def main():
p = args.pro
ppref = p.split('/')[-1].split('.')[0]
l = args.lig
lpref = l.split('.')[0]
if args.clean_lig:
mdtraj.load(l).save_pdb('tidy_' + l)
comb = sr + 'clc/dock/analysis/comb_pl.py ' + p + ' ' + l
call_chimera(comb)
# keep remarks w binding info
fn = ppref + '_' + lpref + '.pdb'
get_remarks = 'grep REMARK ' + l + '>> ' + fn
call_cl(get_remarks)
ref = args.ref
if ref != None:
import numpy as np
# read in combined pdb
lp = mdtraj.load(fn)
# find distance between reference residue and ligand
pi = lp.topology.select('resid ' + ref + ' and name C')
li = lp.topology.select('not protein and name S')
lq = lp.atom_slice(li).xyz[0][0]
pq = lp.atom_slice(pi).xyz[0][0]
dist = np.linalg.norm(pq-lq)
# log results
with open('dists.dat', 'a') as f:
f.write(lpref + ': ' + str(dist) + '\n')
f.close()
# remove comb pdb if beyond cutoff distance
if dist > args.cut:
os.remove(fn)
def main():
df = pd.read_pickle(args.df)
dirs = df.index
for state in dirs:
frames = df.loc[state]
for ndx, IC in enumerate(frames):
if state != 'ab_2_o_13':
continue
if IC == None:
continue
else:
# prep everything
odir = os.path.join('done', 'ICs', state)
t_out = os.path.join(odir, str(ndx) + '.gro')
if not os.path.isdir(odir):
os.makedirs(odir)
fr, top = IC
trace = fr.split('.xtc')[0]
topology = os.path.join(top_pref, top + '.top')
trajectory = os.path.join('ICs', state, str(ndx) + '.gro')
# run grompp
g_out = os.path.join('tpr', trace + '_' + str(ndx) + '.tpr')
run_grompp = os.path.join(gmx_pref, 'grompp') + ' -f files/npt.mdp -c ' \
+ trajectory + ' -p ' + topology + ' -o ' + g_out + ' -maxwarn 1'
call_cl(run_grompp)
# run trjconv
run_trjconv = os.path.join(gmx_pref, 'trjconv') + ' -f ' + trajectory \
+ ' -s ' + g_out + ' -o ' + t_out + ' -pbc mol -center'
call_cl(run_trjconv, pipe_args=[b'MainChain', b'System'])
def main():
ligs = args.clust
od = args.out
pref = ligs.split('/')[-1]
# get length of one pdb w comments
ll = 'grep -n \"TER\" ' + ligs + ' | head -n 1 | awk -F \':\' \'{print $1}\''
lenl = get_num(ll)-1
# get number of clusters
cn = 'grep \"Cluster:\" ' + ligs + ' | tail -n 1 | awk -F \':\' \'{print $2}\''
nc = get_num(cn)
# loop over clusters
for i in range(nc):
# remove pdb if it exists
new_pdb = od + 'c' + str(i) + '_' + pref
try:
os.remove(new_pdb)
except OSError:
pass
# create new pdb
place = 'grep -n \"Cluster: ' + str(i) + '$\" ' + ligs + ' | head -n 1 | awk -F \':\' \'{print $1}\''
clust = get_num(place)
if i == 0:
clust0 = clust
b4, aftr = line_range(clust, lenl, clust0)
pull = 'sed -n \'' + str(b4) + ',' + str(aftr) + 'p;' + str(aftr) + 'q\' ' + ligs + '>> ' + new_pdb
call_cl(pull)
end = 'echo \"END\" >> ' + new_pdb
call_cl(end)
def main():
rec = args.rec
r = mdtraj.load(rec)
lig = args.lig
l = mdtraj.load(lig)
d = args.dist
temp = args.temp
pref = rec.split('.')[0]
