Python transform示例

示例#1

文件： test_rmsd.py 项目： hongbo-zhu-cn/pytraj

 def testsuperpose_alias(self):
     '''testsuperpose_alias'''
     t0 = self.traj[:]
     t1 = self.traj[:]
     pt.transform(t0, ['superpose'])
     pt.transform(t1, ['rms'])
     aa_eq(t0.xyz, t1.xyz)

示例#2

文件： test_rmsd.py 项目： josejames00/pytraj

 def testsuperpose_alias(self):
     '''testsuperpose_alias'''
     t0 = self.traj[:]
     t1 = self.traj[:]
     pt.transform(t0, ['superpose'])
     pt.transform(t1, ['rms'])
     aa_eq(t0.xyz, t1.xyz)

示例#3

文件： test_transform.py 项目： shozebhaider/pytraj

    def test_transforming_trajectory(self):
        traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
        t0 = traj[:]

        t0.transform([
            'autoimage', 'center origin', 'rotate x 30', 'scale x 1.2',
            'translate x 1.3'
        ])
        t1 = traj[:].autoimage().center('origin').rotate('x 30').scale(
            'x 1.2').translate('x 1.3')
        aa_eq(t0.xyz, t1.xyz)

        t2 = traj[:]
        pt.transform(t2, [
            'autoimage', 'center origin', 'rotate x 30', 'scale x 1.2',
            'translate x 1.3'
        ])
        aa_eq(t1.xyz, t2.xyz)

        # another way
        t3 = traj[:]
        t3.autoimage().center('origin')
        pt.rotate(t3, 'x 30')
        pt.scale(t3, 'x 1.2')
        pt.translate(t3, 'x 1.3')
        aa_eq(t3.xyz, t2.xyz)

示例#4

    def test_transform_trajectory_iterator(self):

        traj0 = pt.load(fn, tn)
        traj1 = pt.load(fn, tn)
        traj2 = pt.load(fn, tn)

        # Use ActionList for traj0
        actlist = pt.ActionList(top=traj0.top)
        actlist.add("translate", "x 1.2")
        actlist.add("center", "origin")
        actlist.add("rotate", "x 45.")

        for frame in traj0:
            actlist.compute(frame)

        # use transformation
        itertraj = pt.transform(
            traj1, by=['translate x 1.2', 'center origin', 'rotate x 45.'])
        for frame in itertraj:
            pass

        aa_eq(traj0.xyz, traj1.xyz)

        # use API
        traj2.translate('x 1.2')
        traj2.center('origin')
        traj2.rotate('x 45.')

        aa_eq(traj0.xyz, traj2.xyz)

示例#5

文件： test_transform.py 项目： josejames00/pytraj

    def test_transforming_trajectory(self):
        traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
        t0 = traj[:]

        t0.transform(['autoimage', 'center origin', 'rotate x 30',
                      'scale x 1.2', 'translate x 1.3'])
        t1 = traj[:].autoimage().center('origin').rotate('x 30').scale('x 1.2').translate('x 1.3')
        aa_eq(t0.xyz, t1.xyz)

        t2 = traj[:]
        pt.transform(t2, ['autoimage', 'center origin', 'rotate x 30',
                          'scale x 1.2', 'translate x 1.3'])
        aa_eq(t1.xyz, t2.xyz)

        # another way
        t3 = traj[:]
        t3.autoimage().center('origin')
        pt.rotate(t3, 'x 30')
        pt.scale(t3, 'x 1.2')
        pt.translate(t3, 'x 1.3')
        aa_eq(t3.xyz, t2.xyz)

示例#6

文件： example_actionlist.py 项目： sridharkumarkannam/pytraj

traj0 = pt.load(fn, tn)
traj1 = pt.load(fn, tn)
traj2 = pt.load(fn, tn)
print(traj0.xyz[0, 0], traj1.xyz[0, 0], traj2.xyz[0, 0])

# Use ActionList for traj0
actlist = pt.ActionList(top=traj0.top)
actlist.add("translate", "x 1.2")
actlist.add("center", "origin")
actlist.add("rotate", "x 45.")

for frame in traj0:
    actlist.compute(frame)

# use transformation
itertraj = pt.transform(
    traj1, by=['translate x 1.2', 'center origin', 'rotate x 45.'])
for frame in itertraj:
    pass

aa_eq(traj0.xyz, traj1.xyz)
print(traj0.xyz[0, 0], traj1.xyz[0, 0], traj2.xyz[0, 0])

# use API
traj2.translate('x 1.2')
traj2.center('origin')
traj2.rotate('x 45.')

aa_eq(traj0.xyz, traj2.xyz)
print(traj0.xyz[0, 0], traj1.xyz[0, 0], traj2.xyz[0, 0])