def test_glow():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.glow import GlowEffect
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)]*mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array, [0.1]*mol.n_atoms,
colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time()*10.0)*0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
#v.add_post_processing(SSAOEffect, ssao_power = 5.0)
#v.add_post_processing(FXAAEffect)
#v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_glow():
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)]*mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array, [0.1]*mol.n_atoms,
colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time()*10.0)*0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
v.run()
def test_merge_system():
# take a protein
from chemlab.io import datafile
from chemlab.graphics import display_system
from chemlab.db import ChemlabDB
water = ChemlabDB().get("molecule", "example.water")
prot = datafile("tests/data/3ZJE.pdb").read("system")
# Take a box of water
NWAT = 50000
bsize = 20.0
pos = np.random.random((NWAT, 3)) * bsize
wat = water.copy()
s = System.empty(NWAT, NWAT * 3, box_vectors=np.eye(3) * bsize)
for i in range(NWAT):
wat.move_to(pos[i])
s.add(wat)
prot.r_array += 10
s = merge_systems(s, prot, 0.5)
display_system(s, 'ball-and-stick')
def test_glow():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.glow import GlowEffect
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)] * mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array,
[0.1] * mol.n_atoms, colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time() * 10.0) * 0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
#v.add_post_processing(SSAOEffect, ssao_power = 5.0)
#v.add_post_processing(FXAAEffect)
#v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_outline():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.outline import OutlineEffect
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
#mol = datafile('tests/data/water.gro').read('system')
#mol = datafile('tests/data/benzene.mol').read('molecule')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(AtomRenderer,
mol.r_array,
mol.type_array,
'impostors',
shading='toon')
v.add_post_processing(OutlineEffect, 'depthnormal')
v.add_post_processing(SSAOEffect, ssao_power=4.0)
v.add_post_processing(FXAAEffect)
v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_glow():
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)] * mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array,
[0.1] * mol.n_atoms, colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time() * 10.0) * 0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
v.run()
def test_merge_system():
# take a protein
from chemlab.io import datafile
from chemlab.graphics import display_system
from chemlab.db import ChemlabDB
water = ChemlabDB().get("molecule", "example.water")
prot = datafile("tests/data/3ZJE.pdb").read("system")
# Take a box of water
NWAT = 50000
bsize = 20.0
pos = np.random.random((NWAT, 3)) * bsize
wat = water.copy()
s = System.empty(NWAT, NWAT*3, box_vectors=np.eye(3)*bsize)
for i in range(NWAT):
wat.move_to(pos[i])
s.add(wat)
prot.r_array += 10
s = merge_systems(s, prot, 0.5)
display_system(s, 'ball-and-stick')
def test_random():
'''Testing random made box'''
from chemlab.db import ChemlabDB
cdb = ChemlabDB()
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = cdb.get("molecule", 'gromacs.spce')
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
def test_random():
'''Testing random made box'''
from chemlab.db import ChemlabDB
cdb = ChemlabDB()
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = cdb.get("molecule", 'gromacs.spce')
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
def test_molecular_viewer():
from chemlab.mviewer.qtmolecularviewer import QtMolecularViewer
from chemlab.mviewer.representations import BallAndStickRepresentation
