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R\tvaluesReRRtdefaultiitbuffer_thicknesstasu_is_inside_epsilontoriginal_sitesRt asu_mappingst sym_tableRRR-tshell_asu_tablesRt vdw_distancetdeltas}Cannot automatically determine nonbonded_distance_cutoff: nonbonded_function.residual() not zero beyond maximum VDW distance.tmin_unit_cell_lengthiRRRRRRt%nonbonded_distance_cutoff_plus_buffersInternal error.sBnonbonded_distance_cutoff=%.6g is too small: max_vdw_distance=%.6gs!pair_proxies not defined already.g zo ?g zo ?(;R RRRRR4RRt fractionalizetmaxRt max_defaultRt get_distancesRRtprocess_sites_fractpair_asu_tabletadd_pair_sym_tableR9Rt pair_proxiesRR-R0t max_distanceR8RRYR2R3RRR Rtfind_max_vdw_distanceR RtresidualRR6R7R!tdirect_space_asut!non_crystallographic_asu_mappingsR+tupdate_plain_pair_sym_tableRRRRRRRtvirtual_memory_infot update_maxtnonbonded_proxiestmax_vdw_distanceR(RR\RRtbonded_distance_cutoff_epsilonRRRRRRRRt max_vdw_disttrt-current_nonbonded_distance_cutoff_plus_buffer((RRRRRsO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRsB           1                                            4               cC s=|jd|}|dkr*|j}n|jjd|S(NR\(RR R0Rtdeltas(RR\R((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pytnonbonded_model_distancess  cC stjj|jd|j}|jd|d|jtjd|}|jd|j|j |_ t j j dS(NRRRRtdistance_cutoff(RRRRR+RRRt add_all_pairstextract_pair_sym_tableR5RRR(RRRR((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRs   c 'C sH|dk r$|jdks-tn |j}|dkrQtjjdt}n|jd|d|d| } dgd\ } } }}}}}}}}}|jr| jdk st| j} n|j r|j dk r| j dk st| j } |dkr|j }q|}n|j r3|j}n|jrH|j}n|jr]|j}n|jrr|j}n|jr|j}n|jr|j}n|jr|j}n|jr|j}ntjjd|d| d| d|d |d |d |d |d |d|d|d|d|d|d|d|d|d| d|jS(NRRR\Ri t bond_proxiesRRR"R#R$R%R&R'R(R)R*tcompute_gradientst gradientstdisable_asu_cachet normalizationtextension_objectsR.(R R*R RRRYRRRRRRRtangleR"tdihedralR#treference_dihedralR$t ncs_dihedralR%t chiralityR&t planarityR't parallelityR(tgeneric_restraintsR)tenergiesR.(RR\Rtcustom_nonbonded_functionRRRRR*RRRRRRR"R#R$R%R&R'R(R((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pytenergies_sitessj     .                 c C s;|jdk stt|jdks0t|j|jdjksUtd}tj|jd}x|jdjD]}|j\}}|dkr|} n||||||d} ||||} | | } || | 7}||c| d7<||c| d8||j| nonbonded_clashscore obj Construct nonbonded_clash_info, the non-bonded clashss lists and scores Arguments: sites_cart: sites_cart[i] tuple containing the x,y,z coordinates of atom i site_labels: a list of lables such as " HA LEU A 38 ", for each atom hd_sel: hd_sel[i] retruns True of False, indicating whether an atom i is a Hydrogen or not NOTE: As of Dec. 2013 manipulation of scatterers can produce scatteres which have no lables. In that case, water interaction score will not be accurate Return: self.nonbonded_clash_info NOTE: Be aware to the parameters: assume_hydrogens_all_missing=False, hard_minimum_nonbonded_distance=0.0 The defult values of these are True and 0.001, which will alter the size of the vdw bonds and the clashes that being counted As of Dec. 2013 manipulation of scatterers can produce scatteres whish have no lables. In that case, water interaction score will not be accurate Usage example: mon_lib_srv = mmtbx.monomer_library.server.server() ener_lib = mmtbx.monomer_library.server.ener_lib() pdb = monomer_library.pdb_interpretation.process( file_name=None, raw_records=records, substitute_non_crystallographic_unit_cell_if_necessary=True, mon_lib_srv=mon_lib_srv, ener_lib=ener_lib) grm = pdb.geometry_restraints_manager( assume_hydrogens_all_missing=False, hard_minimum_nonbonded_distance=0.0)) xrs = pdb.xray_structure() sites_cart = xrs.sites_cart() site_labels = xrs.scatterers().extract_labels() hd_sel = xrs.hd_selection() nb_clash_info = grm.get_nonbonded_clashscore( sites_cart=sites_cart, site_labels=site_labels, hd_sel=hd_sel) @author: Youval Dar, LBL 12-2013 R\Rishnonbonded clashscore can't be calculated. PDB file contains unknown type pairs. Please provide cif file.R=Rtnonbonded_listthd_seltfull_connectivty_tabletconnectivty_table_2iN( RRtn_unknown_nonbonded_type_pairsRt get_sortedR tnonbonded_clashscoreRtfull_simple_connectivity(RR\RNRRtproxies_info_nonbondedRMtnonbonded_clash_info((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pytget_nonbonded_clashscorems&=       N("t__name__t __module__R R/RR;R<RIR`R1RRRRRRRRRRRRRRRRRRR RRR<RERW(((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyR s     K  R             = .   [idi2g333333?ii c C sddl} ddlm} ddlm} tjdd} x||f||fgD]x\} }xi| D]a\}}t| j ||| j ||}| j tj d||fd|d|qjWqWWtj d|j d | j}| jd |d |}|jjjd |d |j}tjd|}tj|| jtjjd |dd}g|D]}|j^qz}tj|j d}tj}||jjdd<|jtd|jd|j d|d|d|d|dtj!d|fS(Ni(tuctbx(RKRRER'RDRtbond_simple_proxiesR\t buffer_layerRRt max_shellitDefaultRRRRRRRR,("t$cctbx.crystal.coordination_sequencesRzRZRSRKRtbond_sorted_asu_proxiesR tabstcolRtbond_simple_proxytextract_bond_paramsRR%t;non_crystallographic_unit_cell_with_the_sites_in_its_centerRtspecial_position_settingsRR\RRt add_pairstcoordination_sequencesRRRt std_stringRtdistance_tablet setdefaultR Rtprolsq_repulsion_function(R\tedge_list_bondstedge_list_anglest bond_weightt angle_weightRt+non_crystallographic_unit_cell_buffer_layertasu_mappings_buffer_thicknessR,RzRZRKRRMRDRBRCRRtboxRtbond_asu_tableRtshell_asu_tableRRR((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyt:construct_non_crystallographic_conserving_bonds_and_anglessN    *$             c C s)||gjddks!t|dk r{|dk rZt|t|ksxtq{t|t|ks{tng}ddlm}m}|dk r||}nxpt|D]b\} } xS| jD]E\} } x6| D].} |dk r0| j st||| ||| }n,||| || || }||}|j }||kr| j rd}ndt | }|dkrt | t | }}n|| || }}|dkrd|}n d|}|j d ||||fqqWqWqW|S( Nii(RbtsqrR@R is%7.3fs%.6gsdistance: %s - %s: %s%s( RQR R Rt scitbx.matrixRbRwRfRgRitlengthRR>(ReRRRR\RR@RbRwRRjR)Rltrt_mx_jitd_carttd_fractdisttsstsitsjtsd((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRs<!  !!   !"         ,RScB sVeZdZdZedZdZedZedZdZ RS(s Object processing information on non-bonded steric clashes. When the distance between atoms is smaller than the Van Der Waals distance. @author: Youval Dar (LBL 2013) c C s||_||_||_||_||_|gkry|j}Wn~tk r}|dkrvt|qgggg}|GHn=tk r}t|ntk r}tdnX|d|_ |d|_ |d|_ |d|d|d|_ t |j}t |dd|} t |dd|} t |dd|} | | | } | |_| |_| |_| |_nHd|_d|_d|_d|_g|_ g|_ g|_ g|_ dS(s Arguments: nonbonded_list: a list with items in the following format ([pdb labels], i_seq, j_seq, model, vdw_distance, sym_op_j, rt_mx) i_seq,j_seq: position of residues in the pdb file model: The pdb or other model distance vdw_distance: Van Der Waals distance sym_op_j: is this a product of a symmetry opeation rt_mx: Rotation matrix for symmetry operation hd_sel: hd_sel[i] retruns True of False, indicating whether an atom i is a Hydrogen or not full_connectivty_table: full_connectivty_table[i] is a dictinary constaining a list of all atoms connected to atom i connectivty_table_2: connectivty_table[i] is a dictinary constaining a list of all atoms connected to atom i sites_cart: sites_cart[i] tuple containing the x,y,z coordinates of atom i s#vec3_double' object is not callablesMUnexpected error processing proxies_info_nonbonded in clashscore_clash_list()iiiiN(RMRNRORPR\tclashscore_clash_listt TypeErrorRt Exceptiontnb_clash_proxies_due_to_sym_opt nb_clash_proxies_solvent_solventtnb_clash_proxies_simpletnb_clash_proxies_all_clashesRtnb_clashscore_due_to_sym_optnb_clashscore_solvent_solventtnb_clashscore_simpletnb_clashscore_all_clashes( RRMRNRORPR\t clashlisttetn_atomstclashscore_due_to_sym_optclashscore_solvent_solventtclashscore_simpletclashscore_all_clashes((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyR/*sL                     c C sd}|||||r||s:||}}nt|dfg}|h}|h}x~tddD]m}t} x'|D]} | jt|| } qW| |}|j| }x|D]} ||| bool Check if we have 1-5 interaction between two hydrogen and heavy atom arguments: i_seq,j_seq: are the number of the atoms we are checking in the pdb table hd_sel: hd_sel[i] retruns True of False, indicating whether an atom i is a Hydrogen or not full_connectivty_table: full_connectivty_table[i] is a dictinary constaining a list of all atoms connected to atom retruns: True if we have 1-5 hydrogen and heavy atom interaction cS s|s |o|o| S(N((tatb((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyt~siiiiN(tdicttrangetsettunionR1( RR)RNROtxort atoms_numberstused_connectionstnew_connectionsRBt connectionstkeytnew_atom((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pytis_1_5_interactionos"        c C st|}d}|j|dddd!