hainm

"""calculate RMSD for two proteins with different topologies"""

from pytraj import io as mdio

# create trajectory objects (having frames)
traj_0 = mdio.load("../tests/data/Tc5b.crd", "../tests/data/Tc5b.top")
traj_1 = mdio.load("../tests/data/ala3.dcd", "../tests/data/ala3.psf")

# get new traj objects with given mask
traj_0_new = traj_0[":8-10@CA :frame"]

hainm

# distutils: language = c++
cdef cppclass A:
    void c_test():
        print ("hello from A")

cdef cppclass B(A):
    void SetObject(A* ptr):
        print ("dummy method, hello from B")

cdef class pyA:

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cdef class MyTest (object):
    cdef public object _x
    def __cinit__(self):
        self._x = 0
    
    @property
    def x(self):
        return self._x
    
    @x.setter

hainm

# test get reference Frame from DataSetList
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")

dslist = DataSetList()
dslist.add_set("ref_frame", "myname")
dslist[0].top = traj.top.copy()
# use last Frame for reference
dslist[0].append(traj[-1])

# dslist.get_reference_frame("myname")

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Traceback (most recent call last):
  File "/home/hainm/anaconda3/envs/python2/bin/cython", line 9, in <module>
    load_entry_point('Cython==0.23.dev0', 'console_scripts', 'cython')()
  File "/home/hainm/anaconda3/envs/python2/lib/python2.7/site-packages/Cython-0.23.dev0-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py", line 676, in setuptools_main
    return main(command_line = 1)
  File "/home/hainm/anaconda3/envs/python2/lib/python2.7/site-packages/Cython-0.23.dev0-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py", line 693, in main
    result = compile(sources, options)
  File "/home/hainm/anaconda3/envs/python2/lib/python2.7/site-packages/Cython-0.23.dev0-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py", line 668, in compile
    return compile_multiple(source, options)
  File "/home/hainm/anaconda3/envs/python2/lib/python2.7/site-packages/Cython-0.23.dev0-py2.7-linux-x86_64.egg/Cython/Compiler/Main.py", line 646, in compile_multiple

hainm

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hainm

CPPTRAJ: Trajectory Analysis. V16.00b
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 08/05/15  16:30:04
| Available memory: 132.562 MB

INPUT: Reading Input from file dih.in
  [parm G5.pdb]

hainm

 $ pip install https://github.com/ParmEd/ParmEd/archive/2.0.5.tar.gz
Collecting https://github.com/ParmEd/ParmEd/archive/2.0.5.tar.gz
  Downloading https://github.com/ParmEd/ParmEd/archive/2.0.5.tar.gz
     | 32.0MB 12.1MB/s
Installing collected packages: ParmEd
  Found existing installation: ParmEd 2.3.2
    Uninstalling ParmEd-2.3.2:
      Successfully uninstalled ParmEd-2.3.2
  Running setup.py install for ParmEd ... done
Successfully installed ParmEd-2.3.2

hainm

import pytraj as pt
import numpy as np

traj = pt.iterload('tz2.nc', 'tz2.parm7')
# note: use pt.load method if your trajectory is fit well to memory

c0 = pt.center_of_mass(traj, ':1-3')
c1 = pt.center_of_mass(traj, ':4-7')
c2 = pt.center_of_mass(traj, ':8-10')
c3 = pt.center_of_mass(traj, ':11-13')

hainm

# Q: [AMBER] Working with pytraj

# use all atoms in residue 1
c_o_G = pt.center_of_geometry(traj, mask=':1')

# or
# use given atoms in residue 1
c_o_G = pt.center_of_geometry(traj, mask=':1@C1,N6,C2,C4,N7')

pt.vector.corrplane(traj, mask=':1@C1,N6,C2,C4,N7')