def atom_information(pdbdata, mode):
#analyze pdb file
parser = PDBParser(QUIET=True, PERMISSIVE=True)
structure = parser.get_structure('model', pdbdata)
#DSSP prediction
pmodel = structure[0]
dssp = DSSP(pmodel, pdbdata)
#Set variables
global coordinates
global color
global radius
global chains
global chain_coords
global chain_colors
if mode == 'cpk':
#list of atoms
atoms = [atom for atom in structure.get_atoms()]
natoms = len(atoms)
#atom coordinates
coordinates = np.array([atom.coord for atom in atoms])
center = centroid(coordinates)
coordinates -= center
#atom color
color = [colorrgba(atom.get_id()) for atom in atoms]
#atom radius
radius = np.array([vrad(atom.get_id()) for atom in atoms])
elif mode == 'aminoacid':
#list of atoms
atoms = [
atom for atom in structure.get_atoms()
if atom.get_parent().resname != 'HOH'
]
natoms = len(atoms)
#atom coordinates
coordinates = np.array([atom.coord for atom in atoms])
center = centroid(coordinates)
coordinates -= center
#atom color
color = [
colorrgba(restype(atom.get_parent().resname)) for atom in atoms
]
#atom radius
radius = np.array([vrad(atom.get_id()) for atom in atoms])
elif mode == 'backbone':
#list of atoms
atoms = [
atom for atom in structure.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
]
natoms = len(atoms)
#atom coordinates
coordinates = np.array([atom.coord for atom in atoms])
center = centroid(coordinates)
coordinates -= center
#atom color
color = []
#list of arrays of coordinates and colors for each chain
chains = []
chain_colors = []
chain_coords = []
for chain in structure.get_chains():
chains.append(chain)
can_coord = np.array([
atom.coord for atom in chain.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
])
can_coord -= center
chain_coords.append(can_coord)
chain_length = len(can_coord)
chain_color = np.append(np.random.rand(1, 3), [1.0])
chain_colors.append(chain_color)
color.append(np.tile(chain_color, (chain_length, 1)))
if len(chains) > 1:
color = np.concatenate(color)
#atom radius
radius = np.array([vrad(atom.get_id()) for atom in atoms])
elif mode == 'dssp':
#list of atoms
atoms = [
atom for atom in structure.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
]
natoms = len(atoms)
#atom coordinates
coordinates = np.array([atom.coord for atom in atoms])
center = centroid(coordinates)
coordinates -= center
#atom color
struct3 = [dssp[key][2] for key in list(dssp.keys())]
residues = [
residue for residue in structure.get_residues()
if residue.get_resname() in resdict.keys()
]
color = []
for i in range(len(struct3)):
dsspcolor = crgbaDSSP(struct3[i])
n_atoms = len([
atom for atom in residues[i]
if atom.get_name() == 'CA' or atom.get_name() == 'N'
])
color.append(np.tile(dsspcolor, (n_atoms, 1)))
if len(struct3) > 1:
color = np.concatenate(color)
#list of arrays of coordinates and colors for each chain
chains = []
chain_colors = []
chain_coords = []
for chain in structure.get_chains():
chains.append(chain)
chain_color = np.append(np.random.rand(1, 3), [1.0])
chain_colors.append(chain_color)
can_coord = np.array([
atom.coord for atom in chain.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
])
can_coord -= center
chain_coords.append(can_coord)
#atom radius
radius = np.array([vrad(atom.get_id()) for atom in atoms])
def aa2d():
#Seleccionamos los residuos, solo contando los aminoacidos
for resname, residuetype in resdict.iteritems():
residues = [residue for residue in structure.get_residues() if residue.get_resname() == resname]
