-- This is a port of CineMol to lua
-- CineMol https://github.com/moltools/CineMol was written by David Meijer, Marnix H. Medema & Justin J. J. van der Hooft and is MIT licensed
-- Please consider any edits made to this page as dual licensed MIT & CC-BY-SA 4.0
-- This module provides functions for drawing molecules using atoms and bonds.
local p = {}
local geometry = require( 'Module:CineMol/geometry' )
local style = require( 'Module:CineMol/style' )
local cinemolsvg = require( 'Module:CineMol/svg' )
local model = require( 'Module:CineMol/model' )
local Cylinder = geometry.Cylinder
local CylinderCapType = geometry.CylinderCapType
local Line3D = geometry.Line3D
local Point3D = geometry.Point3D
local Sphere = geometry.Sphere
local get_perpendicular_lines = geometry.get_perpendicular_lines
local checkType = geometry.checkType
local Cartoon = style.Cartoon
local Color = style.Color
local Glossy = style.Glossy
local CoreyPaulingKoltungAtomColor = style.CoreyPaulingKoltungAtomColor
local PubChemAtomRadius = style.PubChemAtomRadius
local Svg = cinemolsvg.Svg
local ViewBox = cinemolsvg.ViewBox
local ModelCylinder = model.ModelCylinder
local ModelSphere = model.ModelSphere
local ModelWire = model.ModelWire
local Scene = model.Scene
p.Style = {
SPACEFILLING = 1,
BALL_AND_STICK = 2,
TUBE = 3,
WIREFRAME = 4
}
local Style = p.Style
p.Look = {
CARTOON = 1,
GLOSSY = 2
}
local Look = p.Look
-- Represents an atom in a molecule.
-- Note: color is not a color object but a plain [r,g,b] table
function p.Atom( index, symbol, coordinates, radius, color, opacity )
checkType( 'Atom', 1, index, 'number' )
checkType( 'Atom', 2, symbol, 'string' )
checkType( 'Atom', 3, coordinates, 'table' )
assert( #coordinates == 3, "Expected 3 coordinates" )
opacity = opacity == nil and 1.0 or opacity
checkType( 'Atom', 6, opacity, 'number' )
return {
_TYPE = 'Atom',
index = index,
symbol = symbol,
coordinates = coordinates,
color = color,
opacity = opacity
}
end
-- A bond between two atoms in a molecule.
-- color is not a Color but a plain table
function p.Bond( start_index, end_index, order, radius, color, opacity )
opacity = opacity == nil and 1.0 or opacity
checkType( 'Bond', 1, start_index, 'number' )
checkType( 'Bond', 2, end_index, 'number' )
checkType( 'Bond', 3, order, 'number' )
checkType( 'Bond', 6, opacity, 'number' )
return {
_TYPE = 'Bond',
start_index = start_index,
end_index = end_index,
order = order,
radius = radius,
color = color,
opacity = opacity
}
end
local function findInTable( table, needle )
for i,v in ipairs( table ) do
if needle == v then
return v
end
end
return false
end
-- Filter atoms and bonds based on the given exclude atoms.
function p.filter_atoms_and_bonds( atoms, bonds, exclude_atoms )
checkType( 'filter_atoms_and_bonds', 1, atoms, 'table' )
checkType( 'filter_atoms_and_bonds', 2, bonds, 'table' )
if exclude_atoms ~= nil then
local filtered_atoms, filtered_bonds, exclude_inds = {}, {}, {}
for _, atom in ipairs( atoms ) do
if findInTable( exclude_atoms, atom.symbol ) == false then
filtered_atoms[#filtered_atoms+1] = atom
else
exclude_inds[#exclude_inds+1] = atom.index
end
end
for _, bond in ipairs( bonds ) do
if findInTable( exclude_inds, bond.start_index ) == false and findInTable( exclude_inds, bond.end_index ) == false then
filtered_bonds[#filtered_bonds+1] = bond
end
end
return filtered_atoms, filtered_bonds
end
return atoms, bonds
end
-- Draw a molecule using the given atoms and bonds in wireframe style.
