o RŀgG@s2dZddlZddlmZddlmZddlmZddlmZddl Z ddl m Z ddl mZdd lmZdd lmZdd lmZdd lmZdd lmZddlmZddlmZddlmZddlmZddlmZddlm Z ddl!m"Z"d8de#de#de$fddZ%  d9dee"eee fde$e&efde#de$e&effddZ'de"fdd Z(d!ede)fd"d#Z*  d:d$e d%e d&ed'ede#d(e$d)e+d*e+ddfd+d,Z,  d:d$e d%e de#d(e$d)e+d*e+ddfd-d.Z-    d;d/ee"eefd0ee"eefde#de#d)e+d*e+de$e&effd1d2Z. d:de"d3e&d4e&d5e&ddf d6d7Z/dS)"z_cmp_res..csrtrurvrxr#r#r$r{#r|csrtrurvrxr#r#r$r{$r|csrtrurvrxr#r#r$r{%r|z rprev error:rpnMismatchCountz rnext error rrNresiduesrJrKrLrd disAtmCountzdisorder disagreement:ra)r;full_idrfr:rAr<r6sortedrprevrnextrgr7 child_dictr=rRrS is_disorderedrprQ)rZr[rr^r_r`r0idr0fidr1fidr*ric0ric1r0prevr1prevr0nextr1nextlongerakr\akndr]da0kr#r#r$_cmp_res sv  .    $$      re0e1cCsi}g|d<d|d<d|d<d|d<d|d<d|d<d|d<d|d <d|d <||d <||d <d |d<d |d<|r t|tr|jjd urt|jjt|jjkrtj|jj|jj|d urddn||d urkdn|drt|jjd|d<t|jjd|d <|d dkrd|d<nd|d<n|jjd urdnt|jjd|d<d|d<nd|d<t | | D]D\}}|jjd urtj|jj|jj|d urdn||d urdn|dr|d t|jjd7<nd|d<|dt|jjd7<q|d |dkr d|d<nst | | D]>\} } d| kr'| krFnnt | j | j D]\} } t| | ||||dq4qt| | ||||dq|d|dkry|d |dkry|d |dkry|ddkryd|d<nd|d<d|d |d |d|d|d|d|d |d |d|d|dsdnd } |ds|d|dkr| d7} |d |d kr| d7} |d |dkr| d7} | |d<|S)aQCompare full IDs and atom coordinates for 2 Biopython PDB entities. Skip DNA and HETATMs. :param Entity e0,e1: Biopython PDB Entity objects (S, M or C). Structures, Models or Chains to be compared :param bool verbose: Whether to print mismatch info, default False :param bool quick: default False. Only check atomArrays are identical, aCoordMatchCount=0 if different :param float rtol, atol: default 1e-03, 1e-03 or round to 3 places. NumPy allclose parameters; default is to round atom coordinates to 3 places and test equal. For 'quick' will use defaults above for comparing atomArrays :returns dict: Result counts for Residues, Full ID match Residues, Atoms, Full ID match atoms, and Coordinate match atoms; report string; error status (bool) rqrrrrrsr}rarrerbid0id1NpassreportgMbP?rdTFrNzv{}:{} {} -- {} of {} residue IDs match; {} residues {} atom coords, {} full IDs of {} atoms ({} disordered) match : {}ERRORzALL OKz -RESIDUE IDS-z -COORDINATES-z -ATOM IDS-)rQrrr6 atomArrayrhshaperlsizerrrErrvaluesrrB)rrrrr_r`r^c0c1rZr[dr0dr1rstrr#r#r$rVs               $   rfilepdbidchainidc Cst|t|dn}zUt|drO|s|jdd}|jdd}t|jdd}|r;|d||p5d|p8d|jd d}|rO|d |d t }| ||j |d d Wnt ynt dt|wWddS1szwYdS)z2Write PDB file with HEADER and TITLE if available.wr2r'Nr3deposition_datezHEADER {:40}{:8} {:4} r4z TITLE  T)preserve_atom_numberingz2write_PDB: argument is not a Biopython PDB Entity )r rr<r2r=rwriterBupperr set_structuresaver?r@r>) rrrrfpr(ddr4ior#r#r$ write_PDBs6     "r)FF)NF)NN)FFNN)0__doc__rRrr itertoolsrtypingrrnumpyrhBio.Filer Bio.PDB.Atomr Bio.PDB.ChainrBio.PDB.internal_coordsr Bio.PDB.Modelr Bio.PDB.PDBExceptionsr Bio.PDB.PDBIOr Bio.PDB.PICIOr rrrBio.PDB.ResiduerrBio.PDB.Structurerbooldictr%r>rrGrTrYfloatrprrrr#r#r#r$s                  )   ` C L