def create_molecules():
""" Creates the molecules """
global GUANINE, ADENINE, CYTOSINE, URACIL
GUANINE = pdb.PDBMolecule('{}/pdb/GMP.pdb'.format(SETTINGS.AppLocation),
center=True)
ADENINE = pdb.PDBMolecule('{}/pdb/AMP.pdb'.format(SETTINGS.AppLocation),
center=True)
CYTOSINE = pdb.PDBMolecule('{}/pdb/CMP.pdb'.format(SETTINGS.AppLocation),
center=True)
URACIL = pdb.PDBMolecule('{}/pdb/UMP.pdb'.format(SETTINGS.AppLocation),
center=True)
def create_molecules():
""" Creates the molecules """
global GUANINE, ADENINE, CYTOSINE, URACIL_ONE, ADENINE_TWO
GUANINE = pdb.PDBMolecule('{}/pdb/GMP.pdb'.format(SETTINGS.AppLocation),
offset=[-100, 0, 0])
ADENINE = pdb.PDBMolecule('{}/pdb/AMP.pdb'.format(SETTINGS.AppLocation),
offset=[-100, 0, 0])
CYTOSINE = pdb.PDBMolecule('{}/pdb/CMP.pdb'.format(SETTINGS.AppLocation),
offset=[-100, 0, 0])
URACIL_ONE = pdb.PDBMolecule('{}/pdb/UMP.pdb'.format(SETTINGS.AppLocation),
offset=[-100, 0, 0])
ADENINE_TWO = pdb.PDBMolecule('{}/pdb/AMP.pdb'.format(
SETTINGS.AppLocation),
offset=[-100, 0, 0])
def alphact_conformational_change(frame, alphact_stage_one_sliced, alphact_stage_two_sliced):
"""
This function simulation the conformational change of the alpha ct peptide with the
alpha helix of the insulin molecule
"""
INSULIN_RECEPTOR = pdb.PDBMolecule(PATH_PDB, center=False)
INSULIN_RECEPTOR.move_to([0,0,0])
frame_start = 270 #the first frame when this function is called upon
for num in range(10014, 10115):
if num < (frame - frame_start) * round(101/60) + 10014:
if num not in alphact_stage_two_sliced:
#remove a portion of the atoms that are not in second stage based on the current frame
alphact_stage_one_sliced.remove(num)
for num in range(10171, 10211):
if num < (frame - frame_start) * round(40/60) + 10171:
#add a portion of atoms that are not in the first stage based on the current frame
alphact_stage_one_sliced.append(num)
alphact_stage_one_sliced_mol = INSULIN_RECEPTOR.divide(alphact_stage_one_sliced, 'alphact_one')
rotation = (frame - frame_start - 60) * -0.01 #set a number for the amount the molecule should rotate based on the frame
alphact_stage_one_sliced_mol.rotate([0,0,1], rotation) #rotate the molecule on the z axis with the rotation variable
insulin_alpha = INSULIN_RECEPTOR.divide(ATOM_POS["N"], "alphact_two")
insulin_alpha.move_offset([0,30,0])
return alphact_stage_one_sliced_mol, insulin_alpha
def molecules():
""" Creates molecules and contains other constants """
global ETHANOL
ETHANOL = pdb.PDBMolecule('{}/pdb/ethanol.pdb'.format(
SETTINGS.AppLocation),
center=True)
def make_molecules(molecules):
"""
make_molecules([frame, molecules])
"""
for obj in ANIMATION_OBJECTS:
molecule_data = ANIMATION_OBJECTS[obj]["molecule"]
if molecule_data[0] and not molecule_data[1]:
# Making normal molecules from pdb file
mol = pdb.PDBMolecule(molecule_data[2], center=True)
molecule = {
"molecule": mol,
"reset": [0, mol.atoms.copy()],
"text": None
}
elif not molecule_data[0]:
# Making basic vapory objects
molecule = {"molecule": molecule_data[1:]}
else:
# Make the molecule a None object until it is time to split the moleucle
molecule = None
molecules[obj] = molecule
return molecules
def frame(step):
""" Renders an Ethanol molecule centered in the scene """
# Dit is een beetje dubbel maar zonder gaat er opnieuw iets mis met self.atom
ETHANOL = pdb.PDBMolecule('{}/pdb/ethanol.pdb'.format(
SETTINGS.AppLocation),
center=True)
camera = Camera('location', [10, 0, 0], 'look_at', [0, 0, 0])
nframes = eval(SETTINGS.NumberFrames)
