def test_makestructure_with_reference(self):
tz2_parm7 = cpptraj_test_dir + '/tz2.parm7'
ref_rst7 = cpptraj_test_dir + '/tz2.rst7'
trajin_rst7 = cpptraj_test_dir + '/Test_MakeStructure/pp2.rst7.save'
# cpptraj
command = """
parm {}
reference {}
trajin {}
makestructure "ref:1-13:tz2.rst7"
rmsd reference
createcrd mycrd
""".format(tz2_parm7, ref_rst7, trajin_rst7)
state = pt.load_cpptraj_state(command)
state.run()
cpp_traj = state.data['mycrd']
# pytraj
traj = pt.load(trajin_rst7, top=tz2_parm7)
ref = pt.load(ref_rst7, top=tz2_parm7)
pt.make_structure(traj, "ref:1-13:1-13", ref=ref)
pt.rmsd(traj, ref=ref)
aa_eq(traj.xyz, cpp_traj.xyz)
def build_protein(seq, command=None):
'''
Parameters
----------
seq : protein sequence
command : None, str or list of str
pytraj command for building secondary structure for a given residue range
if None, build linear sequence
Requires
--------
tleap, pytraj and ParmEd
Examples
--------
>>> # Ala10
>>> seq = "ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA"
>>> parm = build_protein(seq, ['alpha:1-10'])
>>> # visualize in Jupyter notebook
>>> parm.visualize()
>>> # save to pdb file
>>> parm.save("new.pdb")
Returns
-------
parmed.Structure
'''
pdb_fn = 'seq.pdb'
leap_command = """
source leaprc.protein.ff14SB
x = sequence{%s}
savepdb x %s
""" % (seq, pdb_fn)
if command is None:
command = ''
command_str = ' '.join(command) if isinstance(command, list) else command
amberhome = os.getenv('AMBERHOME', '')
if os.path.exists(amberhome + '/dat/leap/cmd/leaprc.ff14SB'):
leap_command = leap_command.replace('protein.ff14SB', 'ff14SB')
with tempfolder():
pdb_out = 'pdb_out.pdb'
leap.run(leap_command)
traj = pytraj.load(pdb_fn)
pytraj.make_structure(traj, command_str)
traj.save(pdb_out, overwrite=True)
return parmed.load_file(pdb_out)
def test_makestructure(self):
# FIXME: What does this test?
# https://github.com/Amber-MD/cpptraj/issues/27
# load only 1st frame
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
# polyproline II dihedral to residues 1-13
t0 = traj[:1].copy()
pt.make_structure(t0, 'pp2:1-13')
pt.write_traj('dummy_test0.pdb', t0, options='model', overwrite=True)
t1 = traj[:1].copy()
pt.make_structure(t1, "chi1:8:N:CA:CB:CG:35")
pt.write_traj('dummy_test1.pdb', t1, options='model', overwrite=True)
def build_protein(seq, command):
'''
Parameters
----------
seq : protein sequence
command : str or list of str
pytraj command for building secondary structure for a given residue range
Requires
--------
tleap, pytraj
Examples
--------
>>> from jamber import build
>>> # Ala10
>>> seq = "ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA"
>>> traj = builder.build_protein(seq, ['alpha:1-10'])
>>> # visualize in Jupyter notebook
>>> traj.visualize()
>>> # save to pdb file
>>> traj.save("new.pdb")
Returns
-------
pytraj.Trajectory
'''
pdb_fn = 'seq.pdb'
leap_command = """
source leaprc.protein.ff14SB
x = sequence{%s}
savepdb x %s
""" % (seq, pdb_fn)
command_str = ' '.join(command) if isinstance(command, list) else command
amberhome = os.getenv('AMBERHOME')
if os.path.exists(amberhome + '/dat/leap/cmd/leaprc.ff14SB'):
leap_command = leap_command.replace('protein.ff14SB', 'ff14SB')
with tempfolder():
leap.run(leap_command)
traj = pt.load(pdb_fn)
pt.make_structure(traj, command_str)
return traj
def test_makestructure(self):
# https://github.com/Amber-MD/cpptraj/issues/27
# load only 1st frame
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# pply polyproline II dihedral to residues 1-13
t0 = traj[:1].copy()
pt.make_structure(t0, 'pp2:1-13')
pt.write_traj('./output/test0.pdb',
t0,
options='model',
overwrite=True)
t1 = traj[:1].copy()
pt.make_structure(t1, "chi1:8:N:CA:CB:CG:35")
pt.write_traj('./output/test1.pdb',
t1,
options='model',
overwrite=True)