function p.draw_bonds_in_wireframe_style( scene, atoms, bonds, wire_width )
wire_width = wire_width == nil and 0.05 or wire_width
checkType( 'draw_bonds_in_wireframe_style', 1, scene, 'Scene' )
checkType( 'draw_bonds_in_wireframe_style', 2, atoms, 'table' )
checkType( 'draw_bonds_in_wireframe_style', 3, bonds, 'table' )
checkType( 'draw_bonds_in_wireframe_style', 4, wire_width, 'number' )
local atom_map = {}
for i,v in ipairs( atoms ) do
atom_map[v.index] = v
end
for _, bond in ipairs(bonds) do
-- Get start atom specifications.
local start_atom = atom_map[bond.start_index]
local start_symbol = start_atom.symbol
local start_color = CoreyPaulingKoltungAtomColor:get_color(start_symbol)
local start_pos = Point3D(start_atom.coordinates[1], start_atom.coordinates[2], start_atom.coordinates[3])
-- Get end atom specifications.
local end_atom = atom_map[bond.end_index]
local end_symbol = end_atom.symbol
local end_color = CoreyPaulingKoltungAtomColor:get_color(end_symbol)
local end_pos = Point3D(end_atom.coordinates[1], end_atom.coordinates[2], end_atom.coordinates[3])
-- Determine color of bond.
if bond.color ~= nil then
start_color = Color(bond.color[1], bond.color[2], bond.color[3])
end_color = Color(bond.color[1], bond.color[2], bond.color[3])
else
if start_atom.color ~= nil then
start_color = Color(start_atom.color[1], start_atom.color[2], start_atom.color[3])
end
if end_atom.color ~= nil then
end_color = Color(end_atom.color[1], end_atom.color[2], end_atom.color[3])
end
end
-- If colors are not the same we split the bond down the middle, and
-- draw two separate wires to represent the bond.
if start_color ~= end_color then
local middle_pos = Point3D(
(start_pos.x + end_pos.x) / 2,
(start_pos.y + end_pos.y) / 2,
(start_pos.z + end_pos.z) / 2
)
scene:add_node(
ModelWire(Line3D(start_pos, middle_pos), start_color, wire_width, bond.opacity)
)
scene:add_node(
ModelWire(Line3D(middle_pos, end_pos), end_color, wire_width, bond.opacity)
)
else
scene:add_node(
ModelWire(Line3D(start_pos, end_pos), start_color, wire_width, bond.opacity)
)
end
end
end
function p.draw_atoms_in_spacefilling_style( scene, atoms, look, stroke_color, stroke_width, radius_scale )
radius_scale = radius_scale == nil and 1.0 or radius_scale
checkType( 'draw_atoms_in_spacefilling_style', 1, scene, 'Scene' )
checkType( 'draw_atoms_in_spacefilling_style', 2, atoms, 'table' )
checkType( 'draw_atoms_in_spacefilling_style', 3, look, 'number' )
checkType( 'draw_atoms_in_spacefilling_style', 4, stroke_color, 'Color' )
checkType( 'draw_atoms_in_spacefilling_style', 5, stroke_width, 'number' )
checkType( 'draw_atoms_in_spacefilling_style', 6, radius_scale, 'number' )
for _, atom in ipairs( atoms) do
-- Get atom specifications.
local atom_symbol = atom.symbol
local atom_color = (
atom.color == nil
and CoreyPaulingKoltungAtomColor:get_color(atom_symbol)
or Color(atom.color[1], atom.color[2], atom.color[3])
)
local atom_radius = PubChemAtomRadius:to_angstrom(atom_symbol) * radius_scale
local atom_pos = Point3D(atom.coordinates[1], atom.coordinates[2], atom.coordinates[3])
-- Determine atom look.
local depiction
if look == Look.CARTOON then
depiction = Cartoon(atom_color, stroke_color, stroke_width, atom.opacity)
elseif look == Look.GLOSSY then
depiction = Glossy(atom_color, atom.opacity)
else
error("Unknown look: " .. look)
end
-- Add atom to scene.
