ó ‚™xTc@ s ddlmZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z ddlmZmZdd lmZdd lZ dd lmZdd lZed „Zed „Zdd„Zedkredejdƒnd S(iÿÿÿÿ(tdivision(tsgtbx(tpointgroup_tools(tsub_lattice_tools(tcrystal(t option_parser(teasy_run(tSorryt multi_out(t show_stringN(tStringIOcC s·|dkrtj}ntj|||ƒ}|dIJ|dIJ|J|dIJ|dIJ|dIJ|dI|jƒIJ|dI|jƒIJ|dItjd|ƒIJ|J|J|d IJ|d IJ|d IJ|d I|j j ƒjƒIJ|d I|j j ƒjƒIJ|d I|j jƒIJ|dItjd|j ƒIJ|J|J|dIJ|dIJ|dIJ|dIJ|dIJ|dIJ|dIJ|J|j ƒ|j d|ƒ|S(NsDA summary of the constructed point group graph object is given belowsD====================================================================s----------------------sInput crystal symmetrys Unit cell: sUnit cell volume: s Space group: tgroups--------------------------sLattice symmetry deductions Niggli cell: sNiggli cell volume: s#Niggli transformed input symmetry: sSymmetry of Niggli cell: sDAll pointgroups that are both a subgroup of the lattice symmetry andsHa supergroup of the Niggli transformed input symmetry wil now be listed,sCas well as their minimal supergroups/maximal subgroups and symmetrysoperators that generate them.sEFor each pointgroup, a list of compatible spacegroups will be listed.sFCare is taken that there are no systematic absence violation with the sprovided input spacegroup.tout(tNonetsyststdouttpgtt"space_group_graph_from_cell_and_sgt parameterstvolumeRtspace_group_infot xs_prim_sett unit_celltpg_hightflushtshow(tinput_uctinput_lst max_deltaR t sg_explorer((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/explore_metric_symmetry.pytdo_pointgroup_trickssJ                   cC sÿ|dkrtj}ntjjddƒ}|dkrHtdƒ‚ntƒ}|jd|ƒdt |ƒt |ƒf}t j d|d|j ƒj ƒƒ}|jdkrÕtd|d j|jƒfƒ‚n|d It |ƒId IJ|d IJdS( Ntcommandtdots_The program "dot" is not on PATH: For information about "dot" visit: http://www.graphviz.org/R s %s -Tpng > %st stdin_linesisFatal error running %s: %ss s A file nameds$contains a graphical representation sof the point group relations.(R RRtlibtbxtpathtfull_command_pathRR tgraphviz_pg_graphR Rtfully_bufferedtgetvaluet splitlinest return_codet RuntimeErrortjoint stderr_lines(t pg_objectt file_nameR tdot_pathtbufferRtrc((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/explore_metric_symmetry.pytmake_graph_of_graphDs$       sphenix.explore_metric_symmetrycC s%td|dddƒjƒjdddddd d d d d ddddƒjddddd dd tddƒjddddd dddƒjddddddddƒjddddddddddƒjddddddddƒjdd ddddddƒjdd!ddd d"d tdd#ƒjdd$dddd dd%d d&ddd d'ƒjdd(ddd d)dd d d*dddd+ƒjdd,dddd-d d.dd/dd0ƒjd1|ƒ}tƒ}|jd2d3d4tj ƒid5d66d7d86d9d:6d;d<6d=d>6d?d@6dAdB6}|j j dk rn|j |j j ƒsn|dC|j j IJ|dDIJdSnd}d}t |ƒdEkr|jjƒdS|jjƒdkrÕ|J|dFIJ|J|jjƒdS|j j dkr"|jjƒdkr"|J|dGIJ|J|jjƒdSn|jjƒdk r]|jjƒjƒs]|dHIJdSn|j j dk r¦tjdI|jjƒdJdK|j j ƒ}||_n|j jrõ|dLIJ|jj|jjƒƒjƒ}tj|dMƒ|_n|j}|j js_t|jƒ|jƒ|j j|ƒ}|j jdk r_t||j j|ƒq_n|j jdk r!|dNIJd}|j jdkrÜ|j j dkr´t!dOƒ‚qýtj|j jdJdK|j j ƒ}n!tj|j jdJ|j jƒ}|j js3t|jƒ|jƒ|j j|ƒ} n|J|J|dPIJ|dQIJ|J|dRIJ|dSIJ|dTIJ|J|J|j j"} | d.krÖt#j$dU|dV|d |j jdW|dX|j j%dY|j j&ƒ} q!|j|jƒƒ} |j|jƒƒ} d}|j j"} d}| jƒj'ƒ| jƒj'ƒkrWt#j(|| ƒ}|}nt#j(|| ƒ}|}|J|dZIJ|J|d[IJ||j)j*ƒIJ|J|d\IJ|Jxnt+|j,|j-|j.ƒD]N\}}}|j/ƒ}|d]IJ|d^IJ|J|d_|dEdE|dEd.|dEd`fIJ|da|d.dE|d.d.|d.d`fIJ|db|d`dE|d`d.