xTc@ saddlmZddlZddlZddlZdZedkr]eejdndS(i(tdivisionNc C sx|D]}tjjd|}|j}|jjdGHx|jD]}d|jGHx|jD]}d|jGHx|j D]}d|j |j fGHx|j D]q}d|j |jfGHxS|jD]E}dG|jGHdG|jGHd G|jGHd G|jGHd |jGHqWqWqWqoWqPWd GHx|jD]}d|jGHx|jD]}d|jGHxx|jD]j} d | j GHxU| jD]G} d| j| j | j fGHx#| jD]}dG|jGHqWqWqWqhWqIWdGHx|jD]}d|jGHxx|jD]j}d|jGHxU|jD]G} d| j| j | j fGHx#| jD]}dG|jGHq{WqMWq.WqWdGHx|jD]}d|jGHx|jD]}d|jGHx|j D]|}d|j |j fGHx^|jD]P} d| j GH| j} d| jGHx#| jD]}dG|jGHqOWqWqWqWqW|j} tj| }|j}|j}|j}|j}|j} | jd|st| j|jkstd|_d|_ d|_d|_ d|_ d|_d|_tjjj }d|_|j!d|dGH|j"dt#GH|j$ddqWdS( Nt file_namesY # Primary "view" of hierarchy: # model, chain, residue_group, atom_group, atoms model: "%s"s chain: "%s"s' residue_group: resseq="%s" icode="%s"s( atom_group: altloc="%s" resname="%s"s s atom.xyz: s atom.occ: s atom.b: s atom.segid: "%s"sd # Secondary (read-only) "view" of the hierarchy: # model, chain, conformer, residue, atoms conformer: "%s"s0 residue: resname="%s" resseq="%s" icode="%s"s # Special case: if there are no alt. conf. you can eliminate one # level of the hierarchy (which may be more intuitive at first).s # A third "view" of the hierarchy: # model, chain, residue_group, conformer, residue, atom # This is useful for handling all conformers of a given residue_group # together. # All meaningful PDB files will only have one residue per conformer.s conformer: altloc="%s"s residue: resname="%s"tothertXYtZtNOPt9999tItQt9tNEWtatoms: # Format entire hierarchy as pdb string and pdb file.t append_endsjunk.pdb(%tiotbxtpdbtinputtconstruct_hierarchytoverall_countstshowtmodelstidtchainstresidue_groupstresseqticodet atom_groupstaltloctresnametatomstformat_atom_recordtxyztocctbtsegidt conformerstresiduest only_residuetrandomtchoicetparenttis_similar_hierarchytAssertionErrort memory_idtnamet hierarchyR t append_atomt as_pdb_stringtTruetwrite_pdb_file( targsRtpdb_inpR,tmodeltchaint residue_groupt atom_groupR t conformertresiduet pdb_atomstroot((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/examples/pdb_hierarchy.pytruns           #       #              t__main__i( t __future__Rt iotbx.pdbR R%tsysR;t__name__targv(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/examples/pdb_hierarchy.pyts     q