scene:add_node(ModelSphere(Sphere(atom_pos, atom_radius), depiction))
end
end
-- Draw a molecule using the given atoms and bonds in tube style.
function p.draw_bonds_in_tube_style( scene, atoms, bonds, tube_bond_style, look, cap_type, stroke_color, stroke_width )
checkType( 'draw_bonds_in_tube_style', 1, scene, 'Scene' )
checkType( 'draw_bonds_in_tube_style', 2, atoms, 'table' )
checkType( 'draw_bonds_in_tube_style', 3, bonds, 'table' )
checkType( 'draw_bonds_in_tube_style', 4, tube_bond_style, 'number' )
checkType( 'draw_bonds_in_tube_style', 5, look, 'number' )
checkType( 'draw_bonds_in_tube_style', 6, cap_type, 'number' )
checkType( 'draw_bonds_in_tube_style', 7, stroke_color, 'Color' )
checkType( 'draw_bonds_in_tube_style', 8, stroke_width, 'number' )
local atom_map = {}
for i,v in ipairs( atoms ) do
atom_map[v.index] = v
end
for _, bond in ipairs(bonds) do
-- Get start atom specifications.
local start_atom = atom_map[bond.start_index]
local start_symbol = start_atom.symbol
local start_color = CoreyPaulingKoltungAtomColor:get_color(start_symbol)
local start_pos = Point3D(start_atom.coordinates[1], start_atom.coordinates[2], start_atom.coordinates[3])
-- Get end atom specifications.
local end_atom = atom_map[bond.end_index]
local end_symbol = end_atom.symbol
local end_color = CoreyPaulingKoltungAtomColor:get_color(end_symbol)
local end_pos = Point3D(end_atom.coordinates[1], end_atom.coordinates[2], end_atom.coordinates[3])
-- Determine color of bond.
if bond.color ~= nil then
start_color = Color(bond.color[1], bond.color[2], bond.color[3])
end_color = Color(bond.color[1], bond.color[2], bond.color[3])
else
if start_atom.color ~= nil then
start_color = Color(start_atom.color[1], start_atom.color[2], start_atom.color[3])
end
if end_atom.color ~= nil then
end_color = Color(end_atom.color[1], end_atom.color[2], end_atom.color[3])
end
end
-- Determine number of cylinders to draw for each bond.
-- Bond order is only used for ball-and-stick style.
local bond_order = tube_bond_style == Style.BALL_AND_STICK and bond.order or 1
local bond_radius = bond.radius ~= nil and bond.radius or 0.2
local temp_bond_radius = bond_radius / bond_order
local line_tmp = Line3D(start_pos, end_pos)
local lines = get_perpendicular_lines(line_tmp, temp_bond_radius * (bond_order + 1), bond_order)
-- Add cylinders to scene.
for __, line in ipairs(lines) do
if start_color ~= end_color then
local middel_pos = Point3D(
(line.start.x + line.endp.x) / 2,
(line.start.y + line.endp.y) / 2,
(line.start.z + line.endp.z) / 2
)
-- First part of bond.
local depiction
if look == Look.CARTOON then
depiction = Cartoon(
start_color, stroke_color, stroke_width, bond.opacity
)
elseif look == Look.GLOSSY then
depiction = Glossy(start_color, bond.opacity)
else
error("Unknown look: " .. look)
end
scene:add_node(
ModelCylinder(
Cylinder(line.start, middel_pos, temp_bond_radius, cap_type), depiction
)
)
-- Second part of bond.
if look == Look.CARTOON then
depiction = Cartoon(end_color, stroke_color, stroke_width, bond.opacity)
elseif look == Look.GLOSSY then
depiction = Glossy(end_color, bond.opacity)
else
error("Unknown look: " .. look)
end
scene:add_node(
ModelCylinder(
Cylinder(middel_pos, line.endp, temp_bond_radius, cap_type), depiction
)
)
else
local depiction
-- Bond as a whole.