rescoord = []
color = colorrgba(residuetype)
for residue in residues:
atoms = [atom for atom in residue.get_atoms()]
coordinates = [atom.coord for atom in atoms]
rescoord.append(np.array(coordinates))
if len(rescoord)>1:
rescoord = np.concatenate(rescoord)
if not len(residues)==0:
x, y, z =zip(*rescoord)
ax.scatter(x, y, z, c=color, marker='o')
#Seleccionamos el resto de 'residuos' que ha determinado el parser, sin incluir aguas
residues_1 = [residue for residue in structure.get_residues() if residue.get_resname() != 'HOH']
residues_2 = [residue for residue in structure.get_residues() if residue.get_resname() in resdict.keys()]
residues_pink = list(set(residues_1)-set(residues_2))
rescoordpink = []
for residue in residues_pink:
atomspink = [atom for atom in residue.get_atoms()]
coordinatespink = [atom.coord for atom in atomspink]
rescoordpink.append(np.array(coordinatespink))
if len(rescoordpink)>1:
rescoordpink = np.concatenate(rescoordpink)
xp, yp, zp = zip(*rescoordpink)
ax.scatter(xp, yp, zp, c='pink', marker='o')
ax.axis("off")
plt.show()
def dssp2d():
ax = fig.add_subplot(111, projection='3d')
#Creamos las listas de residuos vinculadas a su prediccion
residues = [residue for residue in structure.get_residues() if residue.get_resname() in resdict.keys()]
struct3 = [dssp[key][2] for key in list(dssp.keys())]
respred = zip(struct3,residues)
#Creamos la nube de puntos por prediccion
for prediction, color in colorsDSSP.iteritems():
residuesp = [residue[1] for residue in respred if residue[0] == prediction]
predcoord_can = []
for residue in residuesp:
atomsp = [atom for atom in residue.get_atoms() if atom.get_name() == 'CA' or atom.get_name() == 'N']
coordinatesp = [atom.coord for atom in atomsp]
predcoord_can.append(np.array(coordinatesp))
if len(predcoord_can)>1:
predcoord_can = np.concatenate(predcoord_can)
if not len(residuesp)==0:
x, y, z = zip(*predcoord_can)
ax.scatter(x, y, z, c=color, marker='o')
#Creamos las cadenas que unen los atomos
for chain in structure.get_chains():
can_atoms = [atom for atom in chain.get_atoms() if atom.get_name() == 'CA' or atom.get_name() == 'N']
can_coordinates = [atom.coord for atom in can_atoms]
x, y, z = zip(*can_coordinates)
ccolor = np.random.rand(3,1)
ax.plot(x, y, z, c=ccolor, linewidth=1)
ax.axis("off")
plt.show()
def aa2d(self):
"""Draws atoms using a colour palette depending on the type of residue"""
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
#Select residues only if they're aminoacids
for resname, residuetype in resdict.iteritems():
residues = [residue for residue in self.structure.get_residues() if residue.get_resname() == resname]
rescoord = []
color = colorrgba(residuetype)
for residue in residues:
atoms = [atom for atom in residue.get_atoms()]
coordinates = [atom.coord for atom in atoms]
rescoord.append(np.array(coordinates))
if len(rescoord)>1:
rescoord = np.concatenate(rescoord)
if not len(residues)==0:
x, y, z =zip(*rescoord)
ax.scatter(x, y, z, c=color, marker='o')
#Select residues that are not aminoacids, skipping water
residues_1 = [residue for residue in self.structure.get_residues() if residue.get_resname() != 'HOH']
residues_2 = [residue for residue in self.structure.get_residues() if residue.get_resname() in resdict.keys()]
residues_pink = list(set(residues_1)-set(residues_2))
rescoordpink = []
for residue in residues_pink:
atomspink = [atom for atom in residue.get_atoms()]
