def setup_module():
global DATADIR, HMM
DATADIR = tempfile.mkdtemp()
# 4 components and 3 features. Each feature is going to be the x, y, z
# coordinate of 1 atom
HMM = sklearn.hmm.GaussianHMM(n_components=4)
HMM.transmat_ = np.array([[0.9, 0.1, 0.0, 0.0],
[0.1, 0.7, 0.2, 0.0],
[0.0, 0.1, 0.8, 0.1],
[0.0, 0.1, 0.1, 0.8]])
HMM.means_ = np.array([[-10, -10, -10],
[-5, -5, -5],
[5, 5, 5],
[10, 10, 10]])
HMM.covars_ = np.array([[0.1, 0.1, 0.1],
[0.5, 0.5, 0.5],
[1, 1, 1],
[4, 4, 4]])
HMM.startprob_ = np.array([1, 1, 1, 1]) / 4.0
# get a 1 atom topology
topology = md.load(get_mdtraj_fn('native.pdb')).restrict_atoms([1]).topology
# generate the trajectories and save them to disk
for i in range(10):
d, s = HMM.sample(100)
t = md.Trajectory(xyz=d.reshape(len(d), 1, 3), topology=topology)
t.save(os.path.join(DATADIR, 'Trajectory%d.h5' % i))
fetch_alanine_dipeptide()
def setup_module():
global DATADIR, HMM
DATADIR = tempfile.mkdtemp()
# 4 components and 3 features. Each feature is going to be the x, y, z
# coordinate of 1 atom
HMM = sklearn.hmm.GaussianHMM(n_components=4)
HMM.transmat_ = np.array([[0.9, 0.1, 0.0, 0.0], [0.1, 0.7, 0.2, 0.0],
[0.0, 0.1, 0.8, 0.1], [0.0, 0.1, 0.1, 0.8]])
HMM.means_ = np.array([[-10, -10, -10], [-5, -5, -5], [5, 5, 5],
[10, 10, 10]])
HMM.covars_ = np.array([[0.1, 0.1, 0.1], [0.5, 0.5, 0.5], [1, 1, 1],
[4, 4, 4]])
HMM.startprob_ = np.array([1, 1, 1, 1]) / 4.0
# get a 1 atom topology
topology = md.load(get_mdtraj_fn('native.pdb')).restrict_atoms([1
]).topology
# generate the trajectories and save them to disk
for i in range(10):
d, s = HMM.sample(100)
t = md.Trajectory(xyz=d.reshape(len(d), 1, 3), topology=topology)
t.save(os.path.join(DATADIR, 'Trajectory%d.h5' % i))
fetch_alanine_dipeptide()
def test_atomindices_1():
fn = get_mdtraj_fn('2EQQ.pdb')
t = md.load(fn)
with tempdir():
shell('msmb AtomIndices -o all.txt --all -a -p %s' % fn)
shell('msmb AtomIndices -o all-pairs.txt --all -d -p %s' % fn)
atoms = np.loadtxt('all.txt', int)
pairs = np.loadtxt('all-pairs.txt', int)
eq(t.n_atoms, len(atoms))
eq(int(t.n_atoms * (t.n_atoms - 1) / 2), len(pairs))
def test_atomindices_3():
fn = get_mdtraj_fn('2EQQ.pdb')
t = md.load(fn)
with tempdir():
shell('msmb AtomIndices -o alpha.txt --alpha -a -p %s' % fn)
shell('msmb AtomIndices -o alpha-pairs.txt --alpha -d -p %s' % fn)
atoms = np.loadtxt('alpha.txt', int)
pairs = np.loadtxt('alpha-pairs.txt', int)
assert all(t.topology.atom(i).name == 'CA' for i in atoms)
assert sum(1 for a in t.topology.atoms if a.name == 'CA') == len(atoms)
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
def test_atomindices_2():
fn = get_mdtraj_fn('2EQQ.pdb')
t = md.load(fn)
with tempdir():
shell('msmb AtomIndices -o heavy.txt --heavy -a -p %s' % fn)
shell('msmb AtomIndices -o heavy-pairs.txt --heavy -d -p %s' % fn)
atoms = np.loadtxt('heavy.txt', int)
pairs = np.loadtxt('heavy-pairs.txt', int)
assert all(t.topology.atom(i).element.symbol != 'H' for i in atoms)
assert (sum(1 for a in t.topology.atoms
if a.element.symbol != 'H') == len(atoms))
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
