def test_1(self):
datadir = "./data/"
tlist = TopologyList()
# create TopologyList instance with 4 Topology instances
tlist.add_parm(Topology())
tlist.add_parm(datadir + "Tc5b.top")
tlist.add_parm(datadir + "HP36.top")
tlist.add_parm(Topology())
tlist.info()
# test assignment
tlist[0] = tlist[1]
assert tlist[0].n_atoms == tlist[1].n_atoms
print tlist[0].n_atoms
#tlist.info()
#tlist[3].summary()
t_0 = tlist[0]
t_0.copy(tlist[2])
#t_0.summary()
# make sure changing t_0 does not affect tlist[0] since we make a copy
assert t_0.n_atoms != tlist[0].n_atoms
#t_0.summary()
t_0_copy = t_0.copy()
assert t_0_copy != t_0
assert t_0_copy.n_atoms == t_0.n_atoms
print "make sure changing t_0_copy does not affect t_0"
t_0_copy = Topology()
assert t_0_copy.n_atoms != t_0.n_atoms
#t_0.summary()
#t_0_copy.summary()
# clear tlist
tlist.clear()
# testing index out of range
#tlist[0]
tlist.info()
print "adding new Topology instances"
tlist.add_parm(Topology())
tlist.add_parm(Topology())
tlist.add_parm(Topology())
tlist[0]
tlist[1]
tlist[2]
print "test iteration"
print "test adding top instances from python list"
tmplist = [Topology(), Topology(), Topology()]
tlist_2 = TopologyList()
tlist_2.get_parm_from_pylist(tmplist)
def test_write_CHARMMPSF(self):
print "write parm for CHARMM"
parm.writeparm(top=top, filename="output/test.psf", fmt="CHARMMPSF")
top2 = Topology()
parm.readparm(filename="output/test.psf", top=top2)
assert top2.n_atoms == 304
test_generator(top2)
def _cpptraj_rmsd(topname,
refname,
trajname,
first_nframes=100,
mask='',
use_mass=True,
fit=True):
"""
DEMO API
TODO: update this doc
Output: array of rmsd values
Input:
=====
topname : Amber topology file name
refname : Reference file name
trajname : trajectory file name
first_nframes : calc rmsd for first_nframes
mask : AtomMask string
use_mass : bool
fit : fit or no_fit
"""
# not yet supported atom mask
# atm = AtomMask(mask)
# make topology instance
top = Topology(topname)
# create reference frame
ref = ReferenceFrame()
ref.load_ref(refname, top)
refframe = ref.frame
# load trajectory file
trajin = Trajin_Single()
trajin.load(trajname, ArgList(), top)
trajin.prepare_for_read(True)
#create frame to store data from traj iteration
frame = Frame()
frame.set_frame_v(top, trajin.has_vel(), trajin.n_repdim)
# do rmsd
nframes = first_nframes if first_nframes < trajin.total_frames else trajin.total_frames
arr = np.empty(nframes)
trajin.begin_traj(False)
trajin.print_info_line()
for i in range(nframes):
# not added "mask" yet
# just for demo
trajin.get_next_frame(frame)
if fit:
arr[i] = frame.rmsd(refframe, use_mass)
else:
arr[i] = frame.rmsd_no_fit(refframe, use_mass)
trajin.end_traj()
return arr
def test_0(self):
top = Topology()
parm = ParmFile()
print parm.formats()
filename = "./data/Tc5b.top"
print "Read topology file and dump to 'top'"
parm.readparm(top, filename)
assert top.n_atoms == 304
print "\natom_iterator for top"
print parm.filename()
def randomize_ions(frame=Frame(), top=Topology(), command=""):
"""randomize_ions for given Frame with Topology
Return : None
Parameters
---------
frame : Frame instance, default=Frame()
frame coords will be modified
top : Topology instance, default=Topology()
>>> from pycpptraj.misc import randomize_ions
>>> randomize_ions(frame, top, command="randomizeions @Na+ around :1-16 by 5.0 overlap 3.0")
"""
act = allactions.Action_RandomizeIons()
act.master(command=command,
current_top=top,
current_frame=frame,
)
from pycpptraj.DihedralSearch import DihedralSearch
from pycpptraj.Topology import Topology
top = Topology("./data/Tc5b.top")
dhsearch = DihedralSearch()
dhsearch.list_known_types()
dhsearch.offset_help()
import os from pycpptraj.AtomMask import AtomMask from pycpptraj.ReferenceFrame import ReferenceFrame from pycpptraj.Topology import Topology from pycpptraj.FileName import FileName from pycpptraj.Frame import Frame from pycpptraj.CpptrajState import CpptrajState from pycpptraj.Energy import Energy_Amber from pycpptraj.ArgList import ArgList datadir = os.environ['PYCPPTRAJ_HOME'] + "/examples/data/" topname = datadir + "Tc5b.top" filename = "./data/md1_prod.Tc5b.x" top = Topology(topname) #top.summary() ref = ReferenceFrame() #ref.load_ref(filename=filename, top=top, debug=0, arglist=ArgList(), mask="@CA") ref.load_ref(filename, top, arglist=ArgList(), mask="@CA") ref.top.summary() print ref.frame name = ref.frame_name() assert name.full_name == filename #assert name.ext == '.crd' ref.info()
from pycpptraj.Parm_Amber import Parm_Amber as PA
from pycpptraj.Topology import Topology
pa = PA()
print pa.alloc()
pa.write_help()
top = Topology()
pa.read_parm("./data/Tc5b.top", top)
top.summary()
def test_write_TINKER(self):
top2 = Topology()
parm.writeparm(top=top, filename="output/test.arc")
def test_write_mol2(self):
top2 = Topology()
parm.writeparm(top=top, filename="output/test.mol2")
def test_write_GROMACS(self):
top2 = Topology()
parm.writeparm(top=top, filename="output/test.gmxtop")
def test_write_AMBERPARM(self):
top2 = Topology()
parm.writeparm(top=top, filename="output/test.parm7")
parm.readparm(filename="output/test.parm7", top=top2)
assert top2.n_atoms == 304
test_generator(top2)
print "\nres_iterator for top"
for res in top.residueiter:
pass
#print res
print "\nmol_iterator for top"
for mol in top.moliter:
pass
#print mol
for i in range(304):
top.atom_mask_name(i)
top = Topology()
parm = ParmFile()
filename = "./data/Tc5b.top"
parm.readparm(top, filename)
assert top.n_atoms == 304
parm.help()
class TestParmFile(unittest.TestCase):
def test_readpdb(self):
print "test_readpdb +++++++++++++++++++++++++++++++"
pdbtop = mdio.readparm("./test_0_after.pdb")
assert pdbtop.n_atoms == 304
print pdbtop.n_atoms
top2 = pdbtop.copy()
top2.strip_atoms("!@CA")