def test_gninatyping():
m = pybel.readstring('smi', 'c1ccccc1CO')
m.addh()
t = molgrid.GninaIndexTyper()
assert t.num_types() == 28
names = list(t.get_type_names())
assert names[2] == 'AliphaticCarbonXSHydrophobe'
typs = [t.get_atom_type_index(a.OBAtom) for a in m.atoms]
assert len(typs) == 16
acnt = 0
ccnt = 0
ocnt = 0
hcnt = 0
phcnt = 0
for t, r in typs:
if names[t] == 'AromaticCarbonXSHydrophobe':
acnt += 1
assert r == approx(1.9)
if names[t] == 'AliphaticCarbonXSNonHydrophobe':
ccnt += 1
assert r == approx(1.9)
if names[t] == 'OxygenXSDonorAcceptor':
ocnt += 1
assert r == approx(1.7)
if names[t] == 'Hydrogen':
hcnt += 1
assert r == approx(.37)
if names[t] == 'PolarHydrogen':
phcnt += 1
assert r == approx(.37)
assert acnt == 6
assert ccnt == 1
assert ocnt == 1
assert phcnt == 1
assert hcnt == 7
#check covalent rdius
t = molgrid.GninaIndexTyper(True)
typs = [t.get_atom_type_index(a.OBAtom) for a in m.atoms]
assert len(typs) == 16
acnt = 0
ccnt = 0
ocnt = 0
hcnt = 0
phcnt = 0
for t, r in typs:
if names[t] == 'AromaticCarbonXSHydrophobe':
acnt += 1
assert r == approx(0.77)
if names[t] == 'AliphaticCarbonXSNonHydrophobe':
ccnt += 1
assert r == approx(0.77)
if names[t] == 'OxygenXSDonorAcceptor':
ocnt += 1
assert r == approx(.73)
if names[t] == 'Hydrogen':
hcnt += 1
assert r == approx(.37)
if names[t] == 'PolarHydrogen':
phcnt += 1
assert r == approx(.37)
assert acnt == 6
assert ccnt == 1
assert ocnt == 1
assert phcnt == 1
assert hcnt == 7
#!/usr/bin/env python3
'''convert gninatypes file to xyz file'''
import struct, sys, argparse
from functools import partial
import molgrid
names = molgrid.GninaIndexTyper().get_type_names()
def elem(t):
'''convert type index into element string'''
name = names[t]
if 'Hydrogen' in name:
return 'H'
elif 'Carbon' in name:
return 'C'
elif 'Nitrogen' in name:
return 'N'
elif 'Oxygen' in name:
return 'O'
elif 'Sulfur' in name:
return 'S'
elif 'Phosphorus' == name:
return 'P'
elif 'Fluorine' == name:
return 'F'
elif 'Chlorine' == name:
return 'Cl'
elif 'Bromine' == name:
return 'Br'
elif 'Iodine' == name: