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blmol.py
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blmol.py
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"""Scripts for loading molecular geometries into Blender.
Main use is to define the "molecule" object, which can be used to
draw models of molecular coordinates.
Written by Scott Hartley, www.hartleygroup.org and
blog.hartleygroup.org.
Hosted here:
https://github.com/scotthartley/blmol
Some aspects (especially rotating the bond cylinders) based on this
wonderful blog post from Patrick Fuller:
http://patrick-fuller.com/molecules-from-smiles-molfiles-in-blender/
His project is hosted here:
https://github.com/patrickfuller/blender-chemicals
"""
import numpy as np
import time
# Python outside of Blender doesn't play all that well with bpy, so need
# to handle ImportError.
try:
import bpy
import bmesh
bpy_avail = True
except ImportError:
bpy_avail = False
# Dictionary of color definitions (RGB + alpha tuples). Blender RGB
# colors can be conveniently determined by using a uniform png of the
# desired color as a background image, then using the eyedropper. Colors
# with the "_cb" tag are based on colorblind-safe colors as described in
# this Nature Methods editorial DOI:10.1038/nmeth.1618.
COLORS = {
'black': (0, 0, 0, 1.0),
'dark_red': (0.55, 0, 0, 1.0),
'gray': (0.2, 0.2, 0.2, 1.0),
'dark_gray': (0.1, 0.1, 0.1, 1.0),
'green': (0.133, 0.545, 0.133, 1.0),
'dark_green': (0.1, 0.5, 0.1, 1.0),
'indigo': (0.294, 0, 0.509, 1.0),
'light_gray': (0.7, 0.7, 0.7, 1.0),
'orange': (1.0, 0.647, 0, 1.0),
'purple': (0.627, 0.125, 0.941, 1.0),
'red': (0.8, 0, 0, 1.0),
'royal_blue': (0.255, 0.412, 0.882, 1.0),
'white': (1.0, 1.0, 1.0, 1.0),
'yellow': (1.0, 1.0, 0, 1.0),
'violet': (0.561, 0, 1.0, 1.0),
'blue_cb': (0, 0.168, 0.445, 1.0),
'bluish_green_cb': (0, 0.620, 0.451, 1.0),
'orange_cb': (0.791, 0.347, 0, 1.0),
'reddish_purple_cb': (0.800, 0.475, 0.655, 1.0),
'sky_blue_cb': (0.337, 0.706, 0.914, 1.0),
'vermillion_cb': (0.665, 0.112, 0, 1.0),
'yellow_cb': (0.871, 0.776, 0.054, 1.0),
}
ATOMIC_NUMBERS = {
'H': 1,
'LI': 3,
'B': 5,
'C': 6,
'N': 7,
'O': 8,
'F': 9,
'NA': 11,
'MG': 12,
'P': 15,
'S': 16,
'CL': 17,
'K': 19,
'ZN': 30,
'BR': 35,
'RB': 37,
'I': 53,
'CS': 55
}
# Dictionary of Van der Waals radii, by atomic number, from Wolfram
# Alpha.
RADII = {
1: 1.20,
3: 1.82,
5: 1.92, # From wikipedia
6: 1.70,
7: 1.55,
8: 1.52,
9: 1.47,
11: 2.27,
12: 1.73, # From wikipedia
15: 1.80,
16: 1.80,
17: 1.75,
19: 2.75,
30: 1.39, # From wikipedia
35: 1.85,
37: 3.03,
53: 1.98,
55: 3.43
}
# Dictionaries of colors for drawing elements, by atomic number. Used by
# several functions when the `color = 'by_element'` option is passed.
ELEMENT_COLORS = {
1: 'white',
3: 'violet',
5: 'orange',
6: 'gray',
7: 'royal_blue',
8: 'red',
9: 'green',
11: 'violet',
12: 'dark_green',
15: 'orange',
16: 'yellow',
17: 'green',
19: 'violet',
30: 'dark_gray',
35: 'dark_red',
37: 'violet',
53: 'indigo',
55: 'violet'
}
# Conversion factors for 1 BU. Default is typically 1 nm. Assumes
# geometries are input with coords in angstroms.
UNIT_CONV = {
'nm': 0.1,
'A': 1.0
}
def _create_new_material(name, color):
"""Create a new material.
Args:
name (str): Name for the new material (e.g., 'red')
color (tuple): RGB color for the new material (diffuse_color)
(e.g., (1, 0, 0, 1))
Returns:
The new material.
"""
mat = bpy.data.materials.new(name)
mat.diffuse_color = color
mat.roughness = 0.5
mat.specular_color = (1, 1, 1)
mat.specular_intensity = 0.2
return mat
class Atom:
"""A single atom.
