In [10]:

    

import mdtraj as md
from msmbuilder.dataset import dataset
from matplotlib import pyplot as plt
%matplotlib inline


    

In [2]:

    

pdb_top = md.load_prmtop("/Users/je714/Troponin/IAN_Troponin/completehowarthcut/salted/ff99SB/refpdb.prmtop")


    

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indices_pdb = [atom.index for atom in pdb_top.atoms if atom.is_backbone]


    

In [5]:

    

pdb = md.load_restrt("/Users/je714/Troponin/IAN_Troponin/completehowarthcut/salted/ff99SB/refpdb.inpcrd",
                     top="/Users/je714/Troponin/IAN_Troponin/completehowarthcut/salted/ff99SB/refpdb.prmtop",
                     atom_indices=indices_pdb)


    

In [6]:

    

xyz = dataset("/Users/je714/Troponin/IAN_Troponin/completehowarthcut/salted/ff99SB/IAN30ASALT/traj1/05*nc",
             topology="/Users/je714/Troponin/IAN_Troponin/completehowarthcut/salted/ff99SB/IAN30ASALT/WT_ff99SB.prmtop",
             atom_indices = indices_pdb)


    

In [11]:

    

plt.plot(md.rmsd(xyz[0], pdb))


    

    
Out[11]:





[<matplotlib.lines.Line2D at 0x1158823c8>]






    

In [13]:

    

rmsds = []
for traj in xyz:
    rmsd = md.rmsd(traj, pdb)
    rmsds.append(rmsd)


    

In [16]:

    

import numpy as np
plt.plot(np.concatenate(rmsds))


    

    
Out[16]:





[<matplotlib.lines.Line2D at 0x121070908>]






    

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t1.superpose(pdb)


    

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indices_pdb = [atom.index for atom in pdb_top.atoms if atom.is_backbone]


    

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indices_traj = [atom.index for atom in traj_top.atoms if atom.is_backbone]


    

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common_list = []
for i in set(indices_pdb).intersection(set(indices_traj)):
    common_list.append(i)


    

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md.rmsd?


    

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md.rmsd(xyz[0], reference = pdb, atom_indices=common_list)


    

In [ ]:

    

xyz = dataset("/Users/je714/Troponin/IAN_Troponin/completehowarthcut/salted/ff99SB/IAN30ASALT/traj1/05*nc",
             topology="/Users/je714/Troponin/IAN_Troponin/completehowarthcut/salted/ff99SB/IAN30ASALT/WT_ff99SB.prmtop",
             atom_indices = indices_pdb)


    

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md.rmsd(xyz[0], reference = pdb)


    

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