def start_trace():
"""
Function to connect VMD function `connect_plot` with VMD variable change of `vmd_frame`
"""
global fig
molid = evaltcl("molinfo top")
evaltcl("trace variable vmd_frame({}) w connect_plot".format(molid))
fig.canvas.mpl_connect('close_event', stop_trace)
def run(fes_file='fes.dat', colvar='COLVAR', connect=True):
"""
Run routine to plot the free energy surface and connect the current VMD to a point of it.
Parameters
----------
fes_file : str
path to fes file. (Default is 'fes.dat'.)
colvar : str
path to COLVAR file (Default is 'COLVAR'.)
connect : bool
Switch to connect the plot to the current VMD frame.
"""
assert os.path.exists(fes_file), "FES File: {} not found".format(fes_file)
assert os.path.exists(colvar), "COLVAR file: {} not found".format(colvar)
molid = evaltcl("molinfo top")
numframes = int(evaltcl('molinfo {} get numframes'.format(molid)))
current_frame = int(evaltcl('molinfo {} get frame'.format(molid)))
# load files
global colvar_data, fes_edges, fes_data
header, fes_edges, fes_data = load(fes_file)
dimensions = len(fes_edges)
colvar_data = load_colvar(colvar, [cv.name for cv in header])
global fig, ax
if dimensions == 1:
# create plot
fig, ax = plt.subplots()
line = plot_1D(header, fes_data, fes_edges, ax=ax)
elif dimensions == 2:
# create plot
fig, ax = plt.subplots()
img, cbar = plot_2D(header, fes_data, ax=ax)
else:
raise NotImplementedError("Only 1D and 2D free energy landscapes are implemented." + \
"\nFound a {}D landscape!".format(dimensions))
# draw
global point
point, = ax.plot([0], [0], 'r*', markersize=12)
try:
fig.show()
except AttributeError as e:
print(e)
update(current_frame)
if connect:
print("register connect_plot")
register()
print("Connect plot to frames")
start_trace()
print("Stop connect_plot with:\n" +
"trace vdelete vmd_frame({}) w connect_plot".format(molid))
def register():
"""
Function to register VMD function `connect_plot`
which calls the python function `update($frame)` from within VMD
"""
evaltcl("""
proc connect_plot {name index op} {
# name == vmd_frame
# index == molecule id of the newly changed frame
# op == w
set frame [molinfo $index get frame]
gopython -command "update($frame)"
return
}
""")
def set_pbc(xscFile):
"""
Sets the systems periodic boundaries."
"""
xscFile = open(xscFile,"r")
for line in xscFile:
continue
items = line.split()
xDim = items[1]
yDim = items[5]
zDim = items[9]
#set pbd
pbcCommand = ("package require pbctools; pbc set { %s %s %s }"
% (xDim, yDim, zDim))
evaltcl(pbcCommand)
xscFile.close()
def load_assign_data(cond, npyfile):
"""
Function to load and assign data.
Parameters
----------
cond : str
VMD selection string
npyfile : str
path to numpy `.npy` file.
"""
# get number of frames
n_frames = int(evaltcl('molinfo top get numframes'))
# read in data
data = np.load(npyfile)
if n_frames != data.shape[0]:
print("something is off")
# create atomselection and assign data
sel = AtomSel(cond)
for n in range(n_frames):
sel.frame(n)
sel.set('user', data[n, :].tolist())
def expand_data_to_residue(condition, column='user', n_frames=None):
"""
Function to expand the data stored in column from a per atom data to a per residue data.
Parameter
---------
condition : str
condition string to select the atomselect containing the data
column : str, optional
column where the data is stored. Default is `'user'`.
n_frames : int or None, optional
Number of frames to consinder. If `None` all frames are taken.
Default is `None`
Example
-------
>>> expand_data_to_residue(condition='type OW', column='user', n_frames=100)
"""
# get number of frames
if n_frames is None:
n_frames = int(evaltcl('molinfo top get numframes'))
sel_data = AtomSel(condition)
residue = sel_data.get('residue')
sel_residues = AtomSel('same residue as ({})'.format(condition))
# get the list of resdiue IDs
list_residues = sel_residues.get('residue')
# create a dictionay with the counts per residue
dict_counts = dict(
np.array(np.unique(list_residues, return_counts=True)).T)
# get the counts (keep order of the residues as in sel !)
counts_residues = np.vectorize(dict_counts.__getitem__)(residue)
for n in range(n_frames):
sel_data.frame(n)
sel_residues.frame(n)
data = sel_data.get(column)
data_residue = np.repeat(data, counts_residues)
sel_residues.set(column, data_residue.tolist())
def stop_trace():
"""
Function to disconnect VMD function `connect_plot` with VMD variable change of `vmd_frame`
"""
molid = evaltcl("molinfo top")
evaltcl("trace vdelete vmd_frame({}) w connect_plot".format(molid))