Attributes:
at_num (int): The atomic number of the atom.
location (numpy array): The xyz location of the atom, in
Angstroms.
id_num (int): A unique identifier number.
"""
def __init__(self, atomic_number, location, id_num):
self.at_num = atomic_number
self.location = location # np.array
self.id_num = id_num
def draw(self, color='by_element', radius=None, units='nm',
scale=1.0, subsurf_level=2, segments=16):
"""Draw the atom in Blender.
Args:
color (string, ='by_element'): If None, coloring is done by
element. Otherwise specifies the color.
radius (string, =None): If None, draws at the van der Waals
radius. Otherwise specifies the radius in angstroms.
units (sting, ='nm'): 1 BU = 1 nm by default. Can also be
set to angstroms.
scale (float, =1.0): Scaling factor for the atom. Useful
when generating ball-and-stick models.
subsurf_level (int, =2): Subsurface subdivisions that will
be applied.
segments (int, =16): Number of segments in each UV sphere
primitive
Returns:
The blender object.
"""
# The corrected location (i.e., scaled to units.)
loc_corr = tuple(c*UNIT_CONV[units] for c in self.location)
# Work out the sphere radius in BU.
if not radius:
rad_adj = RADII[self.at_num]*UNIT_CONV[units]*scale
else:
rad_adj = radius*UNIT_CONV[units]*scale
# Create sphere as bmesh.
bm = bmesh.new()
bmesh.ops.create_uvsphere(bm,
u_segments=segments,
v_segments=segments,
radius=rad_adj)
for f in bm.faces:
f.smooth = True
# Convert to mesh.
me = bpy.data.meshes.new("Mesh")
bm.to_mesh(me)
bm.free()
# Assign mesh to object and place in space.
atom_sphere = bpy.data.objects.new("atom({})_{}".format(
self.at_num, self.id_num), me)
bpy.context.collection.objects.link(atom_sphere)
atom_sphere.location = loc_corr
# Assign subsurface modifier, if requested
if subsurf_level != 0:
atom_sphere.modifiers.new('Subsurf', 'SUBSURF')
atom_sphere.modifiers['Subsurf'].levels = subsurf_level
# Color atom and assign material
if color == 'by_element':
atom_color = ELEMENT_COLORS[self.at_num]
else:
atom_color = color
if atom_color not in bpy.data.materials:
_create_new_material(atom_color, COLORS[atom_color])
atom_sphere.data.materials.append(bpy.data.materials[atom_color])
return atom_sphere
class Bond:
"""A bond between two atoms.
Attributes:
atom1 (atom): The first atom in the bond.
atom2 (atom): The second atom in the bond.
"""
def __init__(self, atom1, atom2):
self.atom1 = atom1
self.atom2 = atom2
@staticmethod
def _draw_half(location, length, rot_angle, rot_axis, element,
radius=0.2, color='by_element', units='nm',
vertices=64, edge_split=False):
"""Draw half of a bond (static method).
Draws half of a bond, given the location and length. Bonds are
drawn in halves to facilitate coloring by element.
Args:
location (np.array): The center point of the half bond.
length (float): The length of the half bond.
rot_angle (float): Angle by which bond will be rotated.
rot_axis (np.array): Axis of rotation.
element (int): atomic number of element of the bond (for
coloring).
radius (float, =0.2): radius of the bond.
color (string, ='by_element'): color of the bond. If
'by_element', uses element coloring.
units (string, ='nm'): 1 BU = 1 nm, by default. Can change
to angstroms ('A').
vertices (int, =64): Number of vertices in each bond
cylinder.
edge_split (bool, =False): Whether to apply the edge split
modifier to each bond.
Returns:
The new bond (Blender object).
"""
loc_corr = tuple(c*UNIT_CONV[units] for c in location)
len_corr = length * UNIT_CONV[units]
radius_corr = radius * UNIT_CONV[units]
bpy.ops.mesh.primitive_cylinder_add(vertices=vertices,
radius=radius_corr,
depth=len_corr, location=loc_corr,
end_fill_type='NOTHING')