if look == Look.CARTOON then
depiction = Cartoon(start_color, stroke_color, stroke_width, bond.opacity)
elseif look == Look.GLOSSY then
depiction = Glossy(start_color, bond.opacity)
else
error("Unknown look: " .. look)
end
scene:add_node(
ModelCylinder(
Cylinder(line.start, line.endp, temp_bond_radius, cap_type), depiction
)
)
end
end
end
end
function p.draw_molecule(
atoms,
bonds,
style,
look,
resolution,
window, -- Possibly doesn't work
view_box,
rotation_over_x_axis,
rotation_over_y_axis,
rotation_over_z_axis,
scale,
focal_length,
exclude_atoms
)
rotation_over_x_axis = rotation_over_x_axis == nil and 0 or rotation_over_x_axis
rotation_over_y_axis = rotation_over_y_axis == nil and 0 or rotation_over_y_axis
rotation_over_z_axis = rotation_over_z_axis == nil and 0 or rotation_over_z_axis
scale = scale == nil and 1 or scale
checkType( 'draw_molecule', 1, atoms, 'table' )
checkType( 'draw_molecule', 2, bonds, 'table' )
checkType( 'draw_molecule', 3, style, 'number' )
checkType( 'draw_molecule', 4, look, 'number' )
checkType( 'draw_molecule', 5, resolution, 'number' )
checkType( 'draw_molecule', 8, rotation_over_x_axis, 'number' )
checkType( 'draw_molecule', 9, rotation_over_y_axis, 'number' )
checkType( 'draw_molecule', 10, rotation_over_z_axis, 'number' )
checkType( 'draw_molecule', 11, scale, 'number' )
local atoms, bonds = p.filter_atoms_and_bonds(atoms, bonds, exclude_atoms)
local scene = Scene({})
-- Default settings for drawing.
local include_spheres = false
local include_cylinders = false
local include_wires = false
local calculate_sphere_sphere_intersections = false
local calculate_sphere_cylinder_intersections = false
local calculate_cylinder_sphere_intersections = false
local calculate_cylinder_cylinder_intersections = false
-- Default settings for cartoon look.
local stroke_color = Color(0, 0, 0)
local stroke_width = 0.05
-- Wire style has a separate implementation that is faster than for geometric shapes.
if style == Style.WIREFRAME then
include_wires = true
p.draw_bonds_in_wireframe_style(scene, atoms, bonds)
elseif style == Style.SPACEFILLING then
include_spheres = true
calculate_sphere_sphere_intersections = true
p.draw_atoms_in_spacefilling_style(scene, atoms, look, stroke_color, stroke_width)
elseif style == Style.BALL_AND_STICK or style == Style.TUBE then
local cap_type
if style == Style.BALL_AND_STICK then
-- We need to draw atoms a spheres and bonds as cylinders for ball-and-stick
-- style.
include_spheres = true
include_cylinders = true
calculate_cylinder_sphere_intersections = true
cap_type = CylinderCapType.NO_CAP
p.draw_atoms_in_spacefilling_style(
scene,
atoms,
look,
stroke_color,
stroke_width,
1.0 / 3.0 -- Lower the radius of the atoms for ball-and-stick style.
)
elseif style == Style.TUBE then
-- For tube we only draw bonds as cylinders and therefore the intersections
-- between spheres and cylinders are not needed. However, we do need to
-- calculate the intersections between cylinders.
include_cylinders = true
calculate_cylinder_cylinder_intersections = true
cap_type = CylinderCapType.ROUND
end
p.draw_bonds_in_tube_style(
scene, atoms, bonds, style, look, cap_type, stroke_color, stroke_width
)
else
error("Unknown style: " .. style)
end
local viewBox = nil
if view_box ~= nil then
viewBox = ViewBox( view_box[1], view_box[2], view_box[3], view_box[4] )
end
-- Draw scene.
local svg = scene:draw(
resolution,
window,
viewBox,
rotation_over_x_axis,
rotation_over_y_axis,
rotation_over_z_axis,
include_spheres,
include_cylinders,
include_wires,
calculate_sphere_sphere_intersections,
calculate_sphere_cylinder_intersections,
calculate_cylinder_sphere_intersections,
calculate_cylinder_cylinder_intersections,
true,
scale,
focal_length
)
return svg
end
return p