coordinatespink = [atom.coord for atom in atomspink]
rescoordpink.append(np.array(coordinatespink))
if len(rescoordpink)>1:
rescoordpink = np.concatenate(rescoordpink)
xp, yp, zp = zip(*rescoordpink)
ax.scatter(xp, yp, zp, c='pink', marker='o')
ax.axis("off")
plt.show()
def dssp2d(self):
"""Draw CA-N atoms linked by lines, coloured by their tertiary structure prediction"""
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
#Create the residue lists linked to their predictions
residues = [residue for residue in self.structure.get_residues() if residue.get_resname() in resdict.keys()]
struct3 = [self.dssp[key][2] for key in list(self.dssp.keys())]
respred = zip(struct3,residues)
#Create the point cloud depending on the prediction
for prediction, color in colorsDSSP.iteritems():
residuesp = [residue[1] for residue in respred if residue[0] == prediction]
predcoord_can = []
for residue in residuesp:
atomsp = [atom for atom in residue.get_atoms() if atom.get_name() == 'CA' or atom.get_name() == 'N']
coordinatesp = [atom.coord for atom in atomsp]
predcoord_can.append(np.array(coordinatesp))
if len(predcoord_can)>1:
predcoord_can = np.concatenate(predcoord_can)
if not len(residuesp)==0:
x, y, z = zip(*predcoord_can)
ax.scatter(x, y, z, c=color, marker='o')
#Create the chains linking the aminoacids
for chain in self.structure.get_chains():
can_atoms = [atom for atom in chain.get_atoms() if atom.get_name() == 'CA' or atom.get_name() == 'N']
can_coordinates = [atom.coord for atom in can_atoms]
x, y, z = zip(*can_coordinates)
ccolor = np.random.rand(3,1)
ax.plot(x, y, z, c=ccolor, linewidth=1)
ax.axis("off")
plt.show()
def __init__(self):
ShowBase.__init__(self)
self.cloud = False
self.help = False
self.screen_text = []
#Desglosamos archivo PDB
pdbdata = sys.argv[1]
parser = PDBParser(QUIET=True, PERMISSIVE=True)
structure = parser.get_structure('model', pdbdata)
#Hacemos la prediccion DSSP
model = structure[0]
dssp = DSSP(model, pdbdata)
#Creamos los modelos
self.cpknode = render.attachNewNode("CPK")
self.aanode = render.attachNewNode("Aminoacids")
self.bbnode = render.attachNewNode("BackBone")
self.dsspnode = render.attachNewNode("DSSP")
self.nnode = render.attachNewNode("Cloud")
#CPK
for atom in structure.get_atoms():
x, y, z = atom.coord
atomid = atom.get_id()
a = loader.loadModel("data/atom_sphere")
a.setPos(x, y, z)
a.reparentTo(self.cpknode)
a.setColor(colorrgba(atomid))
a.setScale(vrad(atomid))
self.cpknode.flattenStrong()
#Aminoacids
self.residues = [
residue for residue in structure.get_residues()
if residue.get_resname() in resdict.keys()
]
for residue in self.residues:
resid = residue.get_resname()
color = colorrgba(restype(resid))
atoms = [atom for atom in residue.get_atoms()]
for atom in atoms:
x, y, z = atom.coord
atomid = atom.get_id()
a = loader.loadModel("data/atom_sphere")
a.setPos(x, y, z)
a.setColor(color)
a.setScale(vrad(atomid))
a.reparentTo(self.aanode)
self.residues2 = [
residue for residue in structure.get_residues()
if not residue in self.residues and residue.get_resname() != 'HOH'
]
for residue in self.residues2:
atoms = [atom for atom in residue.get_atoms()]
for atom in atoms:
x, y, z = atom.coord
atomid = atom.get_id()
a = loader.loadModel("data/atom_sphere")
a.setPos(x, y, z)
a.setColor(colorrgba(atomid))
a.setScale(vrad(atomid))
a.reparentTo(self.aanode)
self.aanode.flattenStrong()
self.aanode.hide()
#Backbone
for chain in structure.get_chains():
carr = np.random.rand(3, 1)
