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from __future__ import division
import sys
import time
from math import sin, cos, pi, sqrt
from shelxfile import Shelxfile
from shelxfile.atoms.atoms import Atoms
"""
This module is a fork from https://github.com/des4maisons/molecule-viewer
"""
class Coordinate2D(object):
def __init__(self, x, y):
self.x = x
self.y = y
def __mul__(self, const):
return Coordinate2D(self.x * const, self.y * const)
def __add__(self, coor):
return Coordinate2D(self.x + coor.x, self.y + coor.y)
def __sub__(self, coor):
return self + coor * (-1)
def __truediv__(self, const):
return self * (1 / const)
def __repr__(self):
return "(%.02f, %.02f)" % (self.x, self.y)
def __str__(self):
return self.__repr__()
class Atom(object):
def __init__(self, x, y, z, symbol, id):
self.coordinate = Coordinate(x, y, z)
self.symbol = symbol
self.id = int(id)
def __repr__(self):
return str((self.symbol, self.id, self.coordinate))
def __str__(self):
return self.__repr__()
def flatten(self, plane=None):
return self.coordinate.flatten(plane)
# Ugly! return symbol in a randomish ansi colour
def coloured_symbol(self):
return "\x1b[" + str(31 + (self.id % 7)) + "m" + self.symbol
class Coordinate(object):
def __init__(self, x, y, z):
self.x, self.y, self.z = [x, y, z]
def __repr__(self):
return "(%.02f, %.02f, %.02f)" % (self.x, self.y, self.z)
def __str__(self):
return self.__repr__()
def __truediv__(self, const):
return self * (1 / const)
def __mul__(self, const):
return Coordinate(self.x * const, self.y * const, self.z * const)
def __add__(self, coor):
return Coordinate(self.x + coor.x, self.y + coor.y, self.z + coor.z)
# regular dot product
def dot(self, vector):
return self.x * vector.x + self.y * vector.y + self.z * vector.z
def length(self):
return sqrt((self.x ** 2) + (self.y ** 2) + (self.z ** 2))
# project self onto 'onto'
def project(self, onto):
length = onto.length()
scale_factor = self.dot(onto) / (length ** 2)
return onto * scale_factor
# cross product
def cross(self, vector):
a1, a2, a3 = [self.x, self.y, self.z]
b1, b2, b3 = [vector.x, vector.y, vector.z]
return Coordinate(a2 * b3 - a3 * b2,
a3 * b1 - a1 * b3,
a1 * b2 - a2 * b1)
# flatten takes a 2-element list of coordinates. When interpreted as vectors,
# these define a plane in 3-dim'l space
def flatten(self, plane=None):
if plane is None: # defaults to x-y plane
plane = [Coordinate(1, 0, 0), Coordinate(0, 1, 0)]
# copy the list
plane = list(plane)
# get 2 perpendicular vectors that define the same plane
perp = plane[0].cross(plane[1])
plane[0] = perp.cross(plane[1])
# make them unit vectors
plane[0] = plane[0] / (plane[0].length())
plane[1] = plane[1] / (plane[1].length())
proj0 = self.project(plane[0])
proj1 = self.project(plane[1])
ratio0 = None
ratio1 = None
# the (signed) number of times the unit vector fits into the projection
# is the 2 dimensional coordinate we want
# so (2,0) == 2 * (1,0), 2 is what we want. don't divide by zero.
for component in ["x", "y", "z"]:
val = getattr(plane[0], component)
if val != 0:
ratio0 = getattr(proj0, component) / val
val = getattr(plane[1], component)
if val != 0:
ratio1 = getattr(proj1, component) / val
if ratio0 is None or ratio1 is None: # if either are 0
raise ValueError("plane defined with zero vector")
return Coordinate2D(ratio0, ratio1)
class Molecule(object):
def __init__(self, shx_atoms: Atoms):
self.atoms = []
for at in shx_atoms:
self.atoms.append(Atom(at.x, at.y, at.z, at.name, at.resinum))
def parse_atom(self, str):
atype, seqnum, elt, one, x, y, z, who, cares = str.split()
self.atoms.append(Atom(float(x), float(y), float(z), elt, int(seqnum)))
# dimensions is 2-tuple of the number of characters on x and y axis
def draw(self, plane=None, dimensions=None):
if dimensions is None:
dimensions = (80, 29)
screen = Screen(dimensions)
flattened = [a.flatten(plane) for a in self.atoms]
max_extreme = Coordinate2D(max([coor.x for coor in flattened]),
max([coor.y for coor in flattened]))
min_extreme = Coordinate2D(min([coor.x for coor in flattened]),
min([coor.y for coor in flattened]))
span = max_extreme - min_extreme
# make everything fit in our dimensions while maintaining proportions
scale_factor = min((screen.width - 1) / span.x, (screen.height - 1) / span.y)
extra_space = Coordinate2D(screen.width - 1, screen.height - 1) - span * scale_factor
offset = extra_space / 2
for atom in self.atoms:
# shift to be in the 1st quadrant (positive coordinates) close to (0,0)
screen_index = (atom.flatten(plane) - min_extreme) * scale_factor
screen_index = screen_index + offset
screen_index = (int(round(screen_index.x)), int(round(screen_index.y)))
screen.set(screen_index, atom.coloured_symbol())
screen.show()
class Screen(list):
def __init__(self, widthheight):
list.__init__(self)
self.width = widthheight[1]
self.height = widthheight[0]
for i in range(self.width):
self.append([])
for _ in range(self.height):
self[i].append(" ")
def set(self, index, val):
x = index[0]
y = index[1]
self[x][y] = val
def show(self):
for row in self:
print("".join(row))
if __name__ == "__main__":
shx = Shelxfile()
shx.read_file('./tests/resources/p21c.res')
try:
width = sys.argv[2]
height = sys.argv[3]
dims = (int(width), int(height) - 1)
except IndexError:
dims = None
angle = 0
angle_incr = (2 * pi) * (1 / 40) # 40th of a circle
while True:
Molecule(shx.atoms).draw(plane=[Coordinate(0, 1, 0), Coordinate(sin(angle), 0, cos(angle))], dimensions=dims)
angle = angle + angle_incr
time.sleep(0.5)
print("\33[H")
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