hele_rotatie = 2 * math.pi
# When step is below or equal to 40, the ethanol molecule is devided into 2 parts.
if step <= (nframes / 2):
y_ass = (1 / (nframes / 2)) * step
splitsing = ETHANOL.divide([7, 8], 'ethanol', offset=[0, y_ass, 0])
else:
# In the second half of the program, last 40 frames we rotate the molecules 360 degrees.
y_ass = (1 / (nframes / 2)) * 40
splitsing = ETHANOL.divide([7, 8], 'ethanol', offset=[0, y_ass, 0])
step = step - 40
rotatie_per_step = (hele_rotatie / nframes) * step
ETHANOL.rotate([1, 0, 0], rotatie_per_step)
splitsing.rotate([1, 0, 0], rotatie_per_step)
# Return the Scene object for rendering.
return Scene(camera,
objects=[models.default_light] + ETHANOL.povray_molecule +
splitsing.povray_molecule,
included=['colors.inc'])
def frame(step):
global NUCL_1, NUCL_2, NUCL_3, NUCL_4, NUCL_5, NUCL_6, NUCL_7
RNA = pdb.PDBMolecule('{}/pdb/RNA2.pdb'.format(SETTINGS.AppLocation), offset=[-100, 0, 0])
# RNA.show_label(camera=models.default_camera, name=True)
RNA.rotate([0, 1, 1], [0, 3.14, 3.14])
nucleotide_atoms = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]
NUCL_1 = RNA.divide(nucleotide_atoms, 'nucleotide_1')
NUCL_2 = RNA.divide(nucleotide_atoms, 'nucleotide_2')
NUCL_3 = RNA.divide(nucleotide_atoms, 'nucleotide_3')
NUCL_4 = RNA.divide(nucleotide_atoms, 'nucleotide_4')
NUCL_5 = RNA.divide(nucleotide_atoms, 'nucleotide_5')
NUCL_6 = RNA.divide(nucleotide_atoms, 'nucleotide_6')
NUCL_7 = RNA.divide(nucleotide_atoms, 'nucleotide_7')
if step < 15:
RNA.move_to([0, 0, 0])
return Scene(Camera('location', [0, 0, -50], 'look_at', [0, 0, 0]),
objects=[models.default_light] + NUCL_1.povray_molecule + NUCL_4.povray_molecule)
def molecule():
""" Creates a molecule for rendering """
global VIAGRA
VIAGRA = pdb.PDBMolecule('{}/pdb/viagra.pdb'.format(SETTINGS.AppLocation),
center=True)
VIAGRA.move_offset([0, 1, 0])
VIAGRA.scale_atom_distance(1.75)
def alphains_bonded_to_alphact(frame, alphact_stage_two_sliced):
INSULIN_RECEPTOR = pdb.PDBMolecule(PATH_PDB, center=False)
INSULIN_RECEPTOR.move_to([0,0,0])
alphact_complex_insulinalpha_pos = alphact_stage_two_sliced + ATOM_POS["N"] #create a list of atom positions from insulin and the peptide
#create a molecule that is insulin in complex with the peptide
alphact_complex_insulinalpha_mol = INSULIN_RECEPTOR.divide(alphact_complex_insulinalpha_pos, 'alphact_complex_insulinalpha')
return alphact_complex_insulinalpha_mol
def molecule_maker(mol1, mol2, name):
"""Combines two molecules into one"""
