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src/m/d/MDAnalysis-0.8.1/examples/rmsd.py   MDAnalysis(Download)
if __name__ == '__main__':
   from MDAnalysis import *
   from MDAnalysis.tests.datafiles import PSF, DCD, PDB_small
   ref = Universe(PSF, PDB_small)   # reference structure 4AKE
   trj = Universe(PSF, DCD)         # trajectory of change 1AKE->4AKE
 
   print "CA RMSD for %(DCD)r versus first frame" % vars()
   ref = Universe(PSF, DCD)
   ref.trajectory[0]  # go to first frame
   rmsds2 = rmsd_traj(trj, ref, select='name CA')
 
   print "CA RMSD for %(DCD)r versus last frame" % vars()
   ref = Universe(PSF, DCD)

src/m/d/MDAnalysis-0.8.1/examples/rmsd_groups.py   MDAnalysis(Download)
 
import MDAnalysis
from MDAnalysis.tests.datafiles import PSF,DCD,CRD
 
import MDAnalysis.analysis.rms
 
u = MDAnalysis.Universe(PSF,DCD)
ref1 = MDAnalysis.Universe(PSF,DCD)     # reference closed AdK (1AKE) (with the default ref_frame=0)

src/m/d/MDAnalysis-0.8.1/examples/rmsfit_qcp.py   MDAnalysis(Download)
import numpy
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD, PDB_small
import pyqcprot as qcp
 
ref = mda.Universe(PSF, PDB_small)   # reference structure 1AKE
traj = mda.Universe(PSF, DCD)         # trajectory of change 1AKE->4AKE

src/m/d/MDAnalysis-0.8.1/examples/rmsfit.py   MDAnalysis(Download)
if __name__ == '__main__':
    from MDAnalysis import Universe
    from MDAnalysis.tests.datafiles import PSF, DCD, PDB_small
 
    try:
 
    ref = Universe(PSF, PDB_small)   # reference structure 4AKE
    trj = Universe(PSF, DCD)         # trajectory of change 1AKE->4AKE
 
    rms_fit_trj(trj, ref, filename="output/rmsfit.dcd", select="not name H*",

src/m/d/MDAnalysis-0.8.1/examples/dcd2xtc.py   MDAnalysis(Download)
"""
 
from MDAnalysis.tests.datafiles import PDB_small, DCD
from MDAnalysis import Universe, Writer
 
 
import os.path
 
root, ext = os.path.splitext(os.path.basename(DCD))
xtcname = root + '.xtc'  # output format determined by extension
 
u = Universe(PDB_small, DCD)
 
# create a writer instance for the output trajectory
    print "Converted frame %d" % ts.frame
w.close_trajectory()
print "Converted %r --> %r" % (DCD, xtcname)
 

src/m/d/MDAnalysis-0.8.1/examples/nativecontacts.py   MDAnalysis(Download)
"""
import MDAnalysis.analysis.contacts
from MDAnalysis.tests.datafiles import PSF, DCD  # AdK example trajectory
 
try:
    have_matplotlib = False
 
C = MDAnalysis.analysis.contacts.ContactAnalysis(PSF, DCD, targetdir="./output")
C.run()
 

src/m/d/MDAnalysis-0.8.1/examples/GNMExample.py   MDAnalysis(Download)
#!/usr/bin/python
import sys,os
import MDAnalysis
import MDAnalysis.analysis.gnm
from MDAnalysis.tests.datafiles import PSF, DCD
 
u = MDAnalysis.Universe(PSF,DCD)

src/m/d/MDAnalysis-0.8.1/examples/blocks.py   MDAnalysis(Download)
 
if __name__ == "__main__":
    from  MDAnalysis.tests.datafiles import PSF,DCD
    try:
        import matplotlib
        have_matplotlib = False
 
    u = MDAnalysis.Universe(PSF,DCD)
    results = []
    for nblocks in xrange(2,10):

src/m/d/MDAnalysis-0.8.1/examples/backbone_dihedral.py   MDAnalysis(Download)
 
from MDAnalysis import Universe, collection, Timeseries
from MDAnalysis.tests.datafiles import PSF, DCD
 
try:
 
 
universe = Universe(PSF, DCD)
protein = universe.selectAtoms("protein")
 

src/m/d/MDAnalysisTests-0.8.1/MDAnalysisTests/test_atomgroup.py   MDAnalysisTests(Download)
 
import MDAnalysis
from MDAnalysis.tests.datafiles import PSF, DCD, PDB_small, GRO, TRR, \
                                      merge_protein, merge_water, merge_ligand, \
                                      TRZ, TRZ_psf
    def setUp(self):
        """Set up the standard AdK system in implicit solvent."""
        self.universe = MDAnalysis.Universe(PSF, DCD)
        self.atom = self.universe.atoms[1000]  # Leu67:CG
        self.known_pos = array([  3.94543672, -12.4060812 ,  -7.26820087], dtype=float32)
    def setUp(self):
        """Set up the standard AdK system in implicit solvent."""
        self.universe = MDAnalysis.Universe(PSF, DCD)
        self.ag = self.universe.atoms  # prototypical AtomGroup
        self.dih_prec = 2
    def setUp(self):
        self.universe = MDAnalysis.Universe(PSF, DCD)
        self.res = self.universe.residues[100]
 
    def test_type(self):
    def setUp(self):
        """Set up the standard AdK system in implicit solvent."""
        self.universe = MDAnalysis.Universe(PSF, DCD)
        self.rg = self.universe.atoms.residues
 

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