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol.guess_bonds()
v = QtMolecularViewer()
v.run()
def test_molecular_viewer():
from chemlab.mviewer.qtmolecularviewer import QtMolecularViewer
from chemlab.mviewer.representations import BallAndStickRepresentation
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol.guess_bonds()
v = QtMolecularViewer()
v.run()
def test_molecular_viewer():
from chemlab.graphics.qtmolecularviewer import QtMolecularViewer
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('tests/data/3ZJE.pdb').read('system')
#mol = datafile('tests/data/naclwater.gro').read('system')
mol.guess_bonds()
v = QtMolecularViewer(mol)
v.widget.camera.autozoom(mol.r_array)
def on_action1():
if len(v.representation.selection) == 2:
i, j = v.representation.selection
distsq = ((mol.r_array[j] - mol.r_array[i])**2).sum()
print 'distance between', i, j, np.sqrt(distsq)
def select_all_atoms():
which = v.representation.selection[0]
at = mol.type_array[which]
sel = mol.type_array == at
v.representation.make_selection(sel.nonzero()[0])
def select_all_molecules():
which = v.representation.last_modified
if which is None:
return
at = mol.type_array[which]
sel = mol.type_array == at
allmol = mol.atom_to_molecule_indices(sel)
allmol = mol.mol_to_atom_indices(allmol)
v.representation.make_selection(allmol, additive=True)
def change_representation():
BallAndStickRepresentation = 0
# We need two representations
rep = v.add_representation(BallAndStickRepresentation, mol)
rep.set_mask(self.selection)
rep.set_mask(not self.selection)
def scale_radii():
#v.representation.scale_radii(v.representation.selection, 0.9)
v.representation.hide(v.representation.selection)
v.run()
def test_molecular_viewer():
from chemlab.graphics.qtmolecularviewer import QtMolecularViewer
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('tests/data/3ZJE.pdb').read('system')
#mol = datafile('tests/data/naclwater.gro').read('system')
mol.guess_bonds()
v = QtMolecularViewer(mol)
v.widget.camera.autozoom(mol.r_array)
def on_action1():
if len(v.representation.selection) == 2:
i, j = v.representation.selection
distsq = ((mol.r_array[j] - mol.r_array[i])**2).sum()
print 'distance between', i, j, np.sqrt(distsq)
def select_all_atoms():
which = v.representation.selection[0]
at = mol.type_array[which]
sel = mol.type_array == at
v.representation.make_selection(sel.nonzero()[0])
def select_all_molecules():
which = v.representation.last_modified
if which is None:
return
at = mol.type_array[which]
sel = mol.type_array == at
allmol = mol.atom_to_molecule_indices(sel)
allmol = mol.mol_to_atom_indices(allmol)
v.representation.make_selection(allmol, additive=True)
def change_representation():
BallAndStickRepresentation = 0
# We need two representations
rep = v.add_representation(BallAndStickRepresentation, mol)
rep.set_mask(self.selection)
rep.set_mask(not self.selection)
def scale_radii():
#v.representation.scale_radii(v.representation.selection, 0.9)
v.representation.hide(v.representation.selection)
v.run()
def test_molecular_viewer():
from chemlab.graphics.qtmolecularviewer import QtMolecularViewer
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtMolecularViewer(mol)
v.highlight([0, 2, 8])
v.run()
def test_multiple_post_processing():
v = QtViewer()
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('/home/gabriele/projects/LiCl/interface/loafintjc-heat/equilibrium.gro').read('system')
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors', shading='toon')
# Adding multiple post processing effects
v.add_post_processing(SSAOEffect)
v.add_post_processing(GammaCorrectionEffect, 2.0)
#v.add_post_processing(GammaCorrectionEffect, 2.0)
#v.add_post_processing(FXAAEffect)
v.run()
def test_toon_shading():
from chemlab.core.molecule import guess_bonds
cdb = ChemlabDB()
#mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
#v.widget.post_processing = FXAAEffect(v.widget)
#v.widget.post_processing = SSAOEffect(v.widget, kernel_size=64, kernel_radius=1.0, ssao_power=2.0)
