Using InterfaceSasaFilter – Rosetta Commons

This topic has 2 replies, 2 voices, and was last updated 7 years, 2 months ago by Anonymous.

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- October 26, 2017 at 2:53 pm #2760
  Anonymous
  Hi,
  
  I’m trying to use the InterfaceSasaFilter class and am running into an error. Any idea how to get around this issue? A snippet of the code is attached, along with the error message
  
  > sasaFilt = pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter()
  
  > sasaFilt.apply(pose)
  
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.119886 0.0251964 0.992468 -0.887035 0.446241 -0.118479 -0.445865 -0.894558 -0.0311479 -16.5561 15.9674 28.6121
  
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.119886 0.0251964 0.992468 -0.887035 0.446241 -0.118479 -0.445865 -0.894558 -0.0311479 -541.404 478.471 743.192
  
  Error: Could not find calculator sasa – need to register it before use
  
  ERROR:: Exit from: /opt/software/rosetta/rosetta_src_2017.08.59291_bundle/main/source/src/core/pose/metrics/CalculatorFactory.cc line: 95
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x2249c98) [0x7f732bbacc98]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x5a3a3a6) [0x7f732f39d3a6]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x1b8897d) [0x7f732b4eb97d]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x4ae0494) [0x7f732e443494]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x4ae1a89) [0x7f732e444a89]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x4ae11ee) [0x7f732e4441ee]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x4ae1017) [0x7f732e444017]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x3c4260c) [0x7f732d5a560c]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x3c40f9d) [0x7f732d5a3f9d]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0xc730c78) [0x7f7336093c78]
  
  /opt/software/pyrosetta/lib/python2.7/site-packages/pyrosetta-4.0-py2.7.egg/rosetta.so(+0x5e307a8) [0x7f732f7937a8]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x6da2) [0x4cada2]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x44db) [0x4c84db]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x6099) [0x4ca099]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x6099) [0x4ca099]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x6099) [0x4ca099]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x6099) [0x4ca099]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x6099) [0x4ca099]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x68d1) [0x4ca8d1]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python() [0x4de8b8]
  
  /usr/bin/python(PyObject_Call+0x43) [0x4b0cb3]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x2ad1) [0x4c6ad1]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalFrameEx+0x6099) [0x4ca099]
  
  /usr/bin/python(PyEval_EvalCodeEx+0x255) [0x4c2765]
  
  /usr/bin/python(PyEval_EvalCode+0x19) [0x4c2509]
  
  /usr/bin/python() [0x4f1def]
  
  /usr/bin/python(PyRun_FileExFlags+0x82) [0x4ec652]
  
  /usr/bin/python(PyRun_SimpleFileExFlags+0x191) [0x4eae31]
  
  /usr/bin/python(Py_Main+0x68a) [0x49e14a]
  
  /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f7391f0c830]
  
  /usr/bin/python(_start+0x29) [0x49d9d9]
  
  RuntimeError Traceback (most recent call last)
  
  <ipython-input-15-d399225fade1> in <module>()
  
  —-> 1 sasaFilt.apply(mab.pose)
  
  RuntimeError: Caught an unknown exception!
- October 26, 2017 at 3:32 pm #13829
  Anonymous
  This is one of the ugly spots in Rosetta, especially with respect to PyRosetta usage.
  
  You need to register the sasa calculator before InterfaceHolesFilter can use it. In RosettaScripts (where InterfaceHolesFilter is normally used), this is done for you, but in PyRosetta you’ll need to do it manually.
  
  Something like the following should work (though I haven’t tested it in PyRosetta):
```
calculator_factory = core.pose.metrics.CalculatorFactory.Instance()

if not calculator_factory.check_calculator_exists( "sasa" ):

sasa_calculator = core.pose.metrics.simple_calculators.SasaCalculatorLegacy()

calculator_factory.register_calculator( "sasa", sasa_calculator )
```
  Other calculators you might need are “sasa_interface” ( core.pose.metrics.simple_calculators.InterfaceSasaDefinitionCalculator( 1, 2 ) ), “ligneigh” ( core.pose.metrics.simple_calculators.InterfaceNeighborDefinitionCalculator( 1, 2 ) ) , and “liginterfE” (core.pose.metrics.simple_calculators.InterfaceDeltaEnergeticsCalculator( “ligneigh” ) ).
  - October 26, 2017 at 8:30 pm #13830
    Anonymous
    Thanks Rocco – that solved the problem.
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