pele.amber.sanity_checks

Module source

Class containing sanity checks on proteins

Parameters

topopen mm topology object created from prmtop file as

from simtk.openmm.app import AmberPrmtopFile prmtop = AmberPrmtopFile(‘../../examples/amber/coords.prmtop’) top = prmtop.topology

sanity_check.__init__()

Source

def __init__(self, top):

top = OpenMM topology

sanity_check.check_cistrans()

Source

def check_cistrans(self, coords):

Sanity check on the isomer state of peptide bonds

Returns False if the check fails i.e. if any of the peptide bond is CIS

sanity_check.check_CAchirality()

Source

def check_CAchirality(self, coords):

Sanity check on the CA to check if it is L of D

Returns False if the check fails i.e. if any D-amino acid is present