def topology(tmpdir_factory, struct=datafile("1ake_A_protein.pdb")):
# note: use protein-only input 1ake_A_protein.pdb because solvation fails
# if crystal waters are included (in 1ake_A.pdb)
TMPDIR = tmpdir_factory.mktemp('1ake')
with TMPDIR.as_cwd():
topol_args = gromacs.setup.topology(struct=struct, ff="oplsaa", water="tip4p")
return TMPDIR, topol_args
def topology(tmpdir_factory, struct=datafile("1ake_A_protein.pdb")):
# note: use protein-only input 1ake_A_protein.pdb because solvation fails
# if crystal waters are included (in 1ake_A.pdb)
TMPDIR = tmpdir_factory.mktemp('1ake')
with TMPDIR.as_cwd():
topol_args = gromacs.setup.topology(struct=struct,
ff="oplsaa",
water="tip4p")
return TMPDIR, topol_args
def test_grompp_qtot(tmpdir):
pdb = datafile("1ake_A.pdb")
top = tmpdir.mkdir("top")
with top.as_cwd():
f = gromacs.setup.topology(struct=pdb, ff="oplsaa", water="tip4p")
with open('none.mdp','w') as mdp:
mdp.write('; empty mdp file\nrcoulomb = 1\nrvdw = 1\nrlist = 1\n')
qtot = cbook.grompp_qtot(f="none.mdp", c=f['struct'], p=f['top'],
stdout=False, maxwarn=10)
assert_almost_equal(qtot, -4, decimal=5,
err_msg="grompp_qtot() failed to compute total charge correctly")
def test_trj_compact_main(tmpdir):
pdb = datafile("1ake_A.pdb")
top = tmpdir.mkdir("top")
mdpfile = "simple.mdp"
tprfile = "simple.tpr"
outfile = "compact.pdb"
with top.as_cwd():
f = gromacs.setup.topology(struct=pdb, ff="oplsaa", water="tip4p")
with open(mdpfile, 'w') as mdp:
mdp.write('; empty mdp file\nrcoulomb = 1\nrvdw = 1\nrlist = 1\n')
gromacs.grompp(f=mdpfile, o=tprfile, c=f["struct"], p=f["top"])
gromacs.setup.trj_compact_main(s=tprfile, f=f["struct"], o=outfile, input=("protein", "system"))
assert os.path.exists(outfile)
def test_trj_compact_main(tmpdir):
pdb = datafile("1ake_A.pdb")
top = tmpdir.mkdir("top")
mdpfile = "simple.mdp"
tprfile = "simple.tpr"
outfile = "compact.pdb"
with top.as_cwd():
f = gromacs.setup.topology(struct=pdb, ff="oplsaa", water="tip4p")
with open(mdpfile, 'w') as mdp:
mdp.write('; empty mdp file\nrcoulomb = 1\nrvdw = 1\nrlist = 1\n')
gromacs.grompp(f=mdpfile, o=tprfile, c=f["struct"], p=f["top"])
gromacs.setup.trj_compact_main(s=tprfile,
f=f["struct"],
o=outfile,
input=("protein", "system"))
assert os.path.exists(outfile)
def test_energy_minimize_custom_mdp(solvate, low_performance,
mdp=datafile("custom_em.mdp")):
TMPDIR, solvate_args = solvate
nt = 2 if low_performance else 0
with TMPDIR.as_cwd():
try:
em_args = gromacs.setup.energy_minimize(mdrun_args={'nt': nt},
mdp=mdp,
emtol=5000,
**solvate_args)
except gromacs.exceptions.GromacsError as err:
# sometimes the em does not converge at all, e.g. 5.02988e+04 on atom 3277;
# (happens on Travis Linux with Gromacs 4.6.5 but not locally or on Travis OSX) so we
# re-run with a ridiculous tolerance so that we can at least test that the whole
# function can run to completion
em_args = gromacs.setup.energy_minimize(mdrun_args={'nt': nt},
mdp=mdp,
emtol=6e4,
**solvate_args)
assert os.path.exists(em_args['struct'])
assert os.path.exists(em_args['top'])
assert em_args['mainselection'] == '"Protein"'
def test_energy_minimize_custom_mdp(solvate,
low_performance,
mdp=datafile("custom_em.mdp")):
TMPDIR, solvate_args = solvate
nt = 2 if low_performance else 0
with TMPDIR.as_cwd():
try:
em_args = gromacs.setup.energy_minimize(mdrun_args={'nt': nt},
mdp=mdp,
emtol=5000,
**solvate_args)
except gromacs.exceptions.GromacsError as err:
# sometimes the em does not converge at all, e.g. 5.02988e+04 on atom 3277;
# (happens on Travis Linux with Gromacs 4.6.5 but not locally or on Travis OSX) so we
# re-run with a ridiculous tolerance so that we can at least test that the whole
# function can run to completion
em_args = gromacs.setup.energy_minimize(mdrun_args={'nt': nt},
mdp=mdp,
emtol=6e4,
**solvate_args)
assert os.path.exists(em_args['struct'])
assert os.path.exists(em_args['top'])
assert em_args['mainselection'] == '"Protein"'