def main():