Python pairwise_rmsd Examples

Example #1

File: test_rmsd.py Project: hongbo-zhu-cn/pytraj

    def testTwoTrajTypes(self):
        '''test different metrics with different traj objects
        '''
        funclist = [pt.iterload, pt.load]
        txt = '''
        parm {}
        trajin {}
        rms2d @CA metric_holder rmsout tmp.out
        '''.format(tc5b_top, tc5b_trajin)

        for func in funclist:
            traj = func(tc5b_trajin, tc5b_top)
            for metric in ['rms', 'nofit', 'dme']:
                d0 = pt.pairwise_rmsd(traj(mask='@CA'), metric=metric)
                d1 = pt.pairwise_rmsd(traj, mask='@CA', metric=metric)
                d2 = pt.pairwise_rmsd(traj(), mask='@CA', metric=metric)

                txt0 = txt.replace('metric_holder', metric)
                state = pt.load_cpptraj_state(txt0)
                with tempfolder():
                    state.run()
                d3 = state.data[-1].values

                aa_eq(d0, d1)
                aa_eq(d0, d2)
                aa_eq(d0, d3)

Example #2

File: test_rmsd.py Project: josejames00/pytraj

    def testTwoTrajTypes(self):
        '''test different metrics with different traj objects
        '''
        funclist = [pt.iterload, pt.load]
        txt = '''
        parm ./data/Tc5b.top
        trajin ./data/Tc5b.x
        rms2d @CA metric_holder rmsout tmp.out
        '''

        for func in funclist:
            traj = func("./data/Tc5b.x", "./data/Tc5b.top")
            for metric in ['rms', 'nofit', 'dme']:
                d0 = pt.pairwise_rmsd(traj(mask='@CA'), metric=metric)
                d1 = pt.pairwise_rmsd(traj, mask='@CA', metric=metric)
                d2 = pt.pairwise_rmsd(traj(), mask='@CA', metric=metric)

                txt0 = txt.replace('metric_holder', metric)
                state = pt.datafiles.load_cpptraj_output(txt0, dtype='state')
                d3 = state.datasetlist[-1].values

                aa_eq(d0, d1)
                aa_eq(d0, d2)
                aa_eq(d0, d3)

Example #3

File: test_rmsd.py Project: lambdalisue/pytraj

    def testTwoTrajTypes(self):
        '''test different metrics with different traj objects
        '''
        funclist = [pt.iterload, pt.load]
        txt = '''
        parm ./data/Tc5b.top
        trajin ./data/Tc5b.x
        rms2d @CA metric_holder rmsout tmp.out
        '''

        for func in funclist:
            traj = func("./data/Tc5b.x", "./data/Tc5b.top")
            for metric in ['rms', 'nofit', 'dme']:
                d0 = pt.pairwise_rmsd(traj(mask='@CA'), metric=metric)
                d1 = pt.pairwise_rmsd(traj, mask='@CA', metric=metric)
                d2 = pt.pairwise_rmsd(traj(), mask='@CA', metric=metric)

                txt0 = txt.replace('metric_holder', metric)
                state = pt.datafiles.load_cpptraj_output(txt0, dtype='state')
                d3 = state.datasetlist[-1].values

                aa_eq(d0, d1)
                aa_eq(d0, d2)
                aa_eq(d0, d3)

Example #4

File: example_pairwise_rmsd.py Project: sridharkumarkannam/pytraj

import pytraj as pt

traj = pt.iterload('../tests/data/Tc5b.x', '../tests/data/Tc5b.top')

mat = pt.pairwise_rmsd(traj, '@CA')
print(mat)

Example #5

File: 5.Amber_GetEnergies.py Project: kmb413/CADRES

def get_ca_rmsd( traj, mask, metric ):
    
    ca_rmsd = pt.pairwise_rmsd(traj, mask=mask, metric=metric)
    #ca_rmsd = pt.pmap_mpi(pt.rmsd, traj, mask='@CA')

    return ca_rmsd;

Example #6

File: pairwise_rmsd_.py Project: josejames00/pytraj

def calc_pretty(traj, mask='!:WAT', mat_type='cpptraj'):
    return pt.pairwise_rmsd(traj, mask=mask, mat_type=mat_type)

Example #7

File: memory_accumulation.py Project: lambdalisue/pytraj

 def test_pairwise_rmsd():
     pt.pairwise_rmsd(traj(stop=1000), mask='@CA')

Example #8

def calc_pretty(traj, mask='!:WAT', mat_type='cpptraj'):
    return pt.pairwise_rmsd(traj, mask=mask, mat_type=mat_type)

Example #9

File: memory_accumulation.py Project: josejames00/pytraj

 def test_pairwise_rmsd():
     pt.pairwise_rmsd(traj(stop=1000), mask='@CA')