1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
#!/usr/bin/env python
import argparse
import numpy as np
from gridData import Grid, OpenDX
def parse_args():
parser = argparse.ArgumentParser(description='Save grid to PDB a given isovalue')
parser.add_argument('input')
parser.add_argument('output')
parser.add_argument('iso', type=float)
return parser.parse_args()
def extractISOPdb(input, output, iso):
g = Grid(input)
# JD: this is clunky but i'm not sure what's a better way
data = np.array(OpenDX.array(3,g.grid).array.flat)
data = data.reshape((len(data)/3, 3))
x, y, z = 0, 0, 0
counter = 1
lines = []
for point in data:
for pos in point:
if (iso<0 and pos < iso) or (iso > 0 and pos > iso) :
line = 'ATOM %5d C PTH 1 %8.3f%8.3f%8.3f%6.2f%6.2f\n'%(counter,g.origin[0]+float(x)*g.delta[0,0],
g.origin[1]+float(y)*g.delta[1,1],
g.origin[2]+float(z)*g.delta[2,2], 0.0,0.0)
lines.append(line)
counter += 1
z+=1
if z >= g.grid.shape[2]:
z=0
y+=1
if y >=g.grid.shape[1]:
y=0
x+=1
with open(output, "w") as f:
f.writelines(lines)
return g
if __name__ == "__main__":
args = parse_args()
g = extractISOPdb(args.input, args.output, args.iso)
|
