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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 | import os
from subprocess import Popen, PIPE
from input_output.read_msms import read_msms
from triangulation.xyzrn import output_pdb_as_xyzrn
from default_config.global_vars import msms_bin
from default_config.masif_opts import masif_opts
import random
"""
Modified from:
computeMSMS.py - MaSIF
Pablo Gainza - LPDI STI EPFL 2019
"""
# Pablo Gainza LPDI EPFL 2017-2019
# Calls MSMS and returns the vertices.
# Special atoms are atoms with a reduced radius.
import time
def computeMSMS(pdb_file, protonate=True, one_cavity=None):
randnum = random.randint(1,10000000) #+ time.time() + os.getpid()
file_base = masif_opts['tmp_dir']+"/msms_"+str(randnum)
out_xyzrn = file_base+".xyzrn"
if protonate:
output_pdb_as_xyzrn(pdb_file, out_xyzrn)
else:
print("Error - pdb2xyzrn is deprecated.")
sys.exit(1)
# Now run MSMS on xyzrn file
FNULL = open(os.devnull, 'w')
if one_cavity is not None:
args = [msms_bin, "-density", "3.0", "-hdensity", "3.0", "-probe", "1.5",\
"-one_cavity", str(1), str(one_cavity),\
"-if",out_xyzrn,"-of",file_base, "-af", file_base]
else:
args = [msms_bin, "-density", "3.0", "-hdensity", "3.0", "-probe",\
"1.5", "-all_components", "-if",out_xyzrn,"-of",file_base, "-af", file_base]
#print msms_bin+" "+`args`
p2 = Popen(args, stdout=PIPE, stderr=PIPE)
stdout, stderr = p2.communicate()
print(stdout, stderr)
vertices, faces, normals, names = read_msms(file_base)
areas = {}
ses_file = open(file_base+".area")
next(ses_file) # ignore header line
for line in ses_file:
fields = line.split()
areas[fields[3]] = fields[1]
# os.system("rm " + file_base + "*")
return vertices, faces, normals, names, areas
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