v.widget.camera.autozoom(mol.r_array)
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'impostors',
# shading='toon')
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'polygons',
# shading='toon')
ar = v.add_renderer(BallAndStickRenderer,
mol.r_array,
mol.type_array,
guess_bonds(mol.r_array, mol.type_array),
shading='toon')
v.run()
def test_pickers():
from chemlab.graphics.pickers import SpherePicker, CylinderPicker
from chemlab.core.molecule import guess_bonds
#mol = datafile('tests/data/benzene.mol').read('molecule')
mol = ChemlabDB().get('molecule', 'example.water')
centers = mol.r_array
radii = np.array([0.05]*mol.n_atoms)
colors = np.array([[0, 255, 255, 255]]*mol.n_atoms)
bounds = mol.r_array.take(mol.bonds, axis=0)
b_radii = np.array([0.05]*mol.n_bonds)
b_colors = np.array([[0, 255, 255, 255]]*mol.n_bonds)
v = QtViewer()
#v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, centers, radii*1.2, colors, transparent=False)
cr = v.add_renderer(CylinderImpostorRenderer, bounds, b_radii, b_colors)
sp = SpherePicker(v.widget, centers, radii*1.2)
cp = CylinderPicker(v.widget, bounds, b_radii)
def on_click(evt):
x, y = v.widget.screen_to_normalized(evt.x(), evt.y())
a_i, a_d = sp.pick(x, y)
b_i, b_d = cp.pick(x, y)
print('A', a_d)
print('B', b_d)
v.widget.clicked.connect(on_click)
v.run()
def test_multiple_post_processing():
v = QtViewer()
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('/home/gabriele/projects/LiCl/interface/loafintjc-heat/equilibrium.gro').read('system')
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors', shading='toon')
# Adding multiple post processing effects
v.add_post_processing(SSAOEffect)
v.add_post_processing(GammaCorrectionEffect, 2.0)
#v.add_post_processing(GammaCorrectionEffect, 2.0)
#v.add_post_processing(FXAAEffect)
v.run()
def test_local():
db = ChemlabDB()
bz = db.get("molecule", "example.norbornene")
pre_string = bz.tojson()
db = LocalDB("/tmp/testdb/")
db.store("molecule", 'norbornene', bz, nowarn=True)
post_string = db.get('molecule', 'norbornene').tojson()
assert pre_string == post_string
# Do the same thing for a system of 3 norbornenes
s = System([bz.copy() for i in range(3)])
pre_string = s.tojson()
db.store("system", 'norbornene-3', s, nowarn=True)
post_string = db.get('system', 'norbornene-3').tojson()
assert pre_string == post_string
def test_ssao():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(SSAOEffect(v.widget, kernel_size=16, kernel_radius=3.0, ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.run()
def test_local():
db = ChemlabDB()
bz = db.get("molecule", "example.norbornene")
pre_dict = bz.to_dict()
db = LocalDB("/tmp/testdb/")
db.store("molecule", 'norbornene', bz, nowarn=True)
post_dict = db.get('molecule', 'norbornene').to_dict()
npeq_(pre_dict['r_array'], post_dict['r_array'])
# Do the same thing for a system of 3 norbornenes
s = System([bz.copy() for i in range(3)])
pre_dict = s.to_dict()
db.store("system", 'norbornene-3', s, nowarn=True)
post_dict = db.get('system', 'norbornene-3').to_dict()
npeq_(pre_dict['r_array'], post_dict['r_array'])
def test_ssao():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(
SSAOEffect(v.widget, kernel_size=16, kernel_radius=3.0,
ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.run()
def test_outline():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.outline import OutlineEffect
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
#mol = datafile('tests/data/water.gro').read('system')
#mol = datafile('tests/data/benzene.mol').read('molecule')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
'impostors', shading='toon')
v.add_post_processing(OutlineEffect, 'depthonly')
v.add_post_processing(FXAAEffect)
v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_ssao():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(SSAOEffect(v.widget, kernel_size=16,
kernel_radius=3.0, ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.widget.camera.orbit_y(90)
