예제 #1
0
파일: test_bondlib.py 프로젝트: salilab/mdt
    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')
예제 #2
0
파일: test_bondlib.py 프로젝트: salilab/mdt
    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')
예제 #3
0
파일: modlib.py 프로젝트: salilab/mdt
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)
예제 #4
0
파일: modlib.py 프로젝트: salilab/mdt
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)