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mogli.py
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mogli.py
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#!/usr/bin/env python
# coding: utf-8
"""
Simple visualization of molecules.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import itertools
import numpy as np
import numpy.linalg as la
try:
import pybel
except ImportError:
pybel = None
import gr3
import glfw
from OpenGL.GL import glEnable, glDisable, glClear, glBindFramebuffer, glViewport,\
GL_FRAMEBUFFER, GL_DEPTH_TEST, GL_DEPTH_BUFFER_BIT, GL_COLOR_BUFFER_BIT,\
GL_MULTISAMPLE
# Atom color rgb tuples (used for rendering, may be changed by users)
ATOM_COLORS = np.array([(0, 0, 0), # Avoid atomic number to index conversion
(255, 255, 255), (217, 255, 255), (204, 128, 255),
(194, 255, 0), (255, 181, 181), (144, 144, 144),
(48, 80, 248), (255, 13, 13), (144, 224, 80),
(179, 227, 245), (171, 92, 242), (138, 255, 0),
(191, 166, 166), (240, 200, 160), (255, 128, 0),
(255, 255, 48), (31, 240, 31), (128, 209, 227),
(143, 64, 212), (61, 225, 0), (230, 230, 230),
(191, 194, 199), (166, 166, 171), (138, 153, 199),
(156, 122, 199), (224, 102, 51), (240, 144, 160),
(80, 208, 80), (200, 128, 51), (125, 128, 176),
(194, 143, 143), (102, 143, 143), (189, 128, 227),
(225, 161, 0), (166, 41, 41), (92, 184, 209),
(112, 46, 176), (0, 255, 0), (148, 255, 255),
(148, 224, 224), (115, 194, 201), (84, 181, 181),
(59, 158, 158), (36, 143, 143), (10, 125, 140),
(0, 105, 133), (192, 192, 192), (255, 217, 143),
(166, 117, 115), (102, 128, 128), (158, 99, 181),
(212, 122, 0), (148, 0, 148), (66, 158, 176),
(87, 23, 143), (0, 201, 0), (112, 212, 255),
(255, 255, 199), (217, 225, 199), (199, 225, 199),
(163, 225, 199), (143, 225, 199), (97, 225, 199),
(69, 225, 199), (48, 225, 199), (31, 225, 199),
(0, 225, 156), (0, 230, 117), (0, 212, 82),
(0, 191, 56), (0, 171, 36), (77, 194, 255),
(77, 166, 255), (33, 148, 214), (38, 125, 171),
(38, 102, 150), (23, 84, 135), (208, 208, 224),
(255, 209, 35), (184, 184, 208), (166, 84, 77),
(87, 89, 97), (158, 79, 181), (171, 92, 0),
(117, 79, 69), (66, 130, 150), (66, 0, 102),
(0, 125, 0), (112, 171, 250), (0, 186, 255),
(0, 161, 255), (0, 143, 255), (0, 128, 255),
(0, 107, 255), (84, 92, 242), (120, 92, 227),
(138, 79, 227), (161, 54, 212), (179, 31, 212),
(179, 31, 186), (179, 13, 166), (189, 13, 135),
(199, 0, 102), (204, 0, 89), (209, 0, 79),
(217, 0, 69), (224, 0, 56), (230, 0, 46),
(235, 0, 38), (255, 0, 255), (255, 0, 255),
(255, 0, 255), (255, 0, 255), (255, 0, 255),
(255, 0, 255), (255, 0, 255), (255, 0, 255),
(255, 0, 255)], dtype=np.float32)/255.0
# Atom numbers mapped to their symbols
ATOM_NUMBERS = {"H": 1, "HE": 2, "LI": 3, "BE": 4, "B": 5, "C": 6, "N": 7,
"O": 8, "F": 9, "NE": 10, "NA": 11, "MG": 12, "AL": 13,
"SI": 14, "P": 15, "S": 16, "CL": 17, "AR": 18, "K": 19,
"CA": 20, "SC": 21, "TI": 22, "V": 23, "CR": 24, "MN": 25,
"FE": 26, "CO": 27, "NI": 28, "CU": 29, "ZN": 30, "GA": 31,
"GE": 32, "AS": 33, "SE": 34, "BR": 35, "KR": 36, "RB": 37,
"SR": 38, "Y": 39, "ZR": 40, "NB": 41, "MO": 42, "TC": 43,
"RU": 44, "RH": 45, "PD": 46, "AG": 47, "CD": 48, "IN": 49,
"SN": 50, "SB": 51, "TE": 52, "I": 53, "XE": 54, "CS": 55,
