def __init__(self,dcd=None,psf=None,first=0,last=-1,stride=1,waitfor=-1,pdb=None):
self.molID=0
if psf is not None:
self.psf = psf
self.molID=molecule.load('psf',psf)
if (pdb is None) and (dcd is not None):
try:
self.dcd = dcd
self.molID=molecule.new('new')
self.molID=molecule.load('psf',self.psf) # load trajectory
molecule.read(self.molID,'dcd',self.dcd,stride=stride,first=first,last=last,waitfor=waitfor)
print ("DCD file detected id ",self.molID)
except IOError:
print ("Could not read dcd file or psf:", dcd)
raise Exception()
else:
try:
self.molID=molecule.new('pdb')
self.pdb=pdb
molecule.read(molid=self.molID,filetype ='pdb',filename=self.pdb,first=0,last=0)
print ("pdb file detected id ",self.molID)
except IOError:
print ("Could not read dcd file or psf:",pdb)
raise Exception()
def pdb(self,pdb,psf=None):
#sobrecarga para leer pdbs y no dcd
try:
self.molID=molecule.new('pdb')
self.pdb=pdb
if psf is not None:
self.molID=molecule.load('psf',psf)
self.psf=psf # add psf
molecule.read(molid=self.molID,filetype ='pdb',filename=self.pdb,first=0,last=0)
print (self.molID)
except IOError:
print ("Could not read dcd file or psf:",pdb)
raise Exception()
def dcd(self,dcd,psf,first=0,last=-1,stride=1,waitfor=-1):
self.psf = psf
self.dcd = dcd
self.molID=0
try:
self.molID=molecule.new('new')
self.molID=molecule.load('psf',self.psf) # load trajectory
molecule.read(self.molID,'dcd',self.dcd,stride=stride,first=first,last=last,waitfor=waitfor)
print (self.molID)
except IOError:
print ("Could not read dcd file or psf:", dcd)
raise Exception()
def test_read(file_3frames):
m = molecule.load("pdb", file_3frames)
assert molecule.numframes(molid=m) == 3
with pytest.warns(DeprecationWarning):
molecule.read(m, "pdb", filename=file_3frames,
beg=1, end=1, skip=1, waitfor=-1)
assert molecule.numframes(m) == 4
molecule.read(molid=m, filetype="pdb", filename=file_3frames,
waitfor=1)
molecule.cancel(m)
assert molecule.numframes(m) < 6
with pytest.raises(ValueError):
molecule.cancel(molid=m+1)
molecule.delete(m)
def load_data(self, load_data, align=True):
"""Method for loading trajectory data
Parameters
----------
load_data : dict
dictionary of VMD read routine options. See
VMDMolecule.__init__() docs.
"""
if not isinstance(load_data, dict):
raise ValueError("load_data must be a dictionary with "
"key-value pairs corresponding to VMD "
"read command options.")
else:
mol.read(self.molid, **load_data)
if align:
self.self_align()
print("{} frames loaded.".format(mol.numframes(self.molid)))
evaltcl("display resetview")
def load(self, filename, filetype=None, first=0, last=-1, step=1, waitfor=-1, volsets=[0]):
"""
Load molecule data from the given file. The filetype will be guessed from
the filename extension; this can be overridden by setting the filetype
option. first, last, and step control which coordinates frames to load,
if any.
"""
if filetype is None:
filetype = self._guessFiletype(filename)
if molecule.read(self.id, filetype, filename, first, last, step, waitfor, volsets) < 0:
raise IOError("Unable to load file: %s" % filename)
return self
def test_read(file_3frames):
m = molecule.load("pdb", file_3frames)
assert molecule.numframes(molid=m) == 3
with pytest.warns(DeprecationWarning):
molecule.read(m,
"pdb",
filename=file_3frames,
beg=1,
end=1,
skip=1,
waitfor=-1)
assert molecule.numframes(m) == 4
molecule.read(molid=m, filetype="pdb", filename=file_3frames, waitfor=1)
molecule.cancel(m)
assert molecule.numframes(m) < 6
with pytest.raises(ValueError):
molecule.cancel(molid=m + 1)
molecule.delete(m)
def __init__(self,
pdb_file,
load_data=None,
style=None,
name='my_molecule',
flush_pdb_frame=False,
align=True,
center=True):
self.molid = mol.new(name)
mol.rename(self.molid, name)
self.name = name
mol.read(self.molid, 'pdb', pdb_file, beg=0, end=0, skip=1, waitfor=-1)
self.all_atoms = atomsel("all")
if flush_pdb_frame:
mol.delframe(self.molid) # flush trivial frame
if load_data:
self.load_data(load_data, align=align)
if style:
# delete the default representation
molrep.delrep(self.molid, 0)
for rep in style:
molrep.addrep(self.molid, **rep)
def get_cell_size(self,
mem_buf, wat_buf,
molid=None,
filename=None,
zh_mem_full=_MEMBRANE_FULL_THICKNESS / 2.0,
zh_mem_hyd=_MEMBRANE_HYDROPHOBIC_THICKNESS / 2.0):
"""
Gets the cell size of the final system given initial system and
buffers. Detects whether or not a membrane is present. Sets the
size of the system.