combo = mol1.atoms
while len(mol2.atoms) > 0:
combo += [mol2.atoms.pop(0)]
final_combo = pdb.PDBMolecule(name, atoms=combo, center=False)
final_combo.render_molecule()
return final_combo
def create_molecules():
""" Creates the molecules """
global NUCL_1, NUCL_2, NUCL_3, NUCL_4, NUCL_5, NUCL_6, NUCL_7, RNA_2, RNA_1
# Create first RNA molecule
RNA_1 = pdb.PDBMolecule('{}/pdb/RNA.pdb'.format(SETTINGS.AppLocation))
RNA_1.rotate([0, 1, 1], [0, pi, pi])
# Create second RNA molecule
RNA_2 = pdb.PDBMolecule('{}/pdb/RNA.pdb'.format(SETTINGS.AppLocation))
RNA_2.rotate([0, 1, 1], [0, pi, pi])
# Create RNA molecule for the making of nucleotides
rna_to_nucl = pdb.PDBMolecule('{}/pdb/RNA.pdb'.format(
SETTINGS.AppLocation))
rna_to_nucl.rotate([0, 1, 1], [0, pi, pi])
# Determine which atoms make the nucelotides
nucleotide_atoms = [
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31
]
# Creating all the different molecules
NUCL_1 = rna_to_nucl.divide(nucleotide_atoms,
'nucleotide_1',
offset=[-70, 0, 0])
NUCL_2 = rna_to_nucl.divide(nucleotide_atoms,
'nucleotide_2',
offset=[-70, 0, 0])
NUCL_3 = rna_to_nucl.divide(nucleotide_atoms,
'nucleotide_3',
offset=[-70, 0, 0])
NUCL_4 = rna_to_nucl.divide(nucleotide_atoms,
'nucleotide_4',
offset=[-70, 0, 0])
NUCL_5 = rna_to_nucl.divide(nucleotide_atoms,
'nucleotide_5',
offset=[-70, 0, 0])
NUCL_6 = rna_to_nucl.divide(nucleotide_atoms,
'nucleotide_6',
offset=[-70, 0, 0])
NUCL_7 = rna_to_nucl.divide(nucleotide_atoms,
'nucleotide_7',
offset=[-70, 0, 0])
def insulin_bonded_to_ectodomain(frame):
"""
Showing the complete ectodomain of the insulin receptor in complex with one insulin molecule
"""
light = LightSource([0, 0, -100], 'color', [1, 1, 1])
INSULIN_RECEPTOR = pdb.PDBMolecule(PATH_PDB, center=False)
INSULIN_RECEPTOR.move_to([0,0,0])
return INSULIN_RECEPTOR, light
def alphains_binding_alphact(frame, alphact_stage_two_sliced):
INSULIN_RECEPTOR = pdb.PDBMolecule(PATH_PDB, center=False)
INSULIN_RECEPTOR.move_to([0,0,0])
alphact_stage_two_sliced_mol = INSULIN_RECEPTOR.divide(alphact_stage_two_sliced, 'alphact_two')
insulin_alpha = INSULIN_RECEPTOR.divide(ATOM_POS["N"], "insulin_alpha")
frame_start = 330
insulin_offset = (60 - ( frame - frame_start + 1)) / 2 #move the insulin towards the alpha peptide
insulin_alpha.move_offset([0,insulin_offset,0])
return alphact_stage_two_sliced_mol, insulin_alpha
def amino_maker(triplet):
"""Genereerd een aminozuur bij een triplet.
args: triplet: Het triplet waar het aminozuur bij ge genereerd moet worden.