|d|d}|j|dddd!|d|d}|j|d}|j|d}||}dj|}||kr||}}n|||fS(s(str) -> str,str,str Collect atoms keys and coordinates Argumets: record : a clash record, for example: (['pdb=" HA LEU A 38 "', 'pdb="HD23 LEU A 38 "'], 523, 532, 1.8108674716831155, 2.44, '', None) Returns: clash_vec: a unique key for a clash. for example: '0.144,0.323,1.776,0.154,0.327,1.786' key1,key2: are the atoms keys. for example ' HA LEU A 38 ::120::' or ' CB ASN A 55 ::52::sym.op.' "atom1 label::atom1 number::sym.op"" s {0}::{1}::{2}iiiiis/{0:.3f},{1:.3f},{2:.3f},{3:.3f},{4:.3f},{5:.3f}(tlisttformatR\( RtrecordRtkey1tkey2t atomi_xyzt atomj_xyztvect clash_vec((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pytget_clash_keyss ,,  cC sd}d}d}d}|dd!}|dd!}|dd!}|dd!} ||kr|| |} ||| } || |} n|| kr|||} ||| } |||} ni||kr || |} ||| } || |} n-|||} ||| } |||} y-t|| | || || } Wntk rd} nX| S( sI(tuple,tuple) -> float Calculate the cosine used to evaluate wheather the atoms coliding are inline or not Arguments: u,v: lists containing x1,y1,z1,x2,y2,z2 coordinates Returns: cos_angle: the cosine of the angle between center of the common atom and the mid point between the other two atoms. cS s0|d|d|d|d|d|dS(Niii((tutv((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRscS s.gt||D]\}}||d^qS(Ni(R3(RRRty((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRscS s-tj|dd|dd|ddS(Niii(R R (R((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRscS s*gt||D]\}}||^qS(N(R3(tu1tu2RR((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRsiiii(RatZeroDivisionError(RRtu_dot_vtu_mid_vtu_lentmake_vectv1tv2RRtmid_uvtvec1tvec2t cos_angle((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pytcos_vecs8           -  cC se|jd}t|d}t|d}t||gk}t||gk}|od|S(s(str,dict) -> bool retrun true if the two atoms, which number is specified in "key" are single, double or tripple atom molecule Arguments: connectivty_table_2: connectivty_table[i] is a dictinary constaining a list of all atoms connected to atom i key: a list "atom1 lable::atom1 number::sym.op.::atom2 label::atom2 number::sym.op." Return True is both atoms have no connection to atoms two bonds apart s::ii(tsplitRR(RRPRBRCt i_is_solventt j_is_solvent((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pytare_both_solvents cC sgggg}i}i}xb|jD]W}|d}|d}|d}|d}|d} ||} | dkr%|j|||j|js||j|\} } } | | krdj| | g}ndj| | g}||kry| | |g||<| |krg|| [list,list,list] Collect inforamtion of clashing nonbonded proxies (neighboring atoms) for clash score calculation. - proxies considered to clash when model_distance - van_der_waals_distance < -0.41 - For every atom consider only worst clash - Do not double count in-line clashes. for example, C-H1 H2-... if both C and H1 are clashing with H2 count only the worst of them - Exclude 1-5 interaction of Hydrogen and heavy atom Retruns: clashing_atoms_list: [[list of clashes due to sym operation],[list of solvent-solvent clashes],[list of all other clashes]] iiiiig= ףp=ڿs::t,igR@gX9v?(RMRRNRORRR>RRtmaptfloatRRRt iteritemsRRP(Rtclashing_atoms_listtclashing_atoms_dictt clashes_dicttrecRR)tmodeltvdwtsymopRRRRt clash_keyRttemp_clash_listt n_clashesRBRCtvec_itvec_jRRRtclashing_atom_1tclashing_atom_2t remove_keytval((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRsz            - %%$  ( RXRYt__doc__R/t staticmethodRRRRR(((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyRS"s E) 1(t __future__RRzRtcctbx.geometry_restraints.flagst"cctbx.geometry_restraints.energiesRtcctbx.array_familyRtscitbx.python_utils.miscRtlibtbxRRRt libtbx.utilsRR#R RFt boost.pythontboosttpythont import_extR R tobjectR RvRRS(((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/geometry_restraints/manager.pyts6  $  + +