# Generate an orientation matrix from rot_axis to handle changes in
# Blender's API introduced in v 2.8.
rot_matrix_z = rot_axis/np.linalg.norm(rot_axis)
rot_matrix_y = np.cross(rot_matrix_z, [0, 0, 1])
rot_matrix_x = np.cross(rot_matrix_y, rot_matrix_z)
rot_matrix_y = rot_matrix_y/np.linalg.norm(rot_matrix_y)
rot_matrix_x = rot_matrix_x/np.linalg.norm(rot_matrix_x)
rot_matrix = [rot_matrix_x, rot_matrix_y, rot_matrix_z]
bpy.ops.transform.rotate(value=rot_angle, orient_axis='Z',
orient_matrix=rot_matrix,
constraint_axis=(False, False, True))
bpy.ops.object.shade_smooth()
if edge_split:
bpy.ops.object.modifier_add(type='EDGE_SPLIT')
bpy.ops.object.modifier_apply(modifier='EdgeSplit')
if color == 'by_element':
bond_color = ELEMENT_COLORS[element]
else:
bond_color = color
if bond_color not in bpy.data.materials:
_create_new_material(bond_color, COLORS[bond_color])
bpy.context.object.data.materials.append(
bpy.data.materials[bond_color])
return bpy.context.object
def draw(self, radius=0.2, color='by_element', units='nm',
vertices=64, edge_split=False):
"""Draw the bond as two half bonds (to allow coloring).
Args:
radius (float, =0.2): Radius of cylinder in angstroms.
color (string, ='by_element'): Color of the bond. If
'by_element', each half gets element coloring.
units (string, ='nm'): 1 BU = 1 nm, by default. Can change
to angstroms ('A').
vertices (int, =64): Number of vertices in each bond
cylinder.
edge_split (bool, =False): Whether to apply the edge split
modifier to each bond.
Returns:
The bond (Blender object), with both halves joined.
"""
created_objects = []
center_loc = (self.atom1.location + self.atom2.location)/2
bond_vector = self.atom1.location - self.atom2.location
length = np.linalg.norm(bond_vector)
bond_axis = bond_vector/length
cyl_axis = np.array((0, 0, 1))
rot_axis = np.cross(bond_axis, cyl_axis)
# Fix will not draw bond if perfectly aligned along z axis
# because rot_axis becomes (0, 0, 0).
if ((bond_axis == np.array((0, 0, 1))).all()
or (bond_axis == np.array((0, 0, -1))).all()):
rot_axis = np.array((1, 0, 0))
angle = -np.arccos(np.dot(cyl_axis, bond_axis))
start_center = (self.atom1.location + center_loc)/2
created_objects.append(Bond._draw_half(start_center, length/2, angle,
rot_axis, self.atom1.at_num, radius, color,
units, vertices, edge_split))
end_center = (self.atom2.location + center_loc)/2
created_objects.append(Bond._draw_half(end_center, length/2, angle,
rot_axis, self.atom2.at_num, radius, color,
units, vertices, edge_split))
# Deselect all objects in scene.
for obj in bpy.context.selected_objects:
obj.select_set(state=False)
# Select all newly created objects.
for obj in created_objects:
obj.select_set(state=True)
bpy.ops.object.join()
bpy.context.object.name = "bond_{}({})_{}({})".format(
self.atom1.id_num, self.atom1.at_num, self.atom2.id_num,
self.atom2.at_num)
return bpy.context.object
class Molecule:
"""The molecule object.
Attributes:
atoms (list, = []): List of atoms (atom objects) in molecule.
bonds (list, = []): List of bonds (bond objects) in molecule.
"""
def __init__(self, name='molecule', atoms=None, bonds=None):
self.name = name
if atoms is None:
self.atoms = []
else:
self.atoms = atoms
if bonds is None:
self.bonds = []
else:
self.bonds = bonds
def add_atom(self, atom):
"""Adds an atom to the molecule."""
self.atoms.append(atom)
def add_bond(self, a1id, a2id):
"""Adds a bond to the molecule, using atom ids."""
if not self.search_bondids(a1id, a2id):
self.bonds.append(Bond(self.search_atomid(a1id),
self.search_atomid(a2id)))
def search_atomid(self, id_to_search):
"""Searches through atom list and returns atom object
corresponding to (unique) id."""
for atom in self.atoms:
if atom.id_num == id_to_search:
return atom
return None
def search_bondids(self, id1, id2):
"""Searches through bond list and returns bond object
corresponding to (unique) ids."""
for b in self.bonds:
if ((id1, id2) == (b.atom1.id_num, b.atom2.id_num) or
(id2, id1) == (b.atom1.id_num, b.atom2.id_num)):
return b
return None
def draw_bonds(self, caps=True, radius=0.2, color='by_element',
units='nm', join=True, with_H=True, subsurf_level=1,
vertices=64, edge_split=False):
"""Draws the molecule's bonds.