return: De PDBMolecule van het aminozuur"""
locatie = '{a}/pdbeind/{b}.pdb'
aminozuur = bintemplate.TRIPLETTOAMINO[triplet]
amino = pdb.PDBMolecule(locatie.format(a=SETTINGS.AppLocation,
b=aminozuur),
center=True)
return amino
def scene_objects():
""" Creates molecule objects and any other pre-calculated data """
global ETHANOL, VIAGRA, BENZENE, RAD_PER_SCENE, FRONT_LIGHT
FRONT_LIGHT = LightSource([0, 14, -28], 'color', [1, 0.8, 0.4],
'fade_distance', 6, 'fade_power', 2,
'area_light', 3, 3, 12, 12,
'circular orient adaptive', 0)
# Calculate the radians per scene
RAD_PER_SCENE = (math.pi / 180) * 3
# Read in a PDB file and construct a molecule
ETHANOL = pdb.PDBMolecule('pdb/ethanol.pdb',
center=False,
offset=[-10, 8, -5])
VIAGRA = pdb.PDBMolecule('pdb/viagra.pdb',
center=False,
offset=[3, -3, -7])
BENZENE = pdb.PDBMolecule('pdb/benzene.pdb',
center=False,
offset=[0, 8, -5])
def bind_insuline_complete_ectodomain(frame):
"""
Animating the insuline binding to the insulin receptor ectodomain part
"""
light = LightSource([0, 0, -100], 'color', [1, 1, 1])
INSULIN_RECEPTOR = pdb.PDBMolecule(PATH_PDB, center=False) #create a the insulin receptor molecule from the pdb-file
INSULIN_RECEPTOR.move_to([0,0,0]) #move the insulin receptor to the middle of the simulation
insulin = INSULIN_RECEPTOR.divide(INSULIN_ATOM, 'insulin') #create the insulin molecule by dividing the insulin receptor
y = 120 - ( 2 * (frame - 180) ) #setting a y-coordinate for insulin so it moves to the receptor
insulin.move_offset([0, y, 0]) #move the insulin from its original pos to one with the y-coordinate
return INSULIN_RECEPTOR, insulin, light
def frame(step):
global LIPID
LIPID = pdb.PDBMolecule('{}/pdb/lipid_test.pdb'.format(
SETTINGS.AppLocation),
offset=[-100, 0, 0])
# RNA.show_label(camera=models.default_camera, name=True)
# RNA.rotate([0, 1, 1], [0, 3.14, 3.14])
if step < 15:
LIPID.move_to([0, 0, 0])
return Scene(Camera('location', [0, 0, -350], 'look_at', [0, 0, 0]),
objects=[models.default_light] + LIPID.povray_molecule)
def create_molecules():
""" Creates the molecules """
global GTP, GUANINE
GTP = pdb.PDBMolecule('{}/pdb/gtp.pdb'.format(SETTINGS.AppLocation),
center=True)
GTP.rotate([1, 1, 1], [pi * 1.5, pi, pi / 2])
GTP.divide([11, 12, 13, 14, 15, 16, 17, 18], 'phosphate', offset=[
0, 0, 0
]) # removes two phosphate groups to create guanine nucleotide
GUANINE = GTP.divide(
[13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 34, 35],
'guanine',
offset=[4, 0, 0]) # splits into ribose-phosphate and the guanine base
def scene_objects():
""" Creates molecule objects and any other pre-calculated data """
global ATP, FRONT_LIGHT
# Create a light source including some effects
FRONT_LIGHT = LightSource([0, 5, -29], 'color', [1, 1, 1],
'fade_distance', 15, 'fade_power', 2,
'area_light', 3, 3, 12, 12,
'circular orient adaptive', 0)
# Read in a PDB file and construct a molecule
ATP = pdb.PDBMolecule('pdb/ATP_ideal.pdb', center=False)
# Move to the center, and raise a little
ATP.move_to([0, 6, 0])
# Rotate so that the N-tail points downwards a bit
ATP.rotate([0, 1, 1], [0, 1.5, -0.7])
def frame(step):
""" Renders an ATP molecule centered in the scene """
# Feedback to user in terminal about render status
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Calculates the total frames
n_frames = eval(SETTINGS.NumberFrames)
# Calculates distance per frame for the to be splitted molecule parts
x_start = 0
x_end = 8