ccolor = float(carr[0]), float(carr[1]), float(carr[2]), 1.0
can_atoms = [
atom for atom in chain.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
]
can_coordinates = [atom.coord for atom in can_atoms]
for atom in can_atoms:
x, y, z = atom.coord
atomid = atom.get_id()
a = loader.loadModel("data/atom_sphere")
a.setPos(x, y, z)
a.reparentTo(self.bbnode)
a.setColor(ccolor)
a.setScale(vrad(atomid) / 2.5)
lines = LineSegs()
lines.setColor(ccolor)
lines.moveTo(can_coordinates[0][0], can_coordinates[0][1],
can_coordinates[0][2])
for i in range(len(can_atoms))[1:]:
lines.drawTo(can_coordinates[i][0], can_coordinates[i][1],
can_coordinates[i][2])
lines.setThickness(6)
lnode = lines.create()
self.linenp = NodePath(lnode)
self.linenp.instanceTo(self.bbnode)
#Cloud
catoms = [atom for atom in chain.get_atoms()]
for atom in catoms:
x, y, z = atom.coord
atomid = atom.get_id()
a = loader.loadModel("data/atom_sphere")
a.setPos(x, y, z)
a.reparentTo(self.nnode)
a.setColor(ccolor)
a.setScale(vrad(atomid) * 1.1)
self.bbnode.flattenStrong()
self.bbnode.hide()
self.nnode.setTransparency(TransparencyAttrib.MAlpha)
self.nnode.setAlphaScale(0.3)
self.nnode.hide()
#DSSP
self.linenp.instanceTo(self.dsspnode)
self.struct3 = [dssp[key][2] for key in list(dssp.keys())]
for i in range(len(self.struct3)):
dsspcolor = crgbaDSSP(self.struct3[i])
can_atoms = [
atom for atom in self.residues[i]
if atom.get_name() == 'CA' or atom.get_name() == 'N'
]
for atom in can_atoms:
x, y, z = atom.coord
atomid = atom.get_id()
a = loader.loadModel("data/atom_sphere")
a.setPos(x, y, z)
a.reparentTo(self.dsspnode)
a.setColor(dsspcolor)
a.setScale(vrad(atomid) / 2.5)
self.dsspnode.flattenStrong()
self.dsspnode.hide()
#Colocamos la proteina en el centro
self.cpknode.setPos(0, 0, 0)
self.bbnode.setPos(0, 0, 0)
self.aanode.setPos(0, 0, 0)
self.nnode.setPos(0, 0, 0)
#Colocamos la camara en el centro
xc, yc, zc = self.cpknode.getBounds().getCenter()
self.center = xc, yc, zc
self.pradius = self.cpknode.getBounds().getRadius()
self.center_camera()
#Creamos la iluminacion de ambiente
self.ambient = AmbientLight('alight')
self.ambient.setColor(LVecBase4f(0.16, 0.16, 0.17, 1.0))
self.alight = render.attachNewNode(self.ambient)
render.setLight(self.alight)
#Creamos la iluminacion direccional
self.directional = DirectionalLight('dlight')
self.directional.setColor(LVecBase4f(0.8, 0.7, 0.75, 1.0))
self.directional.setShadowCaster(True, 512, 512)
render.setShaderAuto()
self.dlight = render.attachNewNode(self.directional)
self.dlight.setPos(0, -50, 0)
render.setLight(self.dlight)
self.dlight.lookAt(self.cpknode.getBounds().getCenter())
# Post procesado
render.setAntialias(AntialiasAttrib.MAuto)
#Teclado
self.accept('c', self.toggle_cloud)
self.accept('1', self.showmodel, [self.cpknode])
self.accept('2', self.showmodel, [self.aanode])
self.accept('3', self.showmodel, [self.bbnode])
self.accept('4', self.showmodel, [self.dsspnode])
self.accept('x', self.center_camera)
self.accept('arrow_left', self.taskMgr.add,
[self.spinCameraTaskX, "SpinCameraTaskX"])
self.accept('arrow_up', self.taskMgr.add,
[self.spinCameraTaskY, "SpinCameraTaskY"])
self.accept('arrow_down', self.stop_camera)
self.accept('escape', sys.exit)
chain_length = len(can_coord)
chain_color = np.random.rand(1, 3)
chain_colors.append(chain_color)
color.append(np.tile(chain_color, (chain_length, 1)))
chain_radius.append([
vrad(atom.get_id()) for atom in chain.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
