ó º™xTc@ s¬ddlmZddlmZddlmZddlmZddlmZddl m Z ddl m Z m Z ddlmZdd lZd efd „ƒYZd S( iÿÿÿÿ(tdivision(t eigensystem(tflex(tSorry(tnull_out(tmatrix(tacostpi(tpdbNtfab_elbow_anglecB s_eZddddd„Zd„Zd„Zed„Zd„Zd „Zd „Z d „Z RS( tLtHikiqc C sÃ|jd|d|d|d|ƒ||_|jƒ|jjƒdj}|jjƒdj}|jd|d|ƒ}|jd|j d |j ƒ} |jd|jd |jƒ} t j | j jƒƒ} t j | j jƒƒ} |j| ƒ} |j| ƒ}| j|ƒd kr"| }n|jd | d |ƒ}|j|| ƒ}|j| |ƒ}|j|ƒd kr€d |}n||_|j|ƒ|_|j| ƒ|_|j|ƒ|_dS(s3 Get elbow angle for Fragment antigen-binding (Fab) - Default heavy and light chains IDs are: H : heavy, L : light - Default limit (cutoff) between variable and constant parts are residue number 107/113 for light/heavy chains - Variable domain is from residue 1 to limit. Constant domain form limit+1 to end. Reference: ---------- Stanfield, et al., JMB 2006 Usage example: -------------- >>>fab = fab_elbow_angle(pdb_hierarchy=ph,limit_light=114,limit_heavy=118) >>>fab_angle = fab.fab_elbow_angle t chain_ID_Htlimit_Ht chain_ID_Ltlimit_Liÿÿÿÿtstarttendtfixed_selectiontmoving_selectionitvec1tvec2ihN(t select_strt pdb_hierarchytget_pdb_chainst pdb_var_Htatomstxyzt pdb_var_Ltnorm_vectget_transformationt pdb_const_Ht pdb_const_LRtreal_symmetrictrt as_sym_mat3tget_eigenvectortdott get_angletcross_product_as_unit_axisR tcos_H_to_L_with_xaxistcos_H_to_L_with_yaxistcos_H_to_L_with_zaxis(tselfRtchain_id_lighttchain_id_heavyt limit_lightt limit_heavytvh_endtvl_endt mid_H_to_Lttranformation_constttranformation_vart eigen_constt eigen_varteigenvectors_cteigenvectors_vtangletzaxistxaxis((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyt__init__ s>            cC sEtj|ƒtj|ƒ}|jƒ}|dkrA||}n|S(sAretruns normalized vector that starts at "stat" and ends at "end"i(Rtdoubletnorm(R+RRtxtl((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyRQs    cC s]t|ƒ}t|ƒ}tjtj|ƒ|ƒ}|jƒ}|dkrY||}n|S(Ni(ttupleRR=Rtcross_product_matrixR>(R+tatbR?R@((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyR'Ys     cC s“|rJ|rJ|j|ƒ}t|ƒ}|dks9t‚dt|}nd}|dkro|rod|}n|dkr| rd|}n|S(s-retrun the larger angle between vec1 and vec2ii´iZ(R%RtAssertionErrorR(R+RRtlargert angle_costacos_angle_cosR9((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyR&bs    cC sÌ|jƒ}|jƒ}d}xLt|ƒD]>\}}t|tƒs+td|ƒdkri|}Pqiq+q+W| szt‚|||d!}||j|ƒ}|j t j dddgƒƒrÈd}n|S(sA Get the eigen vector for eigen value 1 and normalize it igíµ ÷Æ°>iN( tvectorstvaluestNonet enumeratet isinstancetcomplextabsRER%tall_eqRR=(R+teigentvtetindxtiR?t eigenvector((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyR$os    ! cC sâ|j}|jƒj}|j||jƒƒ|_|j||jƒƒ|_|j||jƒƒ|_ |j||j ƒƒ|_ ||jƒj t ƒdkr±tdƒ‚n||jƒj t ƒdkrÞtdƒ‚ndS(sECreate seperate pdb hierarchy for each on the chains we want to alignis)No atoms in light chain. Check chain names)No atoms in heavy chain. Check chain nameN(Rtatom_selection_cachet selectiontselecttselect_var_str_HRtselect_const_str_HRtselect_var_str_LRtselect_const_str_LR tcounttTrueR(R+tphttest((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyR…s c C sVddlm}|jjƒ}|j|dtƒdtdtd|d|ƒ}|jS(Niÿÿÿÿ(tsuperpose_pdbstlogt write_outputtsave_lsq_fit_objtpdb_hierarchy_fixedtpdb_hierarchy_moving( tphenix.command_lineRbt master_paramstextracttmanagerRtFalseR_t lsq_fit_obj(R+RRRbtparamsR?((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyR”s  cC s„d}d}|j|d||ƒ|_|j||dd|ƒ|_|j|d||ƒ|_|j||dd|ƒ|_dS(stcreate selection strings for the heavy and light chains separating the variable and constant parts of the chainss9pepnames and (name ca or name n or name c) and altloc " "s$chain {0} and resseq {1}:{2} and {3}iRN(tformatRZR[R\R](R+R R RRts1ts2((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyR¤s ( t__name__t __module__R<RR'R_R&R$RRR(((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyR s ?    (t __future__Rt scitbx.linalgRtscitbx.array_familyRt libtbx.utilsRRtscitbxRtmathRRtiotbxRt iotbx.pdbtobjectR (((sI/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/fab_elbow_angle.pyts