def test_atomindices_4():
fn = get_mdtraj_fn('2EQQ.pdb')
t = md.load(fn)
with tempdir():
shell('msmb AtomIndices -o minimal.txt --minimal -a -p %s' % fn)
shell('msmb AtomIndices -o minimal-pairs.txt --minimal -d -p %s' % fn)
atoms = np.loadtxt('minimal.txt', int)
pairs = np.loadtxt('minimal-pairs.txt', int)
assert all(
t.topology.atom(i).name in ['CA', 'CB', 'C', 'N', 'O']
for i in atoms)
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
def test_featurizer():
fn = get_mdtraj_fn('1bpi.pdb')
with tempdir():
shell('hmsm atomindices -o alpha.dat --alpha -a -p %s' % fn)
shell('hmsm featurizer --top %s -o alpha.pickl -a alpha.dat' % fn)
f = np.load('alpha.pickl')
eq(f.atom_indices, np.loadtxt('alpha.dat', int))
with tempdir():
shell('hmsm atomindices -o alphapairs.dat --alpha -d -p %s' % fn)
shell('hmsm featurizer --top %s -o alpha.pickl -d alphapairs.dat' % fn)
f = np.load('alpha.pickl')
eq(f.pair_indices, np.loadtxt('alphapairs.dat', int))
def test_featurizer():
fn = get_mdtraj_fn('1bpi.pdb')
with tempdir():
shell('hmsm atomindices -o alpha.dat --alpha -a -p %s' % fn)
shell('hmsm featurizer --top %s -o alpha.pickl -a alpha.dat' % fn)
f = np.load('alpha.pickl')
eq(f.atom_indices, np.loadtxt('alpha.dat', int))
with tempdir():
shell('hmsm atomindices -o alphapairs.dat --alpha -d -p %s' % fn)
shell('hmsm featurizer --top %s -o alpha.pickl -d alphapairs.dat' % fn)
f = np.load('alpha.pickl')
eq(f.pair_indices, np.loadtxt('alphapairs.dat', int))
def test_dihedralindices():
fn = get_mdtraj_fn('1bpi.pdb')
t = md.load(fn)
with tempdir():
shell('hmsm dihedralindices -o phi.dat --phi -p %s' % fn)
shell('hmsm dihedralindices -o psi.dat --psi -p %s' % fn)
eq(len(np.loadtxt('phi.dat', int)), len(np.loadtxt('psi.dat', int)))
shell('hmsm dihedralindices -o chi1.dat --chi1 -p %s' % fn)
shell('hmsm dihedralindices -o chi2.dat --chi2 -p %s' % fn)
assert len(np.loadtxt('chi2.dat')) < len(np.loadtxt('chi1.dat'))
shell('hmsm dihedralindices -o chi3.dat --chi3 -p %s' % fn)
shell('hmsm dihedralindices -o chi4.dat --chi4 -p %s' % fn)
shell('hmsm dihedralindices -o omega.dat --omega -p %s' % fn)
shell('hmsm dihedralindices -o all.dat --phi --psi --chi1 --chi2 --chi3 --chi4 --omega -p %s' % fn)
def test_dihedralindices():
fn = get_mdtraj_fn('1bpi.pdb')
t = md.load(fn)
with tempdir():
shell('hmsm dihedralindices -o phi.dat --phi -p %s' % fn)
shell('hmsm dihedralindices -o psi.dat --psi -p %s' % fn)
eq(len(np.loadtxt('phi.dat', int)), len(np.loadtxt('psi.dat', int)))
shell('hmsm dihedralindices -o chi1.dat --chi1 -p %s' % fn)
shell('hmsm dihedralindices -o chi2.dat --chi2 -p %s' % fn)
assert len(np.loadtxt('chi2.dat')) < len(np.loadtxt('chi1.dat'))
shell('hmsm dihedralindices -o chi3.dat --chi3 -p %s' % fn)
shell('hmsm dihedralindices -o chi4.dat --chi4 -p %s' % fn)
shell('hmsm dihedralindices -o omega.dat --omega -p %s' % fn)
shell('hmsm dihedralindices -o all.dat --phi --psi --chi1 --chi2 --chi3 --chi4 --omega -p %s' % fn)
def test_atomindices():
fn = get_mdtraj_fn('2EQQ.pdb')
t = md.load(fn)
with tempdir():
