def test_add_trajectory():
view = nv.NGLWidget(default=False)
def update_coords(view=view):
view.frame = 1000
view.frame = 0
p_traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view.add_trajectory(p_traj)
m_traj = md.load(nv.datafiles.XTC, top=nv.datafiles.PDB)
view.add_trajectory(m_traj)
# trigger updating coordinates
update_coords()
assert len(view._coordinates_dict.keys()) == 2
if has_MDAnalysis:
from MDAnalysis import Universe
mda_traj = Universe(nv.datafiles.PDB, nv.datafiles.TRR)
view.add_trajectory(mda_traj)
update_coords()
assert len(view._coordinates_dict.keys()) == 3
if has_HTMD:
from htmd import Molecule
htmd_traj = Molecule(nv.datafiles.PDB)
htmd_traj.filter('protein')
view.add_trajectory(htmd_traj)
update_coords()
if has_MDAnalysis:
assert len(view._coordinates_dict.keys()) == 4
else:
assert len(view._coordinates_dict.keys()) == 3
def test_add_trajectory():
view = nv.NGLWidget()
def update_coords(view=view):
view.frame = 1000
view.frame = 0
p_traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view.add_trajectory(p_traj)
m_traj = md.load(nv.datafiles.XTC, top=nv.datafiles.PDB)
view.add_trajectory(m_traj)
# trigger updating coordinates
update_coords()
assert len(view.coordinates_dict.keys()) == 2
if has_MDAnalysis:
from MDAnalysis import Universe
mda_traj = Universe(nv.datafiles.PDB, nv.datafiles.TRR)
view.add_trajectory(mda_traj)
update_coords()
assert len(view.coordinates_dict.keys()) == 3
if has_HTMD:
from htmd import Molecule
htmd_traj = Molecule(nv.datafiles.PDB)
htmd_traj.filter('protein')
view.add_trajectory(htmd_traj)
update_coords()
if has_MDAnalysis:
assert len(view.coordinates_dict.keys()) == 4
else:
assert len(view.coordinates_dict.keys()) == 3
def listDihedrals(filename):
# This routine gets the names of the atoms in the soft dihedrals
# It's so horrible, since we have to jump through hoops to
# set up the input for gen_soft_list
ll1 = []
ll2 = []
env = Parameterisation._preflight_test(None)
mol = Molecule(filename);
mol = Parameterisation._rename_mol(mol)
mol.bonds = mol._guessBonds()
# make a tempdir
with tempfile.TemporaryDirectory() as td:
# td=tempfile.mkdtemp()
# print(td)
pwd = os.getcwd()
os.chdir(td)
f = open("mol.prm", "w")
f.close()
mol.write("mol.pdb")
mol.write("mol-opt.xyz")
mol.write("mol.xpsf", type="psf")
for charge in range(-1, 2):
ret = subprocess.check_output(
[env['BIN_MATCH'], "-charge", str(charge), "-forcefield", "top_all36_cgenff_new", "mol.pdb"],
stderr=subprocess.STDOUT, shell=False, stdin=None)
ret = subprocess.check_output([env['BIN_GEN_XPSF'], "mol.rtf", "mol.xpsf", "MOL"], stderr=subprocess.STDOUT,
shell=False, stdin=None)
ret = subprocess.check_output([env['BIN_GEN_SOFT_LIST']], stderr=subprocess.STDOUT, shell=False, stdin=None)
f = open("soft-dih-list.txt", "r")
ff = f.readlines()
for l in ff:
ss = []
tt = []
for m in l.split():
tt.append(int(m))
ss.append(mol.name[int(m) - 1].strip().upper())
ll1.append(tt)
ll2.append(ss)
f.close()
os.chdir(pwd)
return (ll1, ll2)
def test_show_htmd():
from htmd import Molecule
fn = nv.datafiles.PDB
traj = Molecule(fn)
view = nv.show_htmd(traj)
# trigger updating cooridnates
view.frame = 100
index = 0
view.frame = index
xyz_htmd = np.squeeze(traj.coords[:, :, index])
aa_eq(view._coordinates_dict[0], xyz_htmd)
def getParameters(self):
import tempfile
if not self.completed:
raise ValueError("Parameterisation is not complete")
# look for the right files in the output directory
dir = os.path.join(self.directory, "999-results")
rtf = os.path.join(dir, "mol.rtf")
prm = os.path.join(dir, "mol.prm")
xyz = os.path.join(dir, "mol.xyz")
pdb = os.path.join(dir, "mol.pdb")
rtf_tmp = tempfile.mkstemp(suffix=".rtf")
prm_tmp = tempfile.mkstemp(suffix=".prm")
pdb_tmp = tempfile.mkstemp(suffix=".pdb")
xyz_tmp = tempfile.mkstemp(suffix=".xyz")
os.close(rtf_tmp[0])
os.close(prm_tmp[0])
os.close(pdb_tmp[0])
os.close(xyz_tmp[0])
shutil.copyfile(rtf, rtf_tmp[1])
shutil.copyfile(prm, prm_tmp[1])
shutil.copyfile(xyz, xyz_tmp[1])
# The Output minimised structure is in XYZ format
# Need to turn it into a PDB with correct atom naming
mol = Molecule(xyz)
Parameterisation._rename_mol(mol) # Canonicalise atom and reside naming
mol.write(pdb_tmp[1])
return {
"RTF": rtf_tmp[1],
"PRM": prm_tmp[1],
"PDB": pdb_tmp[1]
}
def renameStructure(filename):
m = Molecule(filename)
m = Parameterisation._rename_mol(m)
m.write(filename)