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Read_Residue_Data_File_V1.py
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Read_Residue_Data_File_V1.py
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# Created on 2/29/2020 by Staubjr (11:00)
import sys
import numpy as np
import physvis as vis
import matplotlib.pyplot as plt
import os
class atom_builder:
all_atoms = []
def __init__(self, atom_number, atom_type, element, x, y, z):
self.atom_number = atom_number
self.atom_type = atom_type
self.element = element
self.x = float(x)
self.y = float(y)
self.z = float(z)
self.pos = np.array([self.x, self.y, self.z])
atom_builder.all_atoms.append(self)
visual(self)
class bond_builder:
all_bonds = []
def __init__(self, atom1, atom2, number_of_bonds):
self.atom1 = atom1
self.atom2 = atom2
self.number_of_bonds = number_of_bonds
bond_builder.all_bonds.append(self)
visual(self)
class visual:
all_visual_atoms = []
all_visual_bonds = []
atom_colors = { 'carbon' : (0.5, 0.5, 0.5) ,
'hydrogen' : (1., 0., 0.),
'oxygen' : (0., 0., 1.),
'nitrogen' : (1., 0.5, 0.) }
atom_radii = { 'carbon' : 0.25,
'hydrogen' : 0.1,
'oxygen' : 0.35,
'nitrogen' : 0.30 }
bond_color = { 'single' : (0.4, 0.7, 0.9),
'double' : (50/255. , 64/255. , 150/255.) }
def __init__(self, object):
if object.__class__.__name__ == 'atom_builder':
self.atom_object = object
self.visual = vis.sphere(pos = self.atom_object.pos, radius = visual.atom_radii[self.atom_object.element],
color = visual.atom_colors[self.atom_object.element] )
visual.all_visual_atoms.append(self)
if object.__class__.__name__ == 'bond_builder':
self.bond_object = object
if self.bond_object.number_of_bonds == 1:
self.bond_object.bonds = 'single'
if self.bond_object.number_of_bonds == 2:
self.bond_object.bonds = 'double'
self.visual = vis.cylinder(radius = self.bond_object.number_of_bonds * 0.05, pos = self.bond_object.atom1.pos,
axis = self.bond_object.atom2.pos - self.bond_object.atom1.pos,
color = visual.bond_color[self.bond_object.bonds] )
visual.all_visual_bonds.append(self)
def read_txt_file(txt_file):
file_name = str(txt_file)
file = open(file_name, 'r')
rows = file.readlines()
atom_positions = []
bonds = []
for line in rows:
if line[0:5] == str('#Atom'):
atom_position_start = rows.index(line) + 1
if line[0:6] == str('#Bonds'):
atom_position_stop = rows.index(line) - 2
bonds_start = rows.index(line) + 4
bonds_stop = len(rows)
for line in rows[atom_position_start: atom_position_stop + 1]:
values = line.split('\t')
last_value = values[6].strip('\n')
values.pop(6)
values.append(last_value)
atom = atom_builder(values[0], values[1], values[2], values[4], values[5], values[6])
for line in rows[bonds_start: bonds_stop + 1]:
values = line.split('\t')
atoms_in_bond = values[0].split('-')
number_of_bonds = int(values[1].strip('\n'))
formatted_values = []
formatted_values.append(atoms_in_bond[0])
formatted_values.append(atoms_in_bond[1])
formatted_values.append(number_of_bonds)
atom_1_number = formatted_values[0]
atom_2_number = formatted_values[1]
number_of_bonds = formatted_values[2]
for atom in atom_builder.all_atoms:
if atom.atom_number == atom_1_number:
atom_1 = atom
if atom.atom_number == atom_2_number:
atom_2 = atom
bond = bond_builder(atom_1, atom_2, number_of_bonds)
def main():
file_name = str(sys.argv[1])
read_txt_file(file_name)
display = True
disp = vis.scene()
disp.foreground = [1,1,1]
while display == True:
vis.rate(30)
if __name__ == '__main__':
main()