Args:
mem_buf (float) : Membrane (xy) buffer amount
wat_buf (float) : Water (z) buffer amount
molid (int) : VMD molecule ID to consider (can't use with filename)
filename (str) : Filename of system to consider (can't use w molid)
zh_mem_full (float) : Membrane thickness
zh_mem_hyd (float) : Membrane hydrophobic region thickness
Returns:
return dx_sol, dy_sol, dx_tm, dy_tm, dz_full
(float tuple): x solute dimension, y solute dimension,
TM x solute dimension, TM y solute dimension, solute z dimension
Raises:
ValueError: if filename and molid are both specified
"""
# Sanity check
if filename is not None and molid is not None:
raise ValueError("Specified molid and filename to get_cell_size")
if filename is not None:
top = molecule.get_top()
molid = molecule.read(-1, 'mae', filename)
elif molid is None:
molid = molecule.get_top()
# Some options different for water-only systems (no lipid)
if self.water_only:
solute_z = atomsel(self.solute_sel, molid=molid).get('z')
dx_tm = 0.0
dy_tm = 0.0
sol_solute = atomsel(self.solute_sel, molid)
else:
solute_z = atomsel(self.solute_sel, molid=molid).get('z')
tm_solute = atomsel('(%s) and z > %f and z < %f' % (self.solute_sel,
-zh_mem_hyd,
zh_mem_hyd), molid)
if len(tm_solute):
dx_tm = max(tm_solute.get('x')) - min(tm_solute.get('x'))
dy_tm = max(tm_solute.get('y')) - min(tm_solute.get('y'))
else:
dx_tm = dy_tm = 0
sol_solute = atomsel('(%s) and (z < %f or z > %f)' % (self.solute_sel,
-zh_mem_hyd,
zh_mem_hyd), molid)
# Solvent invariant options
dx_sol = max(sol_solute.get('x')) - min(sol_solute.get('x'))
dy_sol = max(sol_solute.get('y')) - min(sol_solute.get('y'))
if self.opts.get('user_x'):
self.size[0] = self.opts['user_x']
else:
self.size[0] = max(dx_tm + 2.*mem_buf, dx_sol + 2.*wat_buf)
if self.opts.get('user_y'):
self.size[1] = self.opts['user_y']
else:
self.size[1] = max(dy_tm + 2.*mem_buf, dy_sol + 2.*wat_buf)
# Z dimension. If there's a membrane, need to account for asymmetry
# in the Z dimension where the protein could be uneven in the membrane
# or even peripheral
if self.opts.get('user_z'):
self.size[2] = self.opts['user_z']
buf = (self.opts['user_z'] - max(solute_z) + min(solute_z))/2
self._zmax = max(solute_z) + buf
self._zmin = min(solute_z) - buf
if zh_mem_full > self._zmax or -zh_mem_full < self._zmin:
raise ValueError("Specified user z of %f is too small to "
"accomodate protein and membrane!"
% self.opts['user_z'])
else:
if self.water_only:
self._zmax = max(solute_z) + wat_buf
self._zmin = min(solute_z) - wat_buf
else:
self._zmax = max(max(solute_z)+wat_buf, zh_mem_full)
self._zmin = min(min(solute_z)-wat_buf, -zh_mem_full)
self.size[2] = self._zmax - self._zmin
# Cleanup temporary file, if read in
if filename is not None:
molecule.delete(molid)
if top != -1:
molecule.set_top(top)
return dx_sol, dy_sol, dx_tm, dy_tm, max(solute_z)-min(solute_z)
def get_cell_size(self,
mem_buf,
wat_buf,
molid=None,
filename=None,
zh_mem_full=_MEMBRANE_FULL_THICKNESS / 2.0,
zh_mem_hyd=_MEMBRANE_HYDROPHOBIC_THICKNESS / 2.0):
"""
Gets the cell size of the final system given initial system and
buffers. Detects whether or not a membrane is present. Sets the
size of the system.