"BA": 56, "LA": 57, "CE": 58, "PR": 59, "ND": 60, "PM": 61,
"SM": 62, "EU": 63, "GD": 64, "TB": 65, "DY": 66, "HO": 67,
"ER": 68, "TM": 69, "YB": 70, "LU": 71, "HF": 72, "TA": 73,
"W": 74, "RE": 75, "OS": 76, "IR": 77, "PT": 78, "AU": 79,
"HG": 80, "TL": 81, "PB": 82, "BI": 83, "PO": 84, "AT": 85,
"RN": 86, "FR": 87, "RA": 88, "AC": 89, "TH": 90, "PA": 91,
"U": 92, "NP": 93, "PU": 94, "AM": 95, "CM": 96, "BK": 97,
"CF": 98, "ES": 99, "FM": 100, "MD": 101, "NO": 102,
"LR": 103, "RF": 104, "DB": 105, "SG": 106, "BH": 107,
"HS": 108, "MT": 109, "DS": 110, "RG": 111, "CN": 112,
"UUB": 112, "UUT": 113, "UUQ": 114, "UUP": 115, "UUH": 116,
"UUS": 117, "UUO": 118}
# Atom valence radii in Å (used for bond calculation)
ATOM_VALENCE_RADII = np.array([0, # Avoid atomic number to index conversion
230, 930, 680, 350, 830, 680, 680, 680, 640,
1120, 970, 1100, 1350, 1200, 750, 1020, 990,
1570, 1330, 990, 1440, 1470, 1330, 1350, 1350,
1340, 1330, 1500, 1520, 1450, 1220, 1170, 1210,
1220, 1210, 1910, 1470, 1120, 1780, 1560, 1480,
1470, 1350, 1400, 1450, 1500, 1590, 1690, 1630,
1460, 1460, 1470, 1400, 1980, 1670, 1340, 1870,
1830, 1820, 1810, 1800, 1800, 1990, 1790, 1760,
1750, 1740, 1730, 1720, 1940, 1720, 1570, 1430,
1370, 1350, 1370, 1320, 1500, 1500, 1700, 1550,
1540, 1540, 1680, 1700, 2400, 2000, 1900, 1880,
1790, 1610, 1580, 1550, 1530, 1510, 1500, 1500,
1500, 1500, 1500, 1500, 1500, 1500, 1600, 1600,
1600, 1600, 1600, 1600, 1600, 1600, 1600, 1600,
1600, 1600, 1600, 1600, 1600, 1600],
dtype=np.float32)/1000.0
# Prevent unintentional changes
ATOM_VALENCE_RADII.flags.writeable = False
# Atom radii in Å (used for rendering, scaled down by factor 0.4, may be
# changed by users)
ATOM_RADII = np.array(ATOM_VALENCE_RADII, copy=True)*0.4
# Bond radius in Å (used for rendering, may be changed by users)
BOND_RADIUS = 0.1
def _create_rotation_matrix(angle, x, y, z):
""" Creates a 3x3 rotation matrix. """
if la.norm((x, y, z)) < 0.0001:
return np.eye(3, dtype=np.float32)
x, y, z = np.array((x, y, z))/la.norm((x, y, z))
matrix = np.zeros((3, 3), dtype=np.float32)
cos = np.cos(angle)
sin = np.sin(angle)
matrix[0, 0] = x*x*(1-cos)+cos
matrix[1, 0] = x*y*(1-cos)+sin*z
matrix[0, 1] = x*y*(1-cos)-sin*z
matrix[2, 0] = x*z*(1-cos)-sin*y
matrix[0, 2] = x*z*(1-cos)+sin*y
matrix[1, 1] = y*y*(1-cos)+cos
matrix[1, 2] = y*z*(1-cos)-sin*x
matrix[2, 1] = y*z*(1-cos)+sin*x
matrix[2, 2] = z*z*(1-cos)+cos
return matrix
_mouse_dragging = False
_previous_mouse_position = None
_camera = None
def _mouse_move_callback(window, x, y):
""" Mouse move event handler for GLFW. """
global _previous_mouse_position, _camera
if _mouse_dragging and _camera is not None:
width, height = glfw.get_window_size(window)
dx = (x-_previous_mouse_position[0])/width
dy = (y-_previous_mouse_position[1])/height
rotation_intensity = la.norm((dx, dy)) * 2
eye, center, up = _camera
camera_distance = la.norm(center-eye)
forward = (center-eye)/camera_distance
right = np.cross(forward, up)
rotation_axis = (up*dx+right*dy)
rotation_matrix = _create_rotation_matrix(-rotation_intensity,
rotation_axis[0],
rotation_axis[1],
rotation_axis[2])
forward = np.dot(rotation_matrix, forward)
up = np.dot(rotation_matrix, up)
eye = center-forward*camera_distance
