnt|dkrQtdn|d krit}n|j}|j|j }t |dkrtd|n|dkrd}n)|dkrdt|}n d|}|j }xd|D]\} || } | j ||| j d} | ||| _|d | j|fIJqWd S( s  Set the charge for selected atoms. Note that both the hierarchy and the xray_structure must be passed here - in the context of the pdbtools app, the scattering_type attributes will override the atom's element and charge when the structure is written out. s8You must specify an atom selection to apply a charge to.i s-The charge must be in the range from -9 to 9.is;No atoms selected for charge modification (selection = %s).s s%1d-s%1d+s %s : set charge to %sN(t isinstanceRJR:RRtabsR tatom_selection_cacheR;RRRIt set_chargetelement_and_charge_symbolstscattering_typetid_str( RRt pdb_atomsR;tchargeRt sel_cachetiselRIti_seqtatomt elem_symbol((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytset_atomic_chargeks0             c sddl}|jjjtdddddg}x|jD]}x|jD]}x|jD]tfd}|rixPjD]?}x6|j D](}|j |kr|j d |qqWqWqiqiWqVWqCWdS( s Remove all protein sidechain atoms beyond C-alpha (as well as all hydrogens). Does not change the chemical identity of the residues. iNs N s CA s C s O s CB c s.x'jD]}|jkr tSq WtS(N(t atom_groupstresnameR7R!(tag(t aa_resnamestrg(s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pythave_amino_acidsR( tiotbx.pdb.amino_acid_codesRtamino_acid_codestone_letter_given_three_letterRRRtresidue_groupsRR2tnamet remove_atom(Rtiotbxtala_atom_namesRRRRR((RRs</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyttruncate_to_poly_alas  c C sx|jD]}x|jD]}x|jD]s}|j}t|dks]t|r?t|dkr|djdkrq3ng}xQ|D]I}|jdkrqntj|j j }|j ||fqW|j dx(|dD]\}} |j d|qW|d\} } d| _q3x9|D]1}|jd krn|j d|qFd|_qFWt|jdkr3|jd|q3q3Wt|jdkr |jd|q q Wq W|j } tj| jd } | j| d S( s Remove all alternate conformers from the hierarchy. Depending on the value of always_keep_one_conformer, this will either remove any atom_group with altloc other than blank or 'A', or it will remove any atom_group beyond the first conformer found. iitcS st|d|dS(Ni(tcmp(Rtb((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytst atom_grouptAt residue_groupRg?N(RR(RRRRRR:taltlocRtmeanR2t extract_occRtsorttremove_atom_grouptremove_residue_groupt remove_chaintdoubleRKtset_occ( Rtalways_keep_one_conformerRRRRtatom_groups_and_occupanciesRtmean_occRt single_confR2tnew_occ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytremove_alt_confss< %     c C s|dkrt}nxA|jD]3}x*|jD]}x|jD]}|jj}|dk r|j|}|jt sqKqn|j } d} x| D]} | jj } t | dkr|j | qn| jjdkrqn| j| ds3td| jn| | d7} qW| dkrn|d|j| fIJnd| } t}t | }x| D]} | j}| jjdks|dkr|dIJ|jtjt |dq|s|j }|j|tjt || |d| j|djfIJt }qqWqKWq8Wq%W|jj }|dk r|jj|ndS( s Reset the sum of occupancies for each residue_group to 1.0. This will fail if any (selected) atom_group has non-uniform occupancies. iRs+Non-uniform occupancies for atom_group '%s'g?s$ residue_group '%s': occupancy=%.2fs$ altloc ' ': set occupancy to 1.0s& altloc '%s': set occupancy to %.2fN(RR RRRR2t extract_i_seqRtall_eqR7RRRRRtstripRRR!RRRRRIR(RR;RRRRRti_seqst selection_rgRt occupancy_sumRtatom_occtgaptresettn_groupsR2R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pyRsV           ! " # c C sd}|j}xt|jD]\}}|jjdkr%|jjdkr%|j}|jdkr|d7}d|_d|_d|_||}d|_ x |jD]}t |_ qWqq%q%W|S( sZ Change the chemical identity of MSE residues to MET, without changing coordinates. itSEtMSEitMETs SD s StS( RIt enumerateR2RRtelementtuppertparentRRR!thetero( RRtn_mseRIRRRt scatterertag_atom((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytconvert_semet_to_mets *       c C s|dkrt}nd}|dk rN|j}|j|j}nx0|jD]"}x|jD] }|dk r|jj}|j |} t | dkrqnqt | t |kr|d|j t | t |fIJqnqn|dkr?d} xd|j D]} | | _ | d7} qWqnx7|j D])} | j} | |7} d| | _ qLWqnWq[WdS(NisRWarning: chain '%s' is only partially selected (%d out of %d) - will not renumber.is%4d(RR RR;RRRR2Rt intersectionRRRtresseqt resseq_as_int( Rt renumber_fromR\Rtselected_i_seqsRRRt chain_i_seqsRRRR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytrenumber_residuess2    &     c C sl|dkst|dkrC|jd|d|dtddn%|dkrh|jd|d|ndS( NRtmmcift file_nameR5t append_endtatoms_reset_serial_first_valuei(spdbR(R:twrite_pdb_fileR7twrite_mmcif_file(RR5Rt output_format((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdbtools.pytwrite_model_file1s     c C st|jdkr+tddn|j}|jd}|jt}|dkru|dIJ||fS|d|IJ|j|}|j|}|j|}|j|} x3|jj D]} |jj | j qW| j |j t| j t|jkoEt|jknsPtxDt|j| j D]'\} } | j| jksltqlW|| fSdS( sg Re-arranges the PDB hierarchy so that waters are located at the end of the atom list. This is done automatically in phenix.refine if water picking is enabled, but the routine here is more flexible. 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