ó ‚™xTc@ s®ddlmZddlZddlmZddlZddlZddlZd dej d„Z d„Z dZ ejje dƒZedkrªe ejd ƒndS( iÿÿÿÿ(tdivisionN(tSorrycC s¸ddl}ddl}|dkre|jjd|dtdddƒ}|jjƒ}t|ƒn|j }g}xè|j D]Ý}d}t |j ƒdkrÈd t j jt j j|ƒƒd }nt j j|ƒsàt‚|jjd |ƒ}|jƒ} xW| jƒD]I} x@| jƒD]2} | jƒsE| jd d ƒr!|jrg| jd|j ƒ} n9|js‹| jdtdtƒ} ndj| jƒƒ} |j rÁt!j"dd| ƒ} ng} d }xT|t | ƒkr#|dd kr| j#dƒn| dc| |7<|d7}qÐWdj| ƒ} |j#d|| j$| fƒq!q!WqWq~W|j%dk r£t&|j%dƒ}|j'dj|ƒƒ|j(ƒndj|ƒGH|j%S(Niÿÿÿÿtargstmaster_phil_stringtNonet pdb_file_defspdb_as_fasta.file_nametis%s it file_namet min_contentgà?tskip_insertionstpads^X*iFs s>%schain '%2s' %stw()t iotbx.pdbt iotbx.philRtphiltprocess_command_line_with_filestmaster_phil_str_templatetworktextracttvalidate_paramst pdb_as_fastaRtlentostpathtsplitexttbasenametisfiletAssertionErrortpdbtinputtconstruct_hierarchytmodelstchainst is_proteintis_natpad_missing_residuestas_padded_sequencetinclude_insertion_residuestTruetFalsetjoint as_sequencet ignore_missing_residues_at_starttretsubtappendtidt output_filetopentwritetclose(Rtparamstouttiotbxtcmdlinet fasta_seqstpdb_filet name_basetpdb_objt hierarchytmodeltchaintseqt seq_linestktf((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/pdb_as_fasta.pytrunsZ        )      , cC s+t|jjƒdkr'tdƒ‚ndS(NisNo PDB files defined!(RRRR(R3((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/pdb_as_fasta.pyR7ssx pdb_as_fasta .short_caption = Extract sequence from PDB file(s) .caption = Only protein and nucleic acid chains are supported by this program. Except for selenomethionine (MSE), non-standard residues and bases will be replaced by 'X' and 'N', respectively. .style = caption_img:icons/custom/phenix.pdbtools.png { file_name = None .type = path .multiple = True .short_caption = PDB file .style = bold noauto file_type:pdb output_file = %s .type = path .style = bold noauto file_type:seq new_file pad_missing_residues = True .type = bool .short_caption = """Use 'X' in place of missing residues""" .style = bold noauto ignore_missing_residues_at_start = False .type = bool .style = bold noauto include_insertion_residues = True .type = bool .short_caption = Include insertion residues .style = bold noauto } spdb_sequences.fat__main__i((t __future__Rt libtbx.philtlibtbxt libtbx.utilsRtsysRR+RtstdoutRBRRRtparset master_philt__name__targv(((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/pdb_as_fasta.pyts $1