])
if len(chains) > 1:
color = np.concatenate(color)
#dssp
color2 = []
struct3 = [dssp[key][2] for key in list(dssp.keys())]
residues = [
residue for residue in structure.get_residues()
if residue.get_resname() in resdict.keys()
]
for i in range(len(struct3)):
dsspcolor = crgbaDSSP(struct3[i])[0:3]
n_atoms = len([
atom for atom in residues[i]
if atom.get_name() == 'CA' or atom.get_name() == 'N'
])
color2.append(np.tile(dsspcolor, (n_atoms, 1)))
if len(struct3) > 1:
color2 = np.concatenate(color2)
#atom radius
radius = [
4 * vrad(atom.get_id()) for atom in atoms
if atom.get_name() == 'CA' or atom.get_name() == 'N'
]
def atom_information(self):
"""Determines the coordinates, colors and sizes of the atoms depending on the mode"""
if self.mode == 'cpk':
#list of atoms
self.atoms = [atom for atom in self.structure.get_atoms()]
self.natoms = len(self.atoms)
#atom coordinates
self.coordinates = np.array([atom.coord for atom in self.atoms])
self.center = centroid(self.coordinates)
self.coordinates -= self.center
#atom color
self.color = [
np.array(colorrgba(atom.get_id())[0:3]) for atom in self.atoms
]
#atom radius
self.radius = [vrad(atom.get_id()) for atom in self.atoms]
elif self.mode == 'aminoacid':
#list of atoms
self.atoms = [
atom for atom in self.structure.get_atoms()
if atom.get_parent().resname != 'HOH'
]
self.natoms = len(self.atoms)
#atom coordinates
self.coordinates = np.array([atom.coord for atom in self.atoms])
self.center = centroid(self.coordinates)
self.coordinates -= self.center
#atom color
self.color = [
colorrgba(restype(atom.get_parent().resname))[0:3]
for atom in self.atoms
]
#atom radius
self.radius = [vrad(atom.get_id()) for atom in self.atoms]
elif self.mode == 'backbone':
#list of atoms
self.atoms = [
atom for atom in self.structure.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
]
self.natoms = len(self.atoms)
#atom coordinates
self.coordinates = np.array([atom.coord for atom in self.atoms])
self.center = centroid(self.coordinates)
self.coordinates -= self.center
#atom color
self.color = []
self.chains = []
for chain in self.structure.get_chains():
self.chains.append(chain)
self.chain_length = len([
atom for atom in chain.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
])
self.chain_color = np.random.rand(1, 3)
self.color.append(
np.tile(self.chain_color, (self.chain_length, 1)))
if len(self.chains) > 1:
self.color = np.concatenate(self.color)
#atom radius
self.radius = [vrad(atom.get_id()) for atom in self.atoms]
elif self.mode == 'dssp':
#list of atoms
self.atoms = [
atom for atom in self.structure.get_atoms()
if atom.get_name() == 'CA' or atom.get_name() == 'N'
]
self.natoms = len(self.atoms)
#atom coordinates
self.coordinates = np.array([atom.coord for atom in self.atoms])
self.center = centroid(self.coordinates)
self.coordinates -= self.center
#atom color
self.struct3 = [
self.dssp[key][2] for key in list(self.dssp.keys())
]
self.residues = [
residue for residue in self.structure.get_residues()
if residue.get_resname() in resdict.keys()
]
self.color = []
for i in range(len(self.struct3)):
self.dsspcolor = crgbaDSSP(self.struct3[i])[0:3]
self.n_atoms = len([
atom for atom in self.residues[i]
if atom.get_name() == 'CA' or atom.get_name() == 'N'
])
self.color.append(np.tile(self.dsspcolor, (self.n_atoms, 1)))
if len(self.struct3) > 1:
self.color = np.concatenate(self.color)
#atom radius
self.radius = [vrad(atom.get_id()) for atom in self.atoms]