_camera = eye, center, up
_previous_mouse_position = (x, y)
def _mouse_click_callback(window, button, status, modifiers):
""" Mouse click event handler for GLFW. """
global _mouse_dragging, _previous_mouse_position
if button == glfw.MOUSE_BUTTON_LEFT:
if status == glfw.RELEASE:
_mouse_dragging = False
_previous_mouse_position = None
elif status == glfw.PRESS:
_mouse_dragging = True
_previous_mouse_position = glfw.get_cursor_pos(window)
class Molecule(object):
"""
A class for storing information about a Molecule. The atomic bonds need to
be explicitly calculated using the calculate_bonds function.
"""
def __init__(self, atomic_numbers, positions):
self.atomic_numbers = atomic_numbers
self.positions = positions
self.bonds = None
self._atomic_radii = None
@property
def atomic_radii(self):
if self._atomic_radii is None:
self._atomic_radii = ATOM_RADII[self.atomic_numbers]
return self._atomic_radii
def calculate_bonds(self, method='radii', param=None):
"""
This function calculates which pair of atoms forms an atomic bond.
Pairs of indices are returned, indicating that the two associated atoms
form a bond.
The method used for this is specified with the parameter 'method'.
Currently two methods are supported:
- using the valence radii of the atoms (optionally multiplied by
param)
- using a constant delta as maximum distance between to bonded atoms
"""
method = method.lower()
if method not in ('radii', 'constant_delta', 'fix_bond'):
raise ValueError("method should be either 'radii' or 'constant "
"delta', not '%s'" % method)
if self.bonds is not None:
# Bonds were calculated for this molecule already.
# Reuse those, if the method and optional parameter are like those
# provided to this function.
if self.bonds.method == method:
if self.bonds.param == param:
return
elif param is None:
# Allow reuse when default param is used.
if method == 'radii' and self.bonds.param == 1.0:
return
if method == 'radii':
radii = ATOM_VALENCE_RADII[self.atomic_numbers]
if param is None:
param = 1.0
if method == 'constant_delta':
if param is None:
raise ValueError("method 'constant_delta' requires param to "
"specify the maximum distance between two "
"atoms to cause a bond between them.")
if method == "fix_bond":
if param is None:
raise ValueError("method 'fix_bond' requires a SMILE expression")
index_pair_list = []
for index, position in enumerate(self.positions):
distance_vectors = self.positions[index+1:] - position
distances_squared = np.sum(np.power(distance_vectors, 2), axis=1)
if method == 'fix_bond':
index_pairs = _smiles2graph(param)
else:
if method == 'radii':
deltas = np.square((radii[index+1:]+radii[index])*param)
elif method == 'constant_delta':
deltas = param**2
nonzero_indices = np.nonzero(distances_squared <= deltas)
num_bonds = len(nonzero_indices[0])
if num_bonds > 0:
index_pairs = np.hstack((np.ones(num_bonds, dtype=np.uint32)
.reshape(num_bonds, 1)*index,
index+1+nonzero_indices[0]
.reshape(num_bonds, 1)))
index_pair_list.append(index_pairs)
if index_pair_list:
index_pairs = np.vstack(index_pair_list)
else:
index_pairs = np.zeros((0, 2))
self.bonds = Bonds(method, param, index_pairs)
class Bonds(object):
"""
A simple class for storing information about atomic bonds in a molecule.