x_distance = x_end - x_start
x_distance_per_frame = (x_distance / (n_frames / 2))
# Variables used for rotating of molecules
full_circle = 2 * pi # One full circle equals exactly 2 times pi
rotation_per_frame = full_circle / (n_frames / 2)
# creating the nucleotide
gtp = pdb.PDBMolecule('{}/pdb/gtp.pdb'.format(SETTINGS.AppLocation),
center=True)
gtp.rotate([1, 1, 1], [pi * 1.5, pi, pi / 2])
gtp.divide([11, 12, 13, 14, 15, 16, 17, 18], 'phosphate', offset=[
0, 0, 0
]) # removes two phosphate groups to create guanine nucleotide
guanine = gtp.divide(
[13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 34, 35],
'base',
offset=[4, 0, 0]) # splits into ribose-phosphate and the gaunine base
# In the first half of the animation: split the guanine nucleotide into guanine and ribose-phosphate
if step in range(0, n_frames // 2):
gtp.move_to([-step * x_distance_per_frame, 0, 0])
guanine.move_to([step * x_distance_per_frame, 0, 0])
# In the second half of the animation: rotate both molecules one full circle
if step in range(n_frames // 2, n_frames):
gtp.rotate([0, 1, 0], rotation_per_frame * (step - (n_frames / 2)))
guanine.rotate([1, 0, 0], rotation_per_frame * (step - (n_frames / 2)))
gtp.move_to([-n_frames // 2 * x_distance_per_frame, 0, 0])
guanine.move_to([n_frames // 2 * x_distance_per_frame, 0, 0])
# Return the Scene object for rendering
return Scene(models.floor_camera,
objects=[models.default_light] + gtp.povray_molecule +
guanine.povray_molecule)
def scene_objects():
""" Creates molecule objects and any other pre-calculated data """
global ETHANOL, RAD_PER_SCENE, FRONT_LIGHT, TRACER
FRONT_LIGHT = LightSource([0, 14, -28], 'color', [1, 0.8, 0.4],
'fade_distance', 6, 'fade_power', 2,
'area_light', 3, 3, 12, 12,
'circular orient adaptive', 0)
# Calculate the radians per scene (one full rotation)
RAD_PER_SCENE = (math.pi / eval(pypovray.SETTINGS.NumberFrames)) * 2
# Create a list holding the 'tracing' spheres that are drawn as the molecule moves
TRACER = []
# Read in a PDB file and construct a molecule
ETHANOL = pdb.PDBMolecule('pdb/ethanol.pdb',
center=False,
offset=[-10, 8, -5])
def nucleo_maker(nucleo_str):
"""Voegt voor elke nucleotide in de nucleotide string een 3d structuur en voegt deze
aan een list toe.
Args: nucleo_str: een string van nucleotiden"""
global nucleomoddel_list
naam = ""
for nucleotide in nucleo_str:
if nucleotide == 'A':
naam = '{}/pdbeind/Adenine.pdb'
elif nucleotide == 'U':
naam = '{}/pdbeind/Uracil.pdb'
elif nucleotide == 'C':
naam = '{}/pdbeind/Guanine.pdb'
elif nucleotide == 'G':
naam = '{}/pdbeind/Thymine.pdb'
nucleomoddel_list.append(
pdb.PDBMolecule(naam.format(SETTINGS.AppLocation), center=True))
def create_molecules():
""" Creates the molecules """
global NUCL_1, NUCL_2, NUCL_3, NUCL_4, NUCL_5, NUCL_6, NUCL_7, RNA
RNA = pdb.PDBMolecule('{}/pdb/RNA2.pdb'.format(SETTINGS.AppLocation)) #, offset=[-100, 0, 0])
# RNA.show_label(camera=models.default_camera, name=True)
RNA.rotate([0, 1, 1], [0, pi, pi])
nucleotide_atoms = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]
NUCL_1 = RNA.divide(nucleotide_atoms, 'nucleotide_1', offset=[-50, 0, 0])
NUCL_2 = RNA.divide(nucleotide_atoms, 'nucleotide_2', offset=[-50, 0, 0])
NUCL_3 = RNA.divide(nucleotide_atoms, 'nucleotide_3', offset=[-50, 0, 0])
NUCL_4 = RNA.divide(nucleotide_atoms, 'nucleotide_4', offset=[-50, 0, 0])
NUCL_5 = RNA.divide(nucleotide_atoms, 'nucleotide_5', offset=[-50, 0, 0])
