def test_write_improperlib(self):
"""Test the write_improperlib function"""
mlib = self.get_mdt_library()
mlib.dihedral_classes.read('data/impgrp.lib')
angtype = mdt.features.DihedralType(mlib)
ang = mdt.features.Dihedral(mlib, bins=mdt.uniform_bins(180, 0.0, 2.0))
m = self.get_test_mdt(mlib, [angtype, ang])
mdt.write_improperlib(open('test.out', 'w'), m)
# Make sure that valid Python code was produced
code = compile(open('test.out').read(), 'test.out', 'exec')
os.unlink('test.out')
def test_write_improperlib(self):
"""Test the write_improperlib function"""
mlib = self.get_mdt_library()
mlib.dihedral_classes.read('data/impgrp.lib')
angtype = mdt.features.DihedralType(mlib)
ang = mdt.features.Dihedral(mlib, bins=mdt.uniform_bins(180, 0.0, 2.0))
m = self.get_test_mdt(mlib, [angtype, ang])
with open('test.out', 'w') as fh:
mdt.write_improperlib(fh, m)
# Make sure that valid Python code was produced
with open('test.out') as fh:
_ = compile(fh.read(), 'test.out', 'exec')
os.unlink('test.out')
from modeller import *
import mdt
import mdt.features
env = environ()
mlib = mdt.Library(env)
mlib.dihedral_classes.read('${LIB}/impgrp.lib')
xray = mdt.features.XRayResolution(mlib, bins=[(0.51, 2.001, 'High res(2.0A)')])
impr_type = mdt.features.DihedralType(mlib)
improper = mdt.features.Dihedral(mlib, bins=mdt.uniform_bins(400, 1.0, 0.0025))
m = mdt.Table(mlib, file='mdt.mdt')
m = m.reshape(features=(xray, impr_type, improper),
offset=(0,0,0), shape=(1,-1,-1))
m = m.integrate(features=(impr_type, improper))
mdt.write_improperlib(file('impropers.py', 'w'), m, density_cutoff=0.1)
from modeller import *
import mdt
import mdt.features
env = Environ()
mlib = mdt.Library(env)
mlib.dihedral_classes.read('${LIB}/impgrp.lib')
xray = mdt.features.XRayResolution(mlib, bins=[(0.51, 2.001, 'High res(2.0A)')])
impr_type = mdt.features.DihedralType(mlib)
improper = mdt.features.Dihedral(mlib, bins=mdt.uniform_bins(400, 1.0, 0.0025))
m = mdt.Table(mlib, file='mdt.mdt')
m = m.reshape(features=(xray, impr_type, improper),
offset=(0,0,0), shape=(1,-1,-1))
m = m.integrate(features=(impr_type, improper))
mdt.write_improperlib(file('impropers.py', 'w'), m, density_cutoff=0.1)