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Biskit :: StructureSlave :: StructureSlave :: Class StructureSlave
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Class StructureSlave

source code

Convert a PDB file to a pickled PDBModel object.

Instance Methods [hide private]
  initialize(self, params)
Copy the parameters that Master is passing in as dict into fields of this class.
  renameAmberRes(self, model)
Rename special residues (from Amber) back into standard names (i.e CYX → CYS).
  renameToAmberAtoms(self, model)
ptraj puts last letter/number of 4-letter atom names first.
dict go(self, dict)
Calculate rmsd values for trajectory and plot them.

Method Details [hide private]

initialize(self, params)

source code 

Copy the parameters that Master is passing in as dict into fields of this class.
Parameters:
  • params (dict) - defined in Master

renameAmberRes(self, model)

source code 

Rename special residues (from Amber) back into standard names (i.e CYX → CYS).
Parameters:
  • model (PDBModel) - model

renameToAmberAtoms(self, model)

source code 

ptraj puts last letter/number of 4-letter atom names first. Undo.
Parameters:
  • model (PDBModel) - model

Note: could be avoided if ptraj would be told: trajout |file| pdb nowrap

go(self, dict)

source code 

Calculate rmsd values for trajectory and plot them.
Parameters:
  • dict (dict) - dictionary with path to pdb files as keys
Returns: dict
dictionary mapping input:output names

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