NUCL_6 = RNA.divide(nucleotide_atoms, 'nucleotide_6', offset=[-50, 0, 0])
NUCL_7 = RNA.divide(nucleotide_atoms, 'nucleotide_7', offset=[-50, 0, 0])
def frame(step):
""" Returns the scene at step number (1 step per frame) """
# Show some information about how far we are with rendering
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Getting the total number of frames, see the configuration file
nframes = eval(SETTINGS.NumberFrames)
# Create molecule
atp = pdb.PDBMolecule('{}/pdb/ATP_ideal.pdb'.format(SETTINGS.AppLocation),
center=True)
atp.move_to([0, 5, 0])
# Creates phospate sliced molecule
phosphate = atp.divide([0, 1, 2, 3, 7, 31, 32], 'phosphate')
# Creates other objects
camera = Camera('location', [25, 5, 10], 'look_at', [0, 5, 0])
light = LightSource([25, 5, 10], 'color', [1, 1, 1])
# Splicing the molecules animation
if step <= 20 and step > 5:
y = (0 - 4 / 15) * (step - 5) # Moves for 15 frames, -4x in total
phosphate.move_offset([0, y, 0])
# Keeping the phospate in it's position after it moved
elif step > 5:
y = (0 - 4 / 15) * (
20 - 5) # Moves it like the 20th frame to keep it's position
phosphate.move_offset([0, y, 0])
# Rotating the molecules
if step >= 30 and step < 70:
phosphate.rotate([1, 0, 0], np.pi * 2 / 40 *
(step - 30)) # Rotates it for 40 frames, 1 - 2pi
atp.rotate([0, 1, 0], np.pi * 2 / 40 * (step - 30))
# Return the Scene object containing all objects for rendering
return Scene(
camera,
objects=[models.checkered_ground, models.default_light, light] +
atp.povray_molecule + phosphate.povray_molecule)
def molecules():
''' Creates molecules and contains other constants '''
global Molecule_name
Molecule_name = pdb.PDBMolecule('{}/pdb/nameofyourmolecule.pdb'.format(
SETTINGS.AppLocation),
center=True)
def create_ethanol():
from pypovray import pypovray, SETTINGS, models, logger, pdb
from vapory import Sphere, Scene, LightSource, Camera
path = "/homes/kdijkstra/thema2/pdb/ethanol.pdb"
ethanol = pdb.PDBMolecule(path, center=False, offset=[-10, 8, -5])
return ethanol
def frame(step):
""" Returns the scene at step number (1 step per frame) """
# Show some information about how far we are with rendering
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Getting the total number of frames, see the configuration file
nframes = eval(SETTINGS.NumberFrames)
if step < 31:
ins_id, atom_pos = get_ins(PATH_LINUX)
camera = Camera('location', [0, 0, -300], 'look_at', [0, 0, 0])
light = LightSource([0, 0, -100], 'color', [1, 1, 1])
insulin_pos = atom_pos["N"] + atom_pos["O"]
#these need to be removed because the used insulin (b chain) is from a sheep, for humans the last aa must be removed
insulin_pos.remove(9997)
insulin_pos.remove(9998)
insulin_pos.remove(9999)
insulin_pos.remove(10000)
insulin_pos.remove(10001)
insulin_pos.remove(10002)
INSULIN_RECEPTOR = pdb.PDBMolecule(PATH_LINUX,
center=False,
offset=[-10, 8, -5])
INSULIN_RECEPTOR.move_to([0, 0, 0])
insulin = INSULIN_RECEPTOR.divide(insulin_pos, 'insulin')
#insulin.move_to([-100,0,0])
x = (30 * 0.1) - (0.1 * step)
y = (30 * 2) - (2 * step)
insulin.move_offset([x, y, 0])
if step > 30:
camera = Camera('location', [-40, 0, -200], 'look_at', [0, 0, 0])
light = LightSource([0, 0, -100], 'color', [1, 1, 1])
ins_id, atom_pos = get_ins(PATH_LINUX)
alphact = atom_pos["P"]
alphact_stage_one_sliced = []
alphact_stage_two_sliced = []
INSULIN_RECEPTOR = pdb.PDBMolecule(PATH_LINUX,
center=False,
offset=[-10, 8, -5])
INSULIN_RECEPTOR.move_to([0, 0, 0])