v.run()
def test_local():
db = ChemlabDB()
bz = db.get("molecule", "example.norbornene")
pre_dict = bz.to_dict()
db = LocalDB("/tmp/testdb/")
db.store("molecule", 'norbornene', bz, nowarn=True)
post_dict = db.get('molecule', 'norbornene').to_dict()
npeq_(pre_dict['r_array'], post_dict['r_array'])
# Do the same thing for a system of 3 norbornenes
s = System([bz.copy() for i in range(3)])
pre_dict = s.to_dict()
db.store("system", 'norbornene-3', s, nowarn=True)
post_dict = db.get('system', 'norbornene-3').to_dict()
npeq_(pre_dict['r_array'], post_dict['r_array'])
def test_glow():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.glow import GlowEffect
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)]*mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array, [0.1]*mol.n_atoms,
colors)
v.add_post_processing(GlowEffect)
#v.add_post_processing(SSAOEffect, ssao_power = 5.0)
#v.add_post_processing(FXAAEffect)
#v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_gamma():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.camera.orbit_y(3.14/3)
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
'impostors', shading='phong')
v.add_post_processing(SSAOEffect, ssao_power=4.0)
v.add_post_processing(GammaCorrectionEffect)
v.run()
)
from ....cclib_patch.parser import gausscomparser
from ....cclib_patch.parser import gaussianparser
_types = {
'gamess': GAMESS,
'gamessuk': GAMESSUK,
'gaussian': gaussianparser.Gaussian,
'gausscom': gausscomparser.Gausscom,
'jaguar': Jaguar,
'molpro': Molpro,
#'nwchem': NWChem,
'orca': ORCA
}
cdb = ChemlabDB()
symbols = cdb.get('data', 'symbols')
def _create_cclib_handler(type):
if type not in _types:
raise FormatNotSupported(type)
class _Handler(IOHandler):
def __init__(self, fd, filetype=type):
super(_Handler, self).__init__(fd)
self.filetype = filetype
self.data = _types[filetype](fd, loglevel=logging.ERROR).parse()
def read(self, feature, *args, **kwargs):
if feature == 'molecular orbitals':
import numpy as np
# CJS changed relative paths to chemlab ones
from chemlab.graphics import colors
from chemlab.db import ChemlabDB
from chemlab.graphics.renderers.base import AbstractRenderer
from chemlab.graphics.renderers.sphere import SphereRenderer
from chemlab.graphics.renderers.sphere_imp import SphereImpostorRenderer
from chemlab.graphics.renderers.point import PointRenderer
vdw_dict = ChemlabDB().get("data", 'vdwdict')
class AtomRenderer(AbstractRenderer):
"""Render atoms by using different rendering methods.
**Parameters**
widget:
The parent QChemlabWidget
r_array: np.ndarray((NATOMS, 3), dtype=float)
The atomic coordinate array
type_array: np.ndarray((NATOMS, 3), dtype=object)
An array containing all the atomic symbols like `Ar`, `H`, `O`.
If the atomic type is unknown, use the `Xx` symbol.
backend: "impostors" | "polygons" | "points"
You can choose the rendering method between the sphere impostors,
polygonal sphere and points.
.. seealso: :py:class:`~chemlab.graphics.renderers.SphereRenderer`
:py:class:`~chemlab.graphics.renderers.SphereImpostorRenderer`
TriangleRenderer, SphereRenderer, SphereImpostorRenderer, PointRenderer,
AtomRenderer, BoxRenderer, LineRenderer, CylinderRenderer, BondRenderer,
BallAndStickRenderer, WireframeRenderer, CylinderImpostorRenderer)
from chemlab.graphics.uis import TextUI
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.qttrajectory import QtTrajectoryViewer, format_time
from chemlab.graphics.postprocessing import (SSAOEffect, FXAAEffect,
GammaCorrectionEffect,
OutlineEffect, GlowEffect,
NoEffect)
cdb = ChemlabDB()
def test_triangle_renderer():
'''To see if we're able to render a triangle'''
vertices = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [2.0, 0.0, 0.0]]
normals = [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]
colors = [colors.blue] * 3
v = QtViewer()
tr = v.add_renderer(TriangleRenderer,
vertices,
normals,
colors,
shading='toon')
v.run()
