File size: 2,038 Bytes
10f2621 | 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 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | import os
import numpy
from subprocess import Popen, PIPE
import pymesh
from default_config.global_vars import apbs_bin, pdb2pqr_bin, multivalue_bin
import random
"""
computeAPBS.py: Wrapper function to compute the Poisson Boltzmann electrostatics for a surface using APBS.
Pablo Gainza - LPDI STI EPFL 2019
This file is part of MaSIF.
Released under an Apache License 2.0
"""
def computeAPBS(vertices, pdb_file, tmp_file_base):
"""
Calls APBS, pdb2pqr, and multivalue and returns the charges per vertex
"""
fields = tmp_file_base.split("/")[0:-1]
directory = "/".join(fields) + "/"
filename_base = tmp_file_base.split("/")[-1]
pdbname = pdb_file.split("/")[-1]
args = [
pdb2pqr_bin,
"--ff=parse",
"--whitespace",
"--noopt",
"--apbs-input",
pdbname,
filename_base,
]
p2 = Popen(args, stdout=PIPE, stderr=PIPE, cwd=directory)
stdout, stderr = p2.communicate()
args = [apbs_bin, filename_base + ".in"]
p2 = Popen(args, stdout=PIPE, stderr=PIPE, cwd=directory)
stdout, stderr = p2.communicate()
vertfile = open(directory + "/" + filename_base + ".csv", "w")
for vert in vertices:
vertfile.write("{},{},{}\n".format(vert[0], vert[1], vert[2]))
vertfile.close()
args = [
multivalue_bin,
filename_base + ".csv",
filename_base + ".dx",
filename_base + "_out.csv",
]
p2 = Popen(args, stdout=PIPE, stderr=PIPE, cwd=directory)
stdout, stderr = p2.communicate()
# Read the charge file
chargefile = open(tmp_file_base + "_out.csv")
charges = numpy.array([0.0] * len(vertices))
for ix, line in enumerate(chargefile.readlines()):
charges[ix] = float(line.split(",")[3])
remove_fn = os.path.join(directory, filename_base)
os.remove(remove_fn)
os.remove(remove_fn+'.csv')
os.remove(remove_fn+'.dx')
os.remove(remove_fn+'.in')
os.remove(remove_fn+'-input.p')
os.remove(remove_fn+'_out.csv')
return charges
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