|d`d`fIJ|J|dcIJ|ddI|j*ƒIJ|deIJ|j0df|dgdhƒ|J|Jt#j$dU|dV|d |j jdW|dX|j j%dY|j j&ƒ} qÌWndS(iNtusages [options]t descriptionsExplore Metric Symmetry. A list of possible unit cells and spacegroups is given for the given specified unit cell and spacegroup combination. If a second unit cell is given, linear combinations of the basis vector of one unit cell are sought that match the other.s --max_deltatactiontstorettypetfloattdefaultg@tdestRthelps|Maximum delta/obliquity used in determining the lattice symmetry, using a modified Le-Page algorithm. Default is 5.0 degreestmetavartFLOATs--start_from_p1t store_truetnigglis^Reduce to Niggli cell and forget the input spacegroup before higher metric symmetry is sought.s--graphskA graphical representation of the graph will be written out. Requires Graphviz to be installed and on PATH.s--centring_typetstrs(Centring type, choose from P,A,B,C,I,R,Fs--other_unit_cells)Other unit cell, for unit cell comparisons10,20,30,90,103.7,90s--other_space_groups9space group for other_unit_cell, for unit cell comparisons--other_centring_types--no_point_group_graphtpg_graphs9Do not carry out the construction of a point group graph.s--relative_length_tolerances;Tolerance for unit cell lengths to be considered equal-ish.gš™™™™™¹?trel_length_tols--absolute_angle_tolerancet abs_angle_tolg$@s)Angular tolerance in unit cell comparisons --max_ordertintitINTs%Maximum volume change for target celltargstlabelRt file_objectt PrimitivetPs A centeredtAs B centeredtBs C centeredtCs Body centeredtIt RombohedraltRs Face centeredtFs)Sorry, the centring type %s is not known.sChoose from P,A,B,C,I,R,F isSorry: Unit cell not specified.s2Sorry: centring type or space group not specified.s1Sorry, Non chiral space groups not yet supported.Rtspace_group_symbols Hall: %s 1s9*Unit cell will be niggli reduced and P1 will be assumed*sP 1s'A second unit cell has been specified. s9No space group or centring type for other cell specified.sUnit cell comparisons--------------------s:The unit cells will be compared. The smallest niggli cell,s9will be used as a (semi-flexible) lego-block to see if its%can construct the larger Niggli cell.txs_atxs_bR trelative_length_tolerancetabsolute_angle_tolerancesFVolume change of largest niggli cell requested via keyword --max_ordersJInput crystal symmetry is tranformed to niggli setting using the operator:sAComparisons for various sublattices of the target cell are listedsC===================================================================s%Niggli cell is expanded using matrix:s /%4i %4i %4i \ is M = |%4i %4i %4i | s \%4i %4i %4i / s.Change of basis operator to reference setting:s sresulting crystal symmetry:tftprefixs (1Rtenable_symmetry_comprehensivetoptionR tFalsetprocessRtregisterRRtoptionst centring_typethas_keytlentparsert show_helptsymmetryRRt space_groupt is_chiralRR?t change_basist!change_of_basis_op_to_niggli_cellRARRtgraphR2tother_unit_celltother_space_grouptother_centring_typeRt max_ordertslttcompare_latticeRBRCRt"make_list_of_target_xs_up_to_ordertbasic_to_niggli_cb_optas_xyztziptxs_listt extra_cb_optmatricestas_list_of_listst show_summary(RFt command_namet command_linetlogtallowed_centring_typestxstother_xstucR-tother_pg_objecttordert sl_objectttmp_attmp_bt modified_xst lego_blockttmp_xstcb_optmat((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/explore_metric_symmetry.pytrun`s€                                                               $        ///    t__main__RFi(t __future__RtcctbxRt cctbx.sgtbxRRRRnRtiotbx.option_parserRR"Rt libtbx.utilsRRtlibtbx.str_utilsR t libtbx.patht cStringIOR RR RR2RŠt__name__targv(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/explore_metric_symmetry.pyts"   2  ÿ