Package Pmv :: Module pdb2pqrCommands
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Module pdb2pqrCommands

source code


This Module implements 'setup_Pdb2Pqr' a command to process molecules using 
    pdb2pqr according to a specified forcefield: 'amber', 'charm' or 'parse'

    Processing options include:
        'debump': whether to debump heavy atoms
        'hopt': whether to run hydrogen optimization
        'hdebump': whether to debump hydrogens  [if not, they are randomized]
        'watopt': whether to optimize water hydrogens
        'hbond': whether to print hydrogen bonding summary

    The processed molecule can be written to a pqr file.

    Additional options include:
        'updateMol': whether to update the current pmv molecule
        'newMol': whether to build a new updated copy of the pmv molecule
    



Classes [hide private]
  SetupPdb2Pqr
This command creates an instance of Pdb2Pqr protein class for a MolKit molecule

Functions [hide private]
  initModule(viewer)

Variables [hide private]
  SetupPdb2PqrCommandGUI = CommandGUI()
  commandList = [{'name': 'setup_Pdb2Pqr', 'cmd': SetupPdb2Pqr(), 'g...

Function Details [hide private]

initModule(viewer)

source code 
None

Variables Details [hide private]

SetupPdb2PqrCommandGUI

None
Value:
CommandGUI()                                                           
      

commandList

None
Value:
[{'name': 'setup_Pdb2Pqr', 'cmd': SetupPdb2Pqr(), 'gui': SetupPdb2PqrC
ommandGUI},]