Args:
mem_buf (float) : Membrane (xy) buffer amount
wat_buf (float) : Water (z) buffer amount
molid (int) : VMD molecule ID to consider (can't use with filename)
filename (str) : Filename of system to consider (can't use w molid)
zh_mem_full (float) : Membrane thickness
zh_mem_hyd (float) : Membrane hydrophobic region thickness
Returns:
return dx_sol, dy_sol, dx_tm, dy_tm, dz_full
(float tuple): x solute dimension, y solute dimension,
TM x solute dimension, TM y solute dimension, solute z dimension
Raises:
ValueError: if filename and molid are both specified
"""
# Sanity check
if filename is not None and molid is not None:
raise ValueError("Specified molid and filename to get_cell_size")
if filename is not None:
top = molecule.get_top()
molid = molecule.read(-1, 'mae', filename)
elif molid is None:
molid = molecule.get_top()
# Some options different for water-only systems (no lipid)
if self.water_only:
solute_z = atomsel(self.solute_sel, molid=molid).get('z')
dx_tm = 0.0
dy_tm = 0.0
sol_solute = atomsel(self.solute_sel, molid)
else:
solute_z = atomsel(self.solute_sel, molid=molid).get('z')
tm_solute = atomsel(
'(%s) and z > %f and z < %f' %
(self.solute_sel, -zh_mem_hyd, zh_mem_hyd), molid)
if len(tm_solute):
dx_tm = max(tm_solute.get('x')) - min(tm_solute.get('x'))
dy_tm = max(tm_solute.get('y')) - min(tm_solute.get('y'))
else:
dx_tm = dy_tm = 0
sol_solute = atomsel(
'(%s) and (z < %f or z > %f)' %
(self.solute_sel, -zh_mem_hyd, zh_mem_hyd), molid)
# Solvent invariant options
dx_sol = max(sol_solute.get('x')) - min(sol_solute.get('x'))
dy_sol = max(sol_solute.get('y')) - min(sol_solute.get('y'))
if self.opts.get('user_x'):
self.size[0] = self.opts['user_x']
else:
self.size[0] = max(dx_tm + 2. * mem_buf, dx_sol + 2. * wat_buf)
if self.opts.get('user_y'):
self.size[1] = self.opts['user_y']
else:
self.size[1] = max(dy_tm + 2. * mem_buf, dy_sol + 2. * wat_buf)
# Z dimension. If there's a membrane, need to account for asymmetry
# in the Z dimension where the protein could be uneven in the membrane
# or even peripheral
if self.opts.get('user_z'):
self.size[2] = self.opts['user_z']
buf = (self.opts['user_z'] - max(solute_z) + min(solute_z)) / 2
self._zmax = max(solute_z) + buf
self._zmin = min(solute_z) - buf
if zh_mem_full > self._zmax or -zh_mem_full < self._zmin:
raise DabbleError("Specified user z of %f is too small to "
"accomodate protein and membrane!" %
self.opts['user_z'])
else:
if self.water_only:
self._zmax = max(solute_z) + wat_buf
self._zmin = min(solute_z) - wat_buf
else:
self._zmax = max(max(solute_z) + wat_buf, zh_mem_full)
self._zmin = min(min(solute_z) - wat_buf, -zh_mem_full)
self.size[2] = self._zmax - self._zmin
# Cleanup temporary file, if read in
if filename is not None:
molecule.delete(molid)
if top != -1:
molecule.set_top(top)
return dx_sol, dy_sol, dx_tm, dy_tm, max(solute_z) - min(solute_z)
def test_volumetric(file_psf, file_dx):
# Test read with a volumetric dataset
m = molecule.load("psf", file_psf)
molecule.read(m, "dx", file_dx, volsets=[0])
# Num volumetric
assert molecule.num_volumetric(m) == 1
with pytest.raises(ValueError):
molecule.num_volumetric(m + 1)
# Test with an invalid dataset index, nothing should be read
molecule.read(m, "dx", file_dx, volsets=[1])
assert molecule.num_volumetric(m) == 1
# Get volumetric
v = molecule.get_volumetric(m, 0)
assert len(v) == 4
assert len(v[0]) == 646875
assert v[1] == (75, 75, 115)
assert v[2] == pytest.approx((-37.0, -37.0, -57.0))
assert len(v[3]) == 9
del v
with pytest.raises(ValueError):
molecule.get_volumetric(m + 1, 0)
with pytest.raises(ValueError):
molecule.get_volumetric(molid=m, dataindex=200)
# Delete volumetric, deprecated invocation
with pytest.warns(DeprecationWarning):
molecule.remove_volumetric(molid=m, dataindex=0)
assert molecule.num_volumetric(m) == 0
# Add volumetric
newvol = list(np.ones((3, 6, 10)).flatten())
# separate size keywords are deprecated
with pytest.warns(DeprecationWarning):
