def __init__(self, fc_length=0.7, cutoff=1.2, factor=46402.):
self.arguments = (fc_length, cutoff, factor)
ForceField.__init__(self, 'deformation')
self.arguments = (fc_length, cutoff, factor)
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
def __init__(self, fc_length = 0.7, cutoff = 1.2, factor = 46402.):
self.arguments = (fc_length, cutoff, factor)
ForceField.__init__(self, 'deformation')
self.arguments = (fc_length, cutoff, factor)
self.fc_length = fc_length
self.cutoff = cutoff
self.factor = factor
def __init__(self, atom1, atom2, atom3, angle, force_constant):
self.atom1 = atom1
self.atom2 = atom2
self.atom3 = atom3
self.angle = angle
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic angle restraint')
def __init__(self, atom1, atom2, atom3, atom4, dihedral, force_constant):
self.index1, self.index2, self.index3, self.index4 = \
self.getAtomParameterIndices((atom1, atom2, atom3, atom4))
self.dihedral = dihedral
self.force_constant = force_constant
self.arguments = (self.index1, self.index2, self.index3, self.index4,
dihedral, force_constant)
ForceField.__init__(self, 'harmonic dihedral restraint')
def __init__(self, atom1, atom2, atom3, angle, force_constant):
self.index1, self.index2, self.index3 = \
self.getAtomParameterIndices((atom1, atom2, atom3))
self.arguments = (self.index1, self.index2, self.index3,
angle, force_constant)
self.angle = angle
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic angle restraint')
def __init__(self, atom1, atom2, atom3, atom4, dihedral, force_constant):
self.index1, self.index2, self.index3, self.index4 = \
self.getAtomParameterIndices((atom1, atom2, atom3, atom4))
self.dihedral = dihedral
self.force_constant = force_constant
self.arguments = (self.index1, self.index2, self.index3, self.index4,
dihedral, force_constant)
ForceField.__init__(self, 'harmonic dihedral restraint')
def __init__(self, atom1, atom2, atom3, angle, force_constant):
self.index1, self.index2, self.index3 = \
self.getAtomParameterIndices((atom1, atom2, atom3))
self.arguments = (self.index1, self.index2, self.index3, angle,
force_constant)
self.angle = angle
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic angle restraint')
def __init__(self, atom1, atom2, atom3, atom4, dihedral, force_constant):
self.atom1 = atom1
self.atom2 = atom2
self.atom3 = atom3
self.atom4 = atom4
self.dihedral = dihedral
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic dihedral restraint')
def __init__(self, cutoff=None, scale_factor=1.):
ForceField.__init__(self, 'anisotropic_network')
self.arguments = (cutoff, )
self.cutoff = cutoff
self.scale_factor = scale_factor
lambda a: np.array([0.0, -a[2], a[1]]),
lambda a: np.array([a[2], 0.0, -a[0]]),
lambda a: np.array([-a[1], a[0], 0.0])
]
u = normal_fns[np.argmin(np.fabs(normal))](normal)
u /= np.linalg.norm(u)
v = np.cross(normal, u)
v /= np.linalg.norm(v)
alpha = np.random.uniform(0.0, np.pi * 2)
return np.cos(alpha) * u + np.sin(alpha) * v
if __name__ == "__main__":
import os, sys
cwd = os.getcwd()
assembled = os.path.abspath(os.path.dirname(str(sys.argv[0])))
os.environ["ASSEMBLEPATH"] = "%s;%s" % (cwd, assembled)
#test mass estimation
from Database import Database
D = Database()
D.load("database\\database.txt", "gromacs")
F = ForceField()
F.load("database\\forcefield\\trappe.ff.txt")
P = Polymer(D, F, "test", "gromacs")
P.chain = "ccctttccCCt"
print(P.get_mass())
def __init__(self, atom1, atom2, distance, force_constant):
self.index1, self.index2 = self.getAtomParameterIndices((atom1, atom2))
self.arguments = (self.index1, self.index2, distance, force_constant)
self.distance = distance
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic distance restraint')
def __init__(self, atom1, atom2, distance, force_constant):
self.atom1 = atom1
self.atom2 = atom2
self.distance = distance
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic distance restraint')
def run(self) -> None:
global terminate
# Collect events until released
with Listener(on_press=self.on_press,
on_release=self.on_release) as listener:
listener.join()
self.env.terminate = True
if __name__ == '__main__':
print('LRAUV project')
# showing vector field
num_obstacles = 3
samples = sampling_locations(num_samples=num_obstacles + 1, sample_dist=15)
obstacles, goal = samples[:num_obstacles], samples[num_obstacles]
FF = ForceField(goal.tolist(), obstacles)
sim = SimView(plt, FF)
tethys = TethysEnv(sim, FF)
IOthread = KeyboardInput(tethys)
IOthread.start()
tethys.start()
while not tethys.terminate:
while not sim.q.empty():
data = sim.q.get()
sim(data)
sim.update()
sleep(0.01)
def __init__(self, parent, title):
self.dirname = ''