"""
def __init__(self, method, param, index_pairs):
self.method = method
self.param = param
self.index_pairs = index_pairs
def __len__(self):
return len(self.index_pairs)
class UnknownFileFormatException(Exception):
"""
This exception will be raised when read() is called with file name that
cannot be mapped to a known file format.
"""
pass
def read(file_name, file_format=None):
"""
Reads molecules from a file. If available, pybel will be used to read the
file, otherwise only xyz files can be read.
If the file_format is unknown, a UnknownFileFormatException will be raised.
"""
if pybel:
if file_format is None:
file_extension = file_name.split('.')[-1]
if file_extension in pybel.informats.keys():
file_format = file_extension
else:
message = ("The file format {format} is not supported by "
"pybel. If the file extension does not match the "
"actual format, please use the file_format "
"parameter.".format(format=file_extension))
raise UnknownFileFormatException(message)
elif file_format not in pybel.informats.keys():
message = ("The file format {format} is not supported by pybel, so"
"mogli cannot understand it yet. Sorry!"
.format(format=file_format))
raise UnknownFileFormatException(message)
try:
# Try reading the file with the 'b' option set. This speeds up
# file reading dramatically for some formats (e.g. pdb).
# If this fails for some reasons, use pybel.readfile().
molecules = []
conv = pybel.ob.OBConversion()
conv.SetOptions("b".encode('ascii'), conv.INOPTIONS)
success = conv.SetInFormat(file_format.encode('ascii'))
if success:
mol = pybel.ob.OBMol()
has_molecule = conv.ReadFile(mol, file_name.encode('ascii'))
while has_molecule:
num_atoms = mol.NumAtoms()
atomic_numbers = np.zeros(num_atoms, dtype=np.uint8)
positions = np.zeros((num_atoms, 3), dtype=np.float32)
for i, atom in enumerate(pybel.ob.OBMolAtomIter(mol)):
atomic_numbers[i] = atom.GetAtomicNum()
positions[i] = (atom.GetX(), atom.GetY(), atom.GetZ())
molecules.append(Molecule(atomic_numbers, positions))
has_molecule = conv.Read(mol)
except:
molecule_file = pybel.readfile(file_format.encode('ascii'),
file_name.encode('ascii'))
molecules = []
for molecule in molecule_file:
atoms = molecule.atoms
atomic_numbers_iterator = (atom.atomicnum for atom in atoms)
atomic_numbers = np.fromiter(atomic_numbers_iterator,
dtype=np.uint8, count=len(atoms))
positions_iterator = itertools.chain.from_iterable(atom.coords
for atom
in atoms)
positions = np.fromiter(positions_iterator,
dtype=np.float32, count=len(atoms)*3)
positions.shape = (len(atoms), 3)
molecules.append(Molecule(atomic_numbers, positions))
return molecules
else:
if (file_format is 'xyz' or
(file_format is None and file_name.endswith('.xyz'))):
with open(file_name, 'r') as input_file:
file_content = input_file.readlines()
molecules = []
while file_content:
num_atoms = int(file_content[0])
atom_strings = file_content[2:2+num_atoms]
file_content = file_content[2+num_atoms:]
atomic_numbers = [ATOM_NUMBERS[atom_string.split()[0].upper()]
for atom_string
in atom_strings]
positions = np.array([(float(atom_string.split()[1]),
float(atom_string.split()[2]),
float(atom_string.split()[3]))
for atom_string
in atom_strings])
molecules.append(Molecule(atomic_numbers, positions))
return molecules
else:
message = ("Failed to import pybel. Currently mogli only supports "
"xyz files if pybel is not installed.")
raise UnknownFileFormatException(message)
def load(file_name,name,smile,scaling=10,fix=np.array([0,0,0])):
with np.load(file_name) as data:
positions = data[name].reshape(-1,3)*scaling
positions[:,:] = positions[:,:]-fix
return from_numpy(positions,smile)
def from_numpy(array,smile):
"""
array must be of [n,3]
"""
smiles = []
for cha in smile:
if cha.isalpha():
smiles.append(cha)
N = len(smiles)
array = array.reshape(-1,N,3)
atomic_numbers = [ATOM_NUMBERS[atom_string] for atom_string in smiles]
molecules = []
for i in range(array.shape[0]):
molecules.append(Molecule(atomic_numbers,array[i]))
return molecules
def show(molecule, width=500, height=500,
show_bonds=True, bonds_method='radii', bonds_param=None,
camera=None, title='mogli'):
"""
Interactively show the given molecule with OpenGL. By default, bonds are
drawn, if this is undesired the show_bonds parameter can be set to False.