Args:
caps (bool, =True): If true, each bond capped with sphere of
radius at atom position. Make false if drawing
ball-and-stick model using separate atom drawings.
radius (float, =0.2): Radius of bonds in angstroms.
color (string, ='by_element'): Color of the bonds. If
'by_element', each gets element coloring.
units (string, ='nm'): 1 BU = 1 nm, by default. Can change
to angstroms ('A').
join (bool, =True): If true, all bonds are joined together
into a single Bl object.
with_H (bool, =True): Include H's.
subsurf_level (int, =1): Subsurface subdivisions that will
be applied to the atoms (end caps).
vertices (int, =64): Number of vertices in each bond
cylinder.
edge_split (bool, =False): Whether to apply the edge split
modifier to each bond.
Returns:
The bonds as a single Blender object, if join=True.
Otherwise, None.
"""
created_objects = []
for b in self.bonds:
if with_H or (b.atom1.at_num != 1 and b.atom2.at_num != 1):
created_objects.append(b.draw(radius=radius,
color=color,
units=units,
vertices=vertices,
edge_split=edge_split))
if caps:
for a in self.atoms:
if with_H or a.at_num != 1:
created_objects.append(a.draw(color=color,
radius=radius,
units=units,
subsurf_level=subsurf_level))
if join:
# # Deselect anything currently selected.
# for obj in bpy.context.selected_objects:
# obj.select = False
# # Select drawn bonds.
# for obj in created_objects:
# obj.select = True
# Deselect all objects in scene.
for obj in bpy.context.selected_objects:
obj.select_set(state=False)
# Select drawn bonds.
for obj in created_objects:
obj.select_set(state=True)
bpy.ops.object.join()
bpy.context.object.name = self.name + '_bonds'
return bpy.context.object
else:
return None
def draw_atoms(self, color='by_element', radius=None, units='nm',
scale=1.0, join=True, with_H=True, subsurf_level=2,
segments=16):
"""Draw spheres for all atoms.
Args:
color (str, ='by_element'): If 'by_element', uses colors in
ELEMENT_COLORS. Otherwise, can specify color for whole
model. Must be defined in COLORS.
radius (float, =None): If specified, gives radius of all
atoms.
units (str, ='nm'): Units for 1 BU. Can also be A.
join (bool, =True): If true, all atoms are joined together
into a single Bl object.
with_H (bool, =True): Include the hydrogens.
subsurf_level (int, =2): Subsurface subdivisions that will
be applied to the atoms.
segments (int, =16): Number of segments in each UV sphere
primitive
Returns:
The atoms as a single Blender object, if join=True.
Otherwise, None.
"""
# Store start time to time script.
start_time = time.time()
# Holds links to all created objects, so that they can be
# joined.
created_objects = []
# Initiate progress monitor over mouse cursor.
bpy.context.window_manager.progress_begin(0, len(self.atoms))
n = 0
for a in self.atoms:
if with_H or a.at_num != 1:
created_objects.append(a.draw(color=color, radius=radius,
units=units, scale=scale,
subsurf_level=subsurf_level,
segments=segments))
n += 1
bpy.context.window_manager.progress_update(n)
# End progress monitor.
bpy.context.window_manager.progress_end()
if join:
# Deselect all objects in scene.
for obj in bpy.context.selected_objects:
obj.select_set(state=False)
# Select all newly created objects.
for obj in created_objects:
obj.select_set(state=True)
bpy.context.view_layer.objects.active = created_objects[0]
bpy.ops.object.join()
bpy.context.object.name = self.name + '_atoms'
print("{} seconds".format(time.time()-start_time))
return
def read_pdb(self, filename):
"""Loads a pdb file into a molecule object. Only accepts atoms
with Cartesian coords through the ATOM/HETATM label and bonds
through the CONECT label.
Args:
filename (string): The target file.
"""
with open(filename) as pdbfile:
for line in pdbfile:
if line[0:4] == "ATOM":
idnum = int(line[6:11])
atnum = ATOMIC_NUMBERS[line[76:78].strip().upper()]
coords = np.array((float(line[30:38]), float(line[38:46]),
float(line[46:54])))
self.add_atom(Atom(atnum, coords, idnum))
elif line[0:6] == "HETATM":
idnum = int(line[6:11])
atnum = ATOMIC_NUMBERS[line[76:78].strip().upper()]
coords = np.array((float(line[30:38]), float(line[38:46]),
float(line[46:54])))
self.add_atom(Atom(atnum, coords, idnum))
elif line[0:6] == "CONECT":
# Loads atoms as a list. First atom is bonded to the
# remaining atoms (up to four).
atoms = line[6:].split()
for bonded_atom in atoms[1:]:
# print(atoms[0], bonded_atom)
self.add_bond(int(atoms[0]), int(bonded_atom))