pmx/example_scripts/test_ffparser.py at 0bed1bce313e2dd7d4da24ebd148a61a20f45f9f · deGrootLab/pmx · GitHub

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import sys, os

from pmx.forcefield2 import ITPFile


def test_ffparser():
    top = ITPFile('./protLig_benchmark/pde2/ligands_cgenff/lig_50181001/MOL.itp')
    ## for atom in top.atoms:
    ##     atom.atomtypeB = 'DUM'
    ##     atom.qB = 0
    ##     atom.mB = atom.m
    top.write('new.itp')


    ## from pmx.ffparser import *
    ## ## from pmx.library import _aacids_dic
    ## rtp = RTPParser( 'ffamber99sb.rtp')
    ## print rtp['ALA']

    ## for name, entry in rtp:
    ##     print name, entry['atoms'][0]
    ## print 'XXX'
    ## for name, entry in rtp:
    ##     print name, entry['atoms'][0]
    ## ala = rtp['ALA']
    ## print _aacids_dic
    ## for aa in _aacids_dic.values():
    ##     try:
    ##         del rtp[aa]
    ##     except:
    ##         pass
    ## rtp.add_entry( "ala", ala )
    ## print "ala" in rtp
    #rtp.write(sys.stdout)
    #print rtp["ALA"]['bonds']

    #nb = NBParser("ffamber99sbnb.itp")
    #print nb