creating a pose from a pdb style string

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    • January 6, 2012 at 9:01 am #1130
      Anonymous

        hello,

        is there any possibility to create a pose from a pdb style string in pyrosetta?

        from the “PyMOLPyrosettaServer.py” script I can see that pymol can be made to listen for a pdb string sent from pyrosetta. i would like to go in the other direction directly passing a pdb string to pyrosetta in order to generate a pose. is this possible? and if so what is the necessary code for this?

        i know that one can generate a pose from a pdb file but i would like to skip this step in order to save the time it costs to read/write from/to disk.

        any help much appreciated,

        merc

      • January 6, 2012 at 3:22 pm #6499
        Anonymous

          It’s possible but there’s no single method to call to get it that I am aware of. In C++, look at the file src/core/import_pose/import_pose.cc, around line 196. This code has just read a file in above it (utility::slurp) and then hands the file contents (a PDB string as you request) off to a function createFileData, then a function build_pose from that FileData. I guess you can work on the python from there?

        • January 9, 2012 at 4:33 pm #6504
          Anonymous

            excellent! thanks to your help i found “rosetta.core.import_pose.pose_from_pdbstring(pose, pdb_str_in)” which does exactly what i want. thanks a bunch!

          • January 9, 2012 at 4:37 pm #6505
            Anonymous

              I thought that function existed! I couldn’t find it when I was looking (brain fart, I guess) so I gave you more vague instructions.

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