for pos in alphact:
if pos in range(10014, 10171):
alphact_stage_one_sliced.append(pos)
if pos in range(10115, 10211):
alphact_stage_two_sliced.append(pos)
if step == 31:
alphact_stage_one_sliced_mol = INSULIN_RECEPTOR.divide(
alphact_stage_one_sliced, 'alphact_one')
alphact_stage_one_sliced_mol.move_to([0, 0, 0])
if step == 32:
alphact_stage_one_sliced_mol = INSULIN_RECEPTOR.divide(
alphact_stage_two_sliced, "alphact_two")
alphact_stage_one_sliced_mol.move_to([0, 0, 0])
if step == 33:
alphact_stage_one_sliced += atom_pos["N"]
alphact_stage_one_sliced_mol = INSULIN_RECEPTOR.divide(
alphact_stage_one_sliced, 'alphact_one')
alphact_stage_one_sliced_mol.move_to([0, 0, 0])
if step == 34:
alphact_stage_two_sliced += atom_pos["N"]
alphact_stage_one_sliced_mol = INSULIN_RECEPTOR.divide(
alphact_stage_two_sliced, "alphact_two")
alphact_stage_one_sliced_mol.move_to([0, 0, 0])
if step == 35:
alphact_stage_two_sliced_mol = INSULIN_RECEPTOR.divide(
alphact_stage_two_sliced, "alphact_two")
insulin_alpha = INSULIN_RECEPTOR.divide(atom_pos["N"],
"alphact_two")
alphact_stage_two_sliced_mol.move_to([0, 0, 0])
insulin_alpha.move_to([50, 0, 0])
return Scene(camera,
objects=[light] + insulin_alpha.povray_molecule +
alphact_stage_two_sliced_mol.povray_molecule)
#simulation
step_start = 36
if step >= step_start:
if step <= step_start + 10:
for num in range(10014, 10115):
if num < (step - step_start) * round(101 / 10) + 10014:
if num not in alphact_stage_two_sliced:
alphact_stage_one_sliced.remove(num)
for num in range(10171, 10211):
if num < (step - step_start) * round(40 / 10) + 10171:
alphact_stage_one_sliced.append(num)
alphact_stage_one_sliced_mol = INSULIN_RECEPTOR.divide(
alphact_stage_one_sliced, 'alphact_one')
rotation = (step - step_start - 10) * -0.1
alphact_stage_one_sliced_mol.rotate([0, 0, 1], rotation)
insulin_alpha = INSULIN_RECEPTOR.divide(
atom_pos["N"], "alphact_two")
insulin_alpha.move_offset([0, 30, 0])
return Scene(camera,
objects=[light] +
alphact_stage_one_sliced_mol.povray_molecule +
insulin_alpha.povray_molecule)
elif step > step_start + 10 and step <= step_start + 20:
alphact_stage_two_sliced_mol = INSULIN_RECEPTOR.divide(
alphact_stage_two_sliced, "alphact_two")
return Scene(camera,
objects=[light] +
alphact_stage_two_sliced_mol.povray_molecule)
return Scene(camera,
objects=[light] +
alphact_stage_one_sliced_mol.povray_molecule)
__author__ = 'Gijs Bakker, Niek Scholten'
import sys
from math import pi
import nonpov
import bintemplate
from pypovray import pypovray, SETTINGS, pdb
from vapory import Scene, Camera, LightSource
nucleomoddel_list = []
triplet_list = []
key_cycle = 0
aminomoddel_list = []
AMINO_AFSTAND = 41
key = pdb.PDBMolecule('{}/pdbeind/tRNA.pdb'.format(SETTINGS.AppLocation),
center=True)
def nucleo_maker(nucleo_str):
"""Voegt voor elke nucleotide in de nucleotide string een 3d structuur en voegt deze
aan een list toe.
Args: nucleo_str: een string van nucleotiden"""
global nucleomoddel_list
naam = ""
for nucleotide in nucleo_str:
if nucleotide == 'A':
naam = '{}/pdbeind/Adenine.pdb'
elif nucleotide == 'U':
naam = '{}/pdbeind/Uracil.pdb'
elif nucleotide == 'C':
naam = '{}/pdbeind/Guanine.pdb'
def create_molecules():
""" Creates the molecules """
global GUANINE, ADENINE
GUANINE = pdb.PDBMolecule('{}/pdb/GMP.pdb'.format(SETTINGS.AppLocation), offset=[-100, 0, 0])
ADENINE = pdb.PDBMolecule('{}/pdb/AMP.pdb'.format(SETTINGS.AppLocation), offset=[-100, 0, 0])
