pele.amber.obsolete.pdb2permlist

pele.amber.obsolete.pdb2permlist.pdb2permList()

Source

def pdb2permList(pdbfname):

Create permutation groups from an Amber pdb file Adapted from svn/SCRIPTS/make_perm.allow/perm-py.pdb

Input:

pdb file name

• with terminal residues start with ‘N’ or ‘C’

  e.g. ALA -> ‘NALA’ or ‘CALA’

• terminated by END

Output:

list of list of groups of atoms numbers to be permuted

e.g.: for alanine dipeptide

[[0, 2, 3], [11, 12, 13], [19, 20, 21]] atom numbers start at 0

TODO: use OpenMM’s pdb parser and get rid of above restrictions

– ss2029, 16Jan2013