For information on the bond calculation, see Molecule.calculate_bonds.
If you pass a tuple of camera position, center of view and an up vector to
the camera parameter, the camera will be set accordingly. Otherwise the
molecule will be viewed in the direction of the z axis, with the y axis
pointing upward.
"""
global _camera
molecule.positions -= np.mean(molecule.positions, axis=0)
max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
if show_bonds:
molecule.calculate_bonds(bonds_method, bonds_param)
# If GR3 was initialized earlier, it would use a different context, so
# it will be terminated first.
gr3.terminate()
# Initialize GLFW and create an OpenGL context
glfw.init()
glfw.window_hint(glfw.SAMPLES, 16)
window = glfw.create_window(width, height, title, None, None)
glfw.make_context_current(window)
glEnable(GL_MULTISAMPLE)
# Set up the camera (it will be changed during mouse rotation)
if camera is None:
camera_distance = -max_atom_distance*2.5
camera = ((0, 0, camera_distance),
(0, 0, 0),
(0, 1, 0))
camera = np.array(camera)
_camera = camera
# Create the GR3 scene
gr3.setbackgroundcolor(255, 255, 255, 0)
_create_gr3_scene(molecule, show_bonds)
# Configure GLFW
glfw.set_cursor_pos_callback(window, _mouse_move_callback)
glfw.set_mouse_button_callback(window, _mouse_click_callback)
glfw.swap_interval(1)
# Start the GLFW main loop
while not glfw.window_should_close(window):
glfw.poll_events()
width, height = glfw.get_window_size(window)
glViewport(0, 0, width, height)
_set_gr3_camera()
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
gr3.drawimage(0, width, 0, height,
width, height, gr3.GR3_Drawable.GR3_DRAWABLE_OPENGL)
glfw.swap_buffers(window)
glfw.terminate()
gr3.terminate()
def draw(molecule,
xmin=0, xmax=1, ymin=0, ymax=1, width=2000, height=2000,
show_bonds=True, bonds_method='radii', bonds_param=None,
camera=None):
"""
Draw the given molecule with the GR framework. By default, bonds are drawn,
if this is undesired the show_bonds parameter can be set to False.
For information on the bond calculation, see Molecule.calculate_bonds.
If you pass a tuple of camera position, center of view and an up vector to
the camera parameter, the camera will be set accordingly. Otherwise the
molecule will be viewed in the direction of the z axis, with the y axis
pointing upward.
"""
global _camera
molecule.positions -= np.mean(molecule.positions, axis=0)
max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
if show_bonds:
molecule.calculate_bonds(bonds_method, bonds_param)
if camera is None:
camera_distance = -max_atom_distance*2.5
camera = ((0, 0, camera_distance),
(0, 0, 0),
(0, 1, 0))
camera = np.array(camera)
_camera = camera
# Create the GR3 scene
gr3.setbackgroundcolor(255, 255, 255, 0)
_set_gr3_camera()
_create_gr3_scene(molecule, show_bonds)
glEnable(GL_DEPTH_TEST)
gr3.setquality(gr3.GR3_Quality.GR3_QUALITY_OPENGL_16X_SSAA)
gr3.drawimage(xmin, xmax, ymin, ymax,
width, height, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
glBindFramebuffer(GL_FRAMEBUFFER, 0)
glDisable(GL_DEPTH_TEST)
def export(molecule, file_name, width=500, height=500,
show_bonds=True, bonds_method='radii', bonds_param=None,
camera=None):
"""
Draw the given molecule into a given file. The file type is determined by
the file extension, e.g. '.png' or '.html'. By default, bonds are drawn,
if this is undesired the show_bonds parameter can be set to False.