# A "-1" in the size parameter instructs wxWidgets to use the default size.
# In this case, we select 200px width and the default height.
wx.Frame.__init__(self, parent, title=title, size=(700, 600))
self.CreateStatusBar() # A Status bar in the bottom of the window
self.SetBackgroundColour("white")
cwd = os.getcwd()
assembled = os.path.abspath(os.path.dirname(str(sys.argv[0])))
os.environ["ASSEMBLEPATH"] = "%s;%s" % (cwd, assembled)
#initialize datastructures
self.db = Database()
self.ff = ForceField()
# Setting up the menu bar
filemenu = wx.Menu()
menuLoad = filemenu.Append(wx.ID_OPEN, "&Load...",
" Load a setup file")
menuSave = filemenu.Append(wx.ID_SAVEAS, "&Save as...",
" Save the current setup")
menuHelp = filemenu.Append(wx.ID_HELP, "&Help",
" Optimization user manual")
menuAbout = filemenu.Append(wx.ID_ABOUT, "&About",
" Information about this program")
filemenu.AppendSeparator()
menuExit = filemenu.Append(wx.ID_EXIT, "E&xit",
" Terminate the program")
# Creating the menu bar
menuBar = wx.MenuBar()
menuBar.Append(filemenu,
"&File") # Adding the "filemenu" to the MenuBar
self.SetMenuBar(menuBar) # Adding the MenuBar to the Frame content.
#panels
self.I = InputData(self)
self.F = InputForceField(self)
self.P = Polymers(self)
self.S = SystemOut(self)
self.make = wx.Button(self, label="MAKE!")
box = wx.BoxSizer(wx.VERTICAL)
box.Add(self.I, 1, wx.EXPAND | wx.ALL, 3)
box.Add(self.F, 0, wx.EXPAND | wx.ALL, 3)
box.Add(self.P, 1, wx.EXPAND | wx.ALL, 3)
box.Add(self.S, 0, wx.EXPAND | wx.ALL, 3)
box.Add(self.make, 0, wx.ALIGN_CENTER | wx.ALL, 3)
self.SetSizer(box)
self.SetSize((800, 700))
self.Centre()
# bind events to menu items
self.Bind(wx.EVT_MENU, self.OnLoad, menuLoad)
self.Bind(wx.EVT_MENU, self.OnSave, menuSave)
self.Bind(wx.EVT_MENU, self.OnHelp, menuHelp)
self.Bind(wx.EVT_MENU, self.OnAbout, menuAbout)
self.Bind(wx.EVT_MENU, self.OnExit, menuExit)
self.Bind(wx.EVT_BUTTON, self.OnMake, self.make)
self.Show()
def __init__(self, cutoff = None, scale_factor = 1.):
ForceField.__init__(self, 'anisotropic_network')
self.arguments = (cutoff,)
self.cutoff = cutoff
self.scale_factor = scale_factor
def __init__(self, name):
ForceField.__init__(self, name)
self.type = 'nonbonded'
def __init__(self, cutoff = None, scale_factor = 1., version=1):
ForceField.__init__(self, 'calpha')
self.arguments = (cutoff,)
self.cutoff = cutoff
self.scale_factor = scale_factor
self.version = version
def __init__(self, atom1, atom2, distance, force_constant):
self.index1, self.index2 = self.getAtomParameterIndices((atom1, atom2))
self.arguments = (self.index1, self.index2, distance, force_constant)
self.distance = distance
self.force_constant = force_constant
ForceField.__init__(self, 'harmonic distance restraint')