#!/usr/bin/python
import fpdb
import sys, os
traj = 'prod/traj.pdb'
os.system("shift_lig.py")
frame = next(fpdb.next_frame(traj))
with open("prod/a1.pdb", 'w') as ofp:
for line in frame:
ofp.write(line)
with open("prod/rec.pdb", 'w') as ofp:
for resi in fpdb.fPDB(frame).topology.get_protein_residues():
resi.write_pdb(ofp)
n = 0
with open("runspa.bash", 'w') as ofp:
ofp.write("#!/bin/bash\n")
ofp.write("source ~/.bashrc\n")
while True:
if os.path.isdir("spa_%d" % n):
os.system("cp prod/a1.pdb spa_%d" % n)
os.system("cp prod/rec.pdb spa_%d" % n)
os.system("cp lig_shift.pdb spa_%d/a1_lig.pdb" % n)
os.system("cp %s/para/SPA.amoeba.para spa_%d/SPA.para" %
(os.environ['SPAHOME'], n))
ofp.write("cd spa_%d\n" % n)
ofp.write("%s/bin/SPA_main SPA.para\n" % os.environ['SPAHOME'])
import sys, os
import fpdb
import pickle
import matplotlib.pyplot as plt
infile = sys.argv[1]
try:
title = sys.argv[2]
except:
title = "RMSF"
# load coords
if True:
coords = list()
f1 = next(fpdb.next_frame(infile))
for line in f1:
if len(line) > 54 and line[17:20] in fpdb.standard_protein_residues:
coords.append(list())
print len(coords)
n_frame = 0
for frame in fpdb.next_frame(infile):
n = 0
for line in frame:
if len(line
) > 54 and line[17:20] in fpdb.standard_protein_residues:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
#!/usr/bin/python
import sys, os
import fpdb
infile = sys.argv[1]
a1_file = 'a1.pdb'
lig_file = 'a1_lig.pdb'
rec_file = 'rec.pdb'
para_source = '/home/fuqiuyu/work/nmr_druggability/md/finished/1dhm/spa/SPA.para'
para_file = 'SPA.para'
print ">>>>> preparing SPA input files"
for model in fpdb.next_frame(infile):
pdb = fpdb.fPDB(model)
pdb.write_pdb(a1_file)
print "----- sys pdb done."
ofp_rec = open(rec_file, 'w')
for residue in pdb.topology.residues:
if residue.name in fpdb.standard_protein_residues:
residue.write_pdb(ofp_rec)
print "----- rec pdb done."
ofp_lig = open(lig_file, 'w')
for line in open(rec_file):
if len(line) >= 6 and line[:6] in ('ATOM ', 'HETATM'):
if line[12:16].strip() not in ('C', 'O', 'N', 'CA'):
#!/usr/bin/python
import sys, os
import fpdb
infile = sys.argv[1]
N = int(sys.argv[2])
count = 0
for frame in fpdb.next_frame(infile):
if count % N == 0:
try:
os.mkdir("spa_%d" % (count / N))
except:
pass
ofp = open("spa_%d/traj.pdb" % (count / N), 'w')
print ">>>>> Traj splited %d" % (count / N)
for line in frame:
ofp.write(line)
print "----- Frame %d" % count
count += 1