def __init__(self):
self.interaction_manager = get_interaction_manager(
*get_twod_signal_manager().get_interaction_data())
#TODO : REMOVE WEIRD POINTS
for x in [[19, 6], [19, 7], [21, 6]]:
print(self.interaction_manager.interaction_matrix[x])
self.interaction_manager.interaction_matrix[x[0]][x[1]] = 0
self.interaction_manager.interaction_matrix[x[1]][x[0]] = 0
self.interaction_matrix = self.interaction_manager.interaction_matrix
self.interaction_matrix[self.interaction_matrix == 9] = 0
self.type_array = self.interaction_manager.type_array
self.shift_data = self.interaction_manager.shift_data
self.number_atoms = self.interaction_manager.number_atoms
self.viewer = QtViewer()
ac = np.random.rand(self.number_atoms, 3) * 3
self.coordinate_manager = CoordinateManager(ac,
self.interaction_manager)
self.renderer = self.viewer.add_renderer(
BallAndStickRenderer, self.coordinate_manager.get_coordinates(),
self.type_array, np.array([]))
def __init__(self):
self.file_manager = FileManager()
system, self.atom_coordinates = self.read_coordinates()
# self.interaction_manager = get_interaction_manager(get_twod_signal_manager().get_interaction_matrix(), system.type_array.tolist(), np.zeros(shape=system.type_array.shape))
self.interaction_manager = get_interaction_manager(*get_twod_signal_manager().get_interaction_data())
self.viewer = QtViewer()
self.best_response_value = 1000000.0
self.best_atom_coordinates = np.copy(self.atom_coordinates)
self.fragments = self.generate_fragments(system)
self.atom_coordinates = self.fix_hydrogen_bond_lengths(system, self.atom_coordinates)
def __init__(self, molecules, interaction_manager):
self.molecules = molecules
for molecule in self.molecules:
molecule.r_array *= 1.85
self.v = QtViewer()
self.renderers = {}
for molecule in self.molecules:
ar = self.v.add_renderer(BallAndStickRenderer, molecule.r_array, molecule.type_array, molecule.bonds)
self.renderers[molecule] = ar
self.best_response_value = 0
self.best_atom_coordinates = None
self.twod_signal_manager = get_twod_signal_manager()
self.interaction_manager = interaction_manager
def __init__(self, coordinates, interaction_manager):
self.viewer = QtViewer()
self.selected_atom = 0
self.active = True
self.coordinates = None
self.atoms = None
self.bonds = None
self.interaction_manager = interaction_manager
self.viewer.widget.on_mouse.append(self.select)
try:
self.update(coordinates, interaction_manager)
if len(coordinates) != len(self.atoms):
raise Exception(
"Atom List does not correspond to coordinate array")
except Exception as e:
self.disable(e)
def __init__(self):
self.interaction_manager = get_interaction_manager(
*get_twod_signal_manager().get_interaction_data())
im = self.interaction_manager.interaction_matrix
im[19][6] = 0
im[19][7] = 0
"""
for x in [9,10,11,12,13,17,18,19,20,21]:
for y in range(self.interaction_manager.number_atoms):
if im[x][y] == 3:
im[x][y] = 0
im[y][x] = 0
"""
self.interaction_matrix = self.interaction_manager.interaction_matrix
self.type_array = self.interaction_manager.type_array
self.shift_data = self.interaction_manager.shift_data
self.number_atoms = self.interaction_manager.number_atoms
self.global_bond_indices = self.interaction_manager.bonds
self.bond_orders = self.interaction_manager.bond_orders
self.viewer = QtViewer()
self.best_response_value = 1000000.0
ac = np.random.rand(self.number_atoms, 3) * 0.001
#ac = FileManager().read_numpy_from_xyz('manual2.xyz') * 0.1
self.iteration_number = 0
self.coordinate_manager = CoordinateManager(self, ac,
self.interaction_manager)
self.fragments = self.generate_fragments_list()
print(self.coordinate_manager.calculate_response_value(True))
self.interaction_manager.print_matrix()
input("")
self.delay = 0
"""
for x in [0,1,2,3,4,5]:
self.interaction_manager.interaction_matrix[self.interaction_manager.interaction_matrix==x] = 9
"""
self.nullfrag = Fragment([], [], [], [], self.viewer,
self.coordinate_manager,
self.interaction_manager, [])
from chemlab.db import CirDB
from chemlab.graphics import QtViewer
from chemlab.graphics.renderers import AtomRenderer
from chemlab.graphics.postprocessing import FXAAEffect, SSAOEffect
# A series of compounds to display
compounds = ["methane", "ethane", "propane", "butane"]
db = CirDB()
# Prepare the viewer
v = QtViewer()
v.widget.initializeGL()
v.add_post_processing(SSAOEffect, kernel_size=128, kernel_radius=1.0)
v.add_post_processing(FXAAEffect)
for compound in compounds:
mol = db.get("molecule", compound)
rend = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array)
v.widget.camera.autozoom(mol.r_array)
# Give some extra zoom
v.widget.camera.mouse_zoom(1.0)
v.widget.toimage(300, 300).save(compound + '.png')
# Cleanup
v.remove_renderer(rend)