shell('msmb AtomIndices -o all.txt --all -a -p %s' % fn)
shell('msmb AtomIndices -o all-pairs.txt --all -d -p %s' % fn)
atoms = np.loadtxt('all.txt', int)
pairs = np.loadtxt('all-pairs.txt', int)
eq(t.n_atoms, len(atoms))
eq(int(t.n_atoms * (t.n_atoms - 1) / 2), len(pairs))
with tempdir():
shell('msmb AtomIndices -o heavy.txt --heavy -a -p %s' % fn)
shell('msmb AtomIndices -o heavy-pairs.txt --heavy -d -p %s' % fn)
atoms = np.loadtxt('heavy.txt', int)
pairs = np.loadtxt('heavy-pairs.txt', int)
assert all(t.topology.atom(i).element.symbol != 'H' for i in atoms)
assert sum(1 for a in t.topology.atoms
if a.element.symbol != 'H') == len(atoms)
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
with tempdir():
shell('msmb AtomIndices -o alpha.txt --alpha -a -p %s' % fn)
shell('msmb AtomIndices -o alpha-pairs.txt --alpha -d -p %s' % fn)
atoms = np.loadtxt('alpha.txt', int)
pairs = np.loadtxt('alpha-pairs.txt', int)
assert all(t.topology.atom(i).name == 'CA' for i in atoms)
assert sum(1 for a in t.topology.atoms if a.name == 'CA') == len(atoms)
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
with tempdir():
shell('msmb AtomIndices -o minimal.txt --minimal -a -p %s' % fn)
shell('msmb AtomIndices -o minimal-pairs.txt --minimal -d -p %s' % fn)
atoms = np.loadtxt('minimal.txt', int)
pairs = np.loadtxt('minimal-pairs.txt', int)
assert all(
t.topology.atom(i).name in ['CA', 'CB', 'C', 'N', 'O']
for i in atoms)
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
def test_atomindices():
fn = get_mdtraj_fn('2EQQ.pdb')
t = md.load(fn)
with tempdir():
shell('msmb AtomIndices -o all.txt --all -a -p %s' % fn)
shell('msmb AtomIndices -o all-pairs.txt --all -d -p %s' % fn)
atoms = np.loadtxt('all.txt', int)
pairs = np.loadtxt('all-pairs.txt', int)
eq(t.n_atoms, len(atoms))
eq(int(t.n_atoms * (t.n_atoms - 1) / 2), len(pairs))
with tempdir():
shell('msmb AtomIndices -o heavy.txt --heavy -a -p %s' % fn)
shell('msmb AtomIndices -o heavy-pairs.txt --heavy -d -p %s' % fn)
atoms = np.loadtxt('heavy.txt', int)
pairs = np.loadtxt('heavy-pairs.txt', int)
assert all(t.topology.atom(i).element.symbol != 'H' for i in atoms)
assert (sum(1 for a in t.topology.atoms if a.element.symbol != 'H') ==
len(atoms))
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
with tempdir():
shell('msmb AtomIndices -o alpha.txt --alpha -a -p %s' % fn)
shell('msmb AtomIndices -o alpha-pairs.txt --alpha -d -p %s' % fn)
atoms = np.loadtxt('alpha.txt', int)
pairs = np.loadtxt('alpha-pairs.txt', int)
assert all(t.topology.atom(i).name == 'CA' for i in atoms)
assert sum(1 for a in t.topology.atoms if a.name == 'CA') == len(atoms)
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
with tempdir():
shell('msmb AtomIndices -o minimal.txt --minimal -a -p %s' % fn)
shell('msmb AtomIndices -o minimal-pairs.txt --minimal -d -p %s' % fn)
atoms = np.loadtxt('minimal.txt', int)
pairs = np.loadtxt('minimal-pairs.txt', int)
assert all(t.topology.atom(i).name in ['CA', 'CB', 'C', 'N', 'O']
for i in atoms)
eq(np.array(list(itertools.combinations(atoms, 2))), pairs)