# can't figure out a non-hacky way to combine pdbs.
cp_receptor = 'head -n -2 ' + rec
receptor, r_err = call_cl(cp_receptor)
cp_ligand = 'tail -n +2 ' + lig
ligand, l_err = call_cl(cp_ligand)
tf = open(temp, 'w')
tf.write(receptor)
tf.write(ligand)
tf.close()
# get indices of receptor within distance d of ligand
comb = mdtraj.load(temp)
# get ligand indices
li = comb.topology.select('not protein')
# find neighbors
neighbors = mdtraj.compute_neighbors(comb, d, li)[0]
# remove ligand from neighbor list (symmetric diff)
n = np.setxor1d(li, neighbors)
# easier to reset sometimes
comb = mdtraj.load(temp)
comb.restrict_atoms(n)
comb.save_pdb(pref + '_trim.pdb')
IPython.embed()
def main():
cwd = os.getcwd()
rec = args.rec
lig = args.lig
d = args.dist
pref = rec.split('.')[0]
ligpref = lig.split('.')[0]
d6bin = '/home/kmckiern/src/dock6/bin/'
# if pdb is gt 15000 atoms, prob need to trim.
if args.trim_rec:
trim_rl(rec, lig, d*3.0)
rec = pref + '_trim.pdb'
pref = rec.split('.')[0]
# generate ligand and receptor (h and no h) mol2 files
gm2 = sr + 'clc/dock/gen_mol2.py '
call_chimera(gm2 + lig)
call_chimera(gm2 + rec)
call_chimera(gm2 + rec + ' --noH')
# write receptor surface file
rnoH = pref + '_noH.mol2'
pnoH = rnoH.split('.')[0]
gsurf = sr + 'clc/dock/gen_surf.py '
call_chimera(gsurf + rnoH)
# fill in all of the dock templates
tmap = {'SURFACE': pnoH, 'SPHERE': pref, 'RECEPTOR': pref, 'LIGAND': ligpref}
template_dir = sr + 'clc/dock/templates/'
tfs = [template_dir + t for t in os.listdir(template_dir)]
for tf in tfs:
gen_templ8(tf, tmap, cwd)
# spheres
try:
os.remove(cwd + '/OUTSPH')
except OSError:
pass
gs = d6bin + 'sphgen -i INSPH -o OUTSPH'
call_cl(gs)
# trim sphere file
ss = d6bin + 'sphere_selector ' + pref + '_big.sph ' + ligpref + '.mol2 ' + str(d*10.0)
call_cl(ss)
# gen box and grid
gb = d6bin + 'showbox < showbox.in'
call_cl(gb)
ggrid = d6bin + 'grid -i grid.in'
grid_out, grid_err = call_cl(ggrid)
write_out('grid_oe.dat', grid_out, grid_err)
# dock some ligands!!
dock = d6bin + 'dock6 -i dock.in'
dock_out, dock_err = call_cl(dock)
write_out('dock_oe.dat', dock_out, dock_err)
def pull_sim():
# make ndx
run_make_ndx, ndx_file = make_ion_ndx(indices, gro)
print(run_make_ndx)
call_cl(run_make_ndx)
# grompp
out_name = gro.replace(".gro", "_pull_1")
run_grompp = grompp_str(pull_mdp, gro, out_name, top, ndx_file)
print(run_grompp)
call_cl(run_grompp)
# mdrun
run_mdrun = mdrun + " -deffnm " + out_name
print(run_mdrun)
call_cl(run_mdrun)
return None
def call_chimera(args):
# MAV requires gui
command = 'chimera --script \'' + args + '\''
call_cl(command)
def call_chimera(args):
command = 'chimera --nogui --script \'' + args + '\''
call_cl(command)
def get_num(cmd):
return int(call_cl(cmd)[0].strip())
def trim_rl(r, l, dist):
rt = 'python ' + sr + 'clc/dock/trim_pdb.py --rec ' + r + ' --lig ' + l + ' --d ' + str(dist)
out, err = call_cl(rt)