def test_write_bondlib(self):
"""Test the write_bondlib function"""
mlib = self.get_mdt_library()
mlib.bond_classes.read('data/bndgrp.lib')
bondtype = mdt.features.BondType(mlib)
bondlen = mdt.features.BondLength(mlib,
bins=mdt.uniform_bins(200, 1.0, 0.005))
m = self.get_test_mdt(mlib, [bondtype, bondlen])
mdt.write_bondlib(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_bondlib(self):
"""Test the write_bondlib function"""
mlib = self.get_mdt_library()
mlib.bond_classes.read('data/bndgrp.lib')
bondtype = mdt.features.BondType(mlib)
bondlen = mdt.features.BondLength(
mlib, bins=mdt.uniform_bins(200, 1.0, 0.005))
m = self.get_test_mdt(mlib, [bondtype, bondlen])
with open('test.out', 'w') as fh:
mdt.write_bondlib(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.bond_classes.read('${LIB}/bndgrp.lib')
xray = mdt.features.XRayResolution(mlib, bins=[(0.51, 2.001, 'High res(2.0A)')])
bond_type = mdt.features.BondType(mlib)
bond_length = mdt.features.BondLength(mlib,
bins=mdt.uniform_bins(400, 1.0, 0.0025))
m = mdt.Table(mlib, file='mdt.mdt')
m = m.reshape(features=(xray, bond_type, bond_length),
offset=(0,0,0), shape=(0,-1,-1))
m = m.integrate(features=(bond_type, bond_length))
mdt.write_bondlib(file('bonds.py', 'w'), m, density_cutoff=0.1)
from modeller import *
import mdt
import mdt.features
env = Environ()
mlib = mdt.Library(env)
mlib.bond_classes.read('${LIB}/bndgrp.lib')
xray = mdt.features.XRayResolution(mlib,
bins=[(0.51, 2.001, 'High res(2.0A)')])
bond_type = mdt.features.BondType(mlib)
bond_length = mdt.features.BondLength(mlib,
bins=mdt.uniform_bins(400, 1.0, 0.0025))
m = mdt.Table(mlib, file='mdt.mdt')
m = m.reshape(features=(xray, bond_type, bond_length),
offset=(0, 0, 0),
shape=(0, -1, -1))
m = m.integrate(features=(bond_type, bond_length))
mdt.write_bondlib(file('bonds.py', 'w'), m, density_cutoff=0.1)