Customize Rosetta codes and make it accessible to PyRosetta

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    • May 24, 2012 at 1:27 pm #1285
      Anonymous

        Hi,

        I’m trying to calculate the atomwise fit scores between specific atoms and nearby electron density maps. It seems that ElectronDensityAtomwise::residue_score() can calculate residue score, while ElectronDensityAtomwise::atom_gradient() can calculate atom score gradient. But neither of them is what I want exactly, and I do not want to compute normalization for the maps which is forcefully done if you want to get the fit scores. I can modify the Rosetta codes to calculate the atom scores I expected, but is it possible to make the modified functions accessible to PyRosetta? Is it difficult to update the PyRosetta bindings manually?

        Many thanks

        xfliu

      • May 24, 2012 at 3:15 pm #7138
        Anonymous

          Our official releases have all code necessary to build PyRoseta. Check src/python/bindings/building.txt for details. So if you using Linux of Mac with compatible OS versions rebuilding should not be too hard. Windows build is much more complicated though, so if you using WIndows I would recommend to look for alternatives.

        • May 24, 2012 at 5:04 pm #7142
          Anonymous

            Mmm that part of the doc is outdated. Right now ~99% is binded so you do not need to modify anything.

          • May 24, 2012 at 5:26 pm #7143
            Anonymous

              Sorry Sergey, but if I understand you correctly, what I need to do is : 1. Modify the Rosetta source codes as I need; 2. Just recompile the python bindings according to building.txt without modifying IncludeDict. Is it correct? I’m using Rosetta3.4 and I find the IncludeDict file is used to decide which modules are going to be binded. But it seems that ElectronDensityAtomwise namespace is not in the IncludeDict attached with Rosetta3.4.

              Cheers

            • May 25, 2012 at 12:19 pm #7150
              Anonymous

                Sergey, I have compiled the PyRosetta as you said. No need to modify the IncludeDict and nearly all of the modules are binded. Sorry for the silly questions above.

              • May 24, 2012 at 4:30 pm #7141
                Anonymous

                  Thank you Sergey. It seems that not all of the namespaces and functions are binded according to building.txt. So if I want to add other namespaces like ElectronDensityAtomwise, should I just add the correspoding header files to the IncludeDict and set them to “True”?

                • May 25, 2012 at 3:58 pm #7151
                  Anonymous

                    I have recompiled PyRosetta. But it seems that the recompiled version may conflict with the rosetta_database in the precompiled PyRosetta package. So I have to use the database in Rosetta3.4. Anyway, it seems OK now.

                  • May 25, 2012 at 6:05 pm #7152
                    Anonymous

                      The version of rosetta_database need to match version of rosetta_source that you used to build PyRosetta, so if you say updated rosetta from SVN (or database from SVN) then you will need to sync them before it will work.

                      But it look like you already figured that out.

                      Best,

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