kyleabeauchamp

from msmbuilder import io
from msmbuilder import MSMLib

ass = io.loadh("~/dat/redesign/NTL9/Ward-2500/Assignments.Fixed.h5")["Data"]
c = MSMLib.get_count_matrix_from_assignments(ass)
m = MSMLib.reversible_MLE_estimator(c)
u = m.optimize()
c0 = c + c.transpose()
c.data[:] = 1.
c3 = MSMLib.mle_reversible_count_matrix(c,initial_guess=c0)

kyleabeauchamp

"""
LH5reporter.py: Output a trajectory in MSMBuilder LH5 format.

This class is for use with the Python OpenMM App.  This class allows OpenMM to directly write an MSMBuilder2 LH5 Trajectory.

Example: After preparing a simulation in OpenMM, the following code allows OpenMM to directly write to a *h5 file.

R1=Trajectory.Trajectory.LoadFromPDB('native.pdb')
simulation.reporters.append(LH5Reporter.LH5Reporter('Trajectories/trj0.lh5', 2000,R1))
"""

kyleabeauchamp

import matplotlib.pyplot as plt
import scipy.cluster
import numpy as np
import fastcluster

num_samples = 1000

similarities = np.loadtxt("./TanimotoMatrix0-1998")
distances0 = -1 * np.log(similarities / 1000.)
distances = scipy.cluster.hierarchy.distance.squareform(distances0)

kyleabeauchamp

MODEL        1                                                                  
ATOM      1  N   ARG A   1       4.346   7.563  -9.808  1.00  0.00           N  
ATOM      2  CA  ARG A   1       4.638   6.110  -9.659  1.00  0.00           C  
ATOM      3  C   ARG A   1       5.735   5.902  -8.620  1.00  0.00           C  
ATOM      4  O   ARG A   1       6.406   4.889  -8.593  1.00  0.00           O  
ATOM      5  CB  ARG A   1       5.074   5.498 -11.002  1.00  0.00           C  
ATOM      6  CG  ARG A   1       6.311   6.214 -11.563  1.00  0.00           C  
ATOM      7  CD  ARG A   1       6.633   5.650 -12.951  1.00  0.00           C  
ATOM      8  NE  ARG A   1       5.490   5.938 -13.863  1.00  0.00           N  
ATOM      9  CZ  ARG A   1       5.575   5.623 -15.127  1.00  0.00           C  

kyleabeauchamp

from sys import stdout
import simtk.openmm as mm
import simtk.openmm.app as app
import simtk.unit as u
import urllib

def write_pdb(pdb_id):
  url = 'http://www.rcsb.org/pdb/files/%s.pdb' % pdb_id
  pdb_text = urllib.urlopen(url).read()
  file_handle = open("%s.pdb" % pdb_id, 'w')

kyleabeauchamp

ATOM      1  N   GLY A   1     -11.791   0.397  -6.281  1.00  0.00           N  
ATOM      2  CA  GLY A   1     -10.447   1.020  -6.222  1.00  0.00           C  
ATOM      3  C   GLY A   1      -9.768   0.819  -4.872  1.00  0.00           C  
ATOM      4  O   GLY A   1     -10.326   0.200  -3.964  1.00  0.00           O  
ATOM      5  H1  GLY A   1     -11.723  -0.596  -6.123  1.00  0.00           H  
ATOM      6  H2  GLY A   1     -12.393   0.795  -5.577  1.00  0.00           H  
ATOM      7  H3  GLY A   1     -12.205   0.552  -7.186  1.00  0.00           H  
ATOM      8  HA2 GLY A   1      -9.814   0.587  -6.997  1.00  0.00           H  
ATOM      9  HA3 GLY A   1     -10.539   2.092  -6.405  1.00  0.00           H  
ATOM     10  N   CYS A   2      -8.548   1.349  -4.721  1.00  0.00           N  

kyleabeauchamp

import mdtraj, mdtraj.geometry
import pandas as pd
import numpy as np

r = mdtraj.load(filename)

data = []
for atom in r.top.atoms:
    data.append((atom.index, atom.name, atom.residue.index, atom.residue.name, atom.residue.chain.index))

kyleabeauchamp

import itertools
import mdtraj, mdtraj.geometry
import pandas as pd

traj = mdtraj.load("./traj.xtc", top="native.pdb")

top, bonds = traj.top.to_dataframe()

atoms = np.array(["H", "HA", "N", "CA", "C", "CB"])

kyleabeauchamp

import mdtraj, mdtraj.geometry
import pandas as pd
 
traj = mdtraj.load("./traj.xtc", top="native.pdb")
 
atom_names = ["H", "N", "CA", "HA"]

resid, atom_indices = mdtraj.geometry.dihedral.atom_sequence_finder(traj, atom_names)

dih = mdtraj.geometry.compute_dihedrals(traj, atom_indices)

kyleabeauchamp

import shutil
import os
import tarfile
import tempfile
import mdtraj
import itertools
import pandas as pd

min_num_gen = 50