molecule.add_volumetric(molid=m,
name="testvol",
xsize=3,
ysize=6,
zsize=10,
data=newvol)
assert molecule.num_volumetric(m) == 1
nv = molecule.get_volumetric(m, 0)
assert nv[0] == newvol
assert nv[1] == (3, 6, 10)
assert nv[2] == (0, 0, 0)
assert nv[3] == tuple(np.identity(3).flatten())
# Test a reasonable invocation of add with most keywords
molecule.add_volumetric(m,
"testvol",
size=(3, 6, 10),
data=newvol,
origin=(10, 20, -10),
xaxis=(0, 1, 0))
assert molecule.num_volumetric(molid=m) == 2
nv = molecule.get_volumetric(m, 1)
assert nv[0] == newvol
assert nv[1] == (3, 6, 10)
assert nv[2] == (10, 20, -10)
assert nv[3][:3] == (0, 1, 0)
# Invalid size
with pytest.raises(ValueError):
molecule.add_volumetric(m, "wrongsize", size=(1, 0, 1), data=[3])
# Not matching dimensions
with pytest.raises(ValueError):
molecule.add_volumetric(m, "wrondim", size=(10, 1, 3), data=newvol)
# Data not a sequence
with pytest.raises(TypeError):
molecule.add_volumetric(m, "wrongtype", size=(2, 3, 2), data=True)
# Non-float items in data
with pytest.raises(TypeError):
molecule.add_volumetric(m,
"wrongdata",
size=(1, 1, 2),
data=[3.0, True])
# Delete correctly
molecule.delete_volumetric(molid=m, dataindex=1)
assert molecule.num_volumetric(m) == 1
# Delete wrong things
with pytest.raises(ValueError):
molecule.delete_volumetric(m + 1, dataindex=0)
with pytest.raises(ValueError):
molecule.delete_volumetric(m, 1)
molecule.delete(m)
def test_volumetric(file_psf, file_dx):
# Test read with a volumetric dataset
m = molecule.load("psf", file_psf)
molecule.read(m, "dx", file_dx, volsets=[0])
# Num volumetric
assert molecule.num_volumetric(m) == 1
with pytest.raises(ValueError):
molecule.num_volumetric(m+1)
# Test with an invalid dataset index, nothing should be read
molecule.read(m, "dx", file_dx, volsets=[1])
assert molecule.num_volumetric(m) == 1
# Get volumetric
v = molecule.get_volumetric(m, 0)
assert len(v) == 4
assert len(v[0]) == 646875
assert v[1] == (75, 75, 115)
assert v[2] == pytest.approx((-37.0, -37.0, -57.0))
assert len(v[3]) == 9
del v
with pytest.raises(ValueError):
molecule.get_volumetric(m+1, 0)
with pytest.raises(ValueError):
molecule.get_volumetric(molid=m, dataindex=200)
# Delete volumetric, deprecated invocation
with pytest.warns(DeprecationWarning):
molecule.remove_volumetric(molid=m, dataindex=0)
assert molecule.num_volumetric(m) == 0
# Add volumetric
newvol = list(np.ones((3,6,10)).flatten())
# separate size keywords are deprecated
with pytest.warns(DeprecationWarning):
molecule.add_volumetric(molid=m, name="testvol", xsize=3, ysize=6,
zsize=10, data=newvol)
assert molecule.num_volumetric(m) == 1
nv = molecule.get_volumetric(m, 0)
assert nv[0] == newvol
assert nv[1] == (3, 6, 10)
assert nv[2] == (0, 0, 0)
assert nv[3] == tuple(np.identity(3).flatten())
# Test a reasonable invocation of add with most keywords
molecule.add_volumetric(m, "testvol", size=(3,6,10), data=newvol,
origin=(10,20,-10), xaxis=(0, 1, 0))
assert molecule.num_volumetric(molid=m) == 2
nv = molecule.get_volumetric(m, 1)
assert nv[0] == newvol
assert nv[1] == (3, 6, 10)
assert nv[2] == (10, 20, -10)
assert nv[3][:3] == (0, 1, 0)
# Invalid size
with pytest.raises(ValueError):
molecule.add_volumetric(m, "wrongsize", size=(1, 0, 1), data=[3])
# Not matching dimensions
with pytest.raises(ValueError):
molecule.add_volumetric(m, "wrondim", size=(10, 1, 3), data=newvol)
# Data not a sequence
with pytest.raises(TypeError):
molecule.add_volumetric(m, "wrongtype", size=(2,3,2), data=True)
# Non-float items in data
with pytest.raises(TypeError):
molecule.add_volumetric(m, "wrongdata", size=(1,1,2), data=[3.0, True])
# Delete correctly
molecule.delete_volumetric(molid=m, dataindex=1)
assert molecule.num_volumetric(m) == 1
# Delete wrong things
with pytest.raises(ValueError):
molecule.delete_volumetric(m+1, dataindex=0)
with pytest.raises(ValueError):
molecule.delete_volumetric(m, 1)
molecule.delete(m)