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--></style></head><body lang=en-FR link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>Dear CCTBX developers,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>I am a postdoc at EPFL working with HHpred for homology modeling of membrane proteins.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>I have been trying to write my own HHpred alignment parser until I found the python script under “cctbx_fork/iotbx/bioinformatics/__init__.py/” that contains an HHpred parser.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>My goal is to correctly parse the raw HHpred output file (.hhr), which involves unwrapping every alignment, parsing out a lot of text to finally obtain something like this:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>>pdb_name<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>query-sequence<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>column score<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>Example:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>>4U15<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>VYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWS<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>+........+..+..++|+++|++++.++.+.++++ +..+.++.+|+++|++.++...+........ +...|..<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>Being somewhat new to python, I was wondering whether the people who wrote this script are still around and could help me figure out whether the parser could be implemented in such a way.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>Thanks for any help you can provide!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>Best,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt'>Louis D<o:p></o:p></span></p></div></body></html>