File: generate_mmff.py

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# python
import pymol
from chempy import io
from chempy import protein
from chempy import protein_mmff
from chempy import bond_mmff

#
#print 'normal'
#protein_mmff.check_sum(protein_mmff.normal)
#print 'n_terminal'
#protein_mmff.check_sum(protein_mmff.n_terminal)
#print 'c_terminal'
#protein_mmff.check_sum(protein_mmff.c_terminal)
from inspect import getsourcefile
current_file_dir = os.path.dirname(os.path.abspath(getsourcefile(lambda:0)))
model= io.pdb.fromFile(os.path.join(current_file_dir, "../../test/dat/pept.pdb"))

model= protein.generate(model,forcefield=protein_mmff,bondfield=bond_mmff)

for a in model.atom:
   a.numeric_type = protein_mmff.alpha_map[a.text_type]
   
sm = 0
for a in model.atom:
   sm = sm + a.partial_charge

print(" prot: net partial charge on protein is %8.3f" % sm)
print(" prot: (this should be integral)!")

io.pkl.toFile(model,"generate_mmff.pkl")