def test_basic_load(file_3nob):
assert molecule.num() == 0
assert molecule.listall() == []
m = molecule.load("mae", file_3nob)
assert molecule.num() == 1
assert molecule.listall() == [m]
assert molecule.exists(m)
assert not molecule.exists(m + 1)
assert molecule.name(m) == "3nob.mae"
with pytest.raises(ValueError):
molecule.name(m + 1)
molecule.rename(m, "newname")
assert molecule.name(m) == "newname"
with pytest.raises(ValueError):
molecule.rename(name="wrong id", molid=m + 1)
assert molecule.numatoms(molid=m) == 2481
with pytest.raises(ValueError):
molecule.numatoms(m + 1)
molecule.delete(m)
with pytest.raises(ValueError):
molecule.delete(m)
def test_basic_load(file_3nob):
assert molecule.num() == 0
assert molecule.listall() == []
m = molecule.load("mae", file_3nob)
assert molecule.num() == 1
assert molecule.listall() == [m]
assert molecule.exists(m)
assert not molecule.exists(m+1)
assert molecule.name(m) == "3nob.mae"
with pytest.raises(ValueError):
molecule.name(m+1)
molecule.rename(m, "newname")
assert molecule.name(m) == "newname"
with pytest.raises(ValueError):
molecule.rename(name="wrong id", molid=m+1)
assert molecule.numatoms(molid=m) == 2481
with pytest.raises(ValueError):
molecule.numatoms(m+1)
molecule.delete(m)
with pytest.raises(ValueError):
molecule.delete(m)
def __init__(self, name=None, id=None, atoms=0):
"""
Creating a new Molecule instance with no arguments will create a new
empty molecule in VMD. Passing a valid molecule id will make the
Molecule instance mirror the state of the corresponding molecule in VMD.
If id is None, and a name is given, the new molecule will have that name.
"""
if id is None:
if name is None:
name = "molecule"
self.id = molecule.new(name, atoms)
else:
self.id = id
self.atoms = molecule.numatoms(self.id)
if not molecule.exists(self.id):
raise ValueError("Molecule with id %d does not exist." % self.id)
def num_waters_remaining(molid, water_sel='water and element O'):
"""
Returns the number of waters remaining in the system, indicated
by the value of the beta flag.
Args:
molid (int): VMD molecule id to consider
sel (str): VMD atom selection that counts as water, defaults
to 'water and element O'
Returns:
(int) number of water molecules remaining in the system
Raises:
ValueError if empty water selection
ValueError if non-existent molecule given
"""
if not len(water_sel):
raise ValueError("Empty water selection string")
if not molecule.exists(molid):
raise ValueError("Invalid molecule %d" % molid)
return len(atomsel_remaining(molid, water_sel))
def num_waters_remaining(molid, water_sel='water and element O'):
"""
Returns the number of waters remaining in the system, indicated
by the value of the beta flag.
Args:
molid (int): VMD molecule id to consider
sel (str): VMD atom selection that counts as water, defaults
to 'water and element O'
Returns:
(int) number of water molecules remaining in the system
Raises:
ValueError if empty water selection
ValueError if non-existent molecule given
"""
if not water_sel:
raise ValueError("Empty water selection string")
if not molecule.exists(molid):
raise ValueError("Invalid molecule %d" % molid)
return len(atomsel_remaining(molid, water_sel))
def num_lipids_remaining(molid, lipid_sel):
"""
Returns the number of lipids remaining in the system, indicated
by the value of the beta flag. Uses the fragment notation to count
the number of lipids.
Args:
molid (int): VMD molecule ID to consider
lipid_sel (str): VMD atom selection that counts as lipid
Returns:
(int) number of lipid molecules remaining in the system
Raises:
ValueError if empty lipid selection
ValueError if non-existent molecule given
"""
if not len(lipid_sel):
raise ValueError("Empty lipid selection string")
if not molecule.exists(molid):
raise ValueError("Invalid molecule %d" % molid)
return np.unique(atomsel_remaining(molid, lipid_sel).get('fragment')).size
def num_lipids_remaining(molid, lipid_sel):
"""
Returns the number of lipids remaining in the system, indicated
by the value of the beta flag. Uses the fragment notation to count
the number of lipids.
Args:
molid (int): VMD molecule ID to consider
lipid_sel (str): VMD atom selection that counts as lipid
Returns:
(int) number of lipid molecules remaining in the system
Raises:
ValueError if empty lipid selection
ValueError if non-existent molecule given
"""
if not lipid_sel:
raise ValueError("Empty lipid selection string")
if not molecule.exists(molid):
raise ValueError("Invalid molecule %d" % molid)
return np.unique(atomsel_remaining(molid, lipid_sel).fragment).size