For information on the bond calculation, see Molecule.calculate_bonds.
If you pass a tuple of camera position, center of view and an up vector to
the camera parameter, the camera will be set accordingly. Otherwise the
molecule will be viewed in the direction of the z axis, with the y axis
pointing upward.
"""
global _camera
molecule.positions -= np.mean(molecule.positions, axis=0)
max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
if show_bonds:
molecule.calculate_bonds(bonds_method, bonds_param)
if camera is None:
if _camera is None:
camera_distance = -max_atom_distance*2.5
camera = ((0, 0, camera_distance),
(0, 0, 0),
(0, 1, 0))
else:
camera = _camera
camera = np.array(camera)
_camera = camera
# Create the GR3 scene
gr3.setbackgroundcolor(255, 255, 255, 0)
_set_gr3_camera()
_create_gr3_scene(molecule, show_bonds)
glEnable(GL_DEPTH_TEST)
gr3.setquality(gr3.GR3_Quality.GR3_QUALITY_OPENGL_16X_SSAA)
gr3.export(file_name, width, height)
glBindFramebuffer(GL_FRAMEBUFFER, 0)
glDisable(GL_DEPTH_TEST)
def _smiles2graph(smiles):
onhand = 0
former = 0
root = 0
rootFlag = False
graph = []
for char in smiles:
if char == "(":
root = former
rootflag = True
elif char.isalpha():
if rootFlag:
graph.append([root,onhand])
else:
graph.append([former,onhand])
former = onhand
onhand += 1
elif char == ")":
rootFlag = False
former = root
return np.array(graph[1:])
def _set_gr3_camera():
""" Set the GR3 camera, using the global _camera variable. """
eye, center, up = _camera
gr3.cameralookat(eye[0], eye[1], eye[2],
center[0], center[1], center[2],
up[0], up[1], up[2])
def _create_gr3_scene(molecule, show_bonds=True):
"""
Create the GR3 scene from the provided molecule and - if show_bonds is
True (default) - the atomic bonds in the molecule.
"""
gr3.clear()
num_atoms = len(molecule.atomic_numbers)
gr3.drawspheremesh(num_atoms,
molecule.positions,
ATOM_COLORS[molecule.atomic_numbers],
molecule.atomic_radii)
if show_bonds and len(molecule.bonds.index_pairs) > 0:
index_pairs = molecule.bonds.index_pairs
num_bonds = len(molecule.bonds)
bond_positions = molecule.positions[index_pairs[:, 0]]
bond_directions = molecule.positions[index_pairs[:, 1]]-bond_positions
bond_lengths = la.norm(bond_directions, axis=1)
bond_directions /= bond_lengths.reshape(num_bonds, 1)
bond_radii = np.ones(num_bonds, dtype=np.float32)*BOND_RADIUS
bond_colors = np.ones((num_bonds, 3), dtype=np.float32)*0.3
gr3.drawcylindermesh(num_bonds, bond_positions, bond_directions,
bond_colors, bond_radii, bond_lengths)
def main():
"""
Command line interface
"""
parser = argparse.ArgumentParser()
show_bonds_group = parser.add_mutually_exclusive_group()
show_bonds_group.add_argument('--show_bonds',
action='store_true', default=True,
help='show atomic bonds (default)')
show_bonds_group.add_argument('--hide_bonds',
action='store_false', dest='show_bonds',
help='do not show atomic bonds')
parser.add_argument('-m', '--bond_method',
default='radii', choices=['radii', 'constant_delta'])
parser.add_argument('-p', '--bond_param', default=1.0, type=float)
parser.add_argument('-i', '--molecule', default=0, type=int,
help='the molecule index for files with multiple'
' molecules')
parser.add_argument('-f', '--format', type=str)
parser.add_argument('file_name')
args, unknown = parser.parse_known_args()
if unknown:
print('The following arguments were ignored:')
print(' '.join(unknown))
molecules = read(args.file_name, args.format)
show(molecules[args.molecule],
show_bonds=args.show_bonds,
bonds_method=args.bond_method,
bonds_param=args.bond_param)
if __name__ == '__main__':
main()