extracting and plotting atomic coordinates from pdb file python - regex

Question

I am trying to extract just the alpha carbon coordinates and plot them in a 3D representation. The top half of the following code works fine, but I can't seem to plot my results.
import re
import glob
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
coord = []
pattern = re.compile('ATOM\s{5,}\d+\s{2}CA\s{2,}\w{3}\s\w\s{2,}\d+\s{6}\d+\.\d+\s\d+\.\d+\s{2}\d+\.\d+', flags=re.S)
for file in glob.glob('file_rank_1.pdb'):
with open(file) as fp:
for result in pattern.findall(fp.read()):
output = result[-22:]
coord = " ".join(output.split())
coord = coord.replace(" ",",")
c = coord.split(',')
print(c)
X,Y,Z = (c)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.plot_wireframe(X,Y,Z)
ax.set_xlabel('x axis')
ax.set_ylabel('y axis')
ax.set_zlabel('z axis')
plt.show()
My results from running the above looks like...
['72.438', '109.283', '43.980']
['75.664', '110.907', '45.079']
['74.354', '111.094', '48.594']
['73.380', '107.449', '48.722']
['76.614', '106.603', '46.958']
['79.740', '105.625', '48.895']
['82.425', '107.703', '47.318']
['80.088', '110.405', '46.265']
['78.710', '110.389', '49.818']
['82.235', '110.471', '51.200']
['82.841', '113.550', '49.133']
['79.233', '114.754', '49.675']
['78.633', '113.745', '53.295']
['77.041', '117.182', '53.503']
['73.963', '116.530', '51.505']
['73.696', '113.058', '52.933']
TypeError: Cannot cast array data from dtype('float64') to dtype('<U32') according to the rule 'safe'
The above code opens the graph interface, but it remains blank. There is also a full screen of red file messages from the interactive shell that I left off to try to save space in this question.
How can I plot the numbers found in c? Thanks

Answer 1

There are a few things to point out:
1) In the following block, c is a list of strings not floats.
with open(file) as fp:
for result in pattern.findall(fp.read()):
output = result[-22:]
coord = " ".join(output.split())
coord = coord.replace(" ",",")
c = coord.split(',')
print(c)
You can change them using:
[float(i) for i in c]
2) When you set X,Y,Z = (c), that c is only the last item in the loop. So you should append each c within the loop to collect all coordinates.
3) You might want to use numpy for array manipulations.
So hopefully the following will work:
import re
import numpy as np
import glob
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
points = []
pattern = re.compile('ATOM\s{5,}\d+\s{2}CA\s{2,}\w{3}\s\w\s{2,}\d+\s{6}\d+\.\d+\s\d+\.\d+\s{2}\d+\.\d+', flags=re.S)
for file in glob.glob('file_rank_1.pdb'):
with open(file) as fp:
for result in pattern.findall(fp.read()):
output = result[-22:]
coord = " ".join(output.split())
coord = coord.replace(" ",",")
c = coord.split(',')
c = [float(i) for i in c] # change them to float
points.append(c)
print(c)
X,Y,Z=np.array(points).T
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.plot_wireframe(X,Y,Z)
ax.set_xlabel('x axis')
ax.set_ylabel('y axis')
ax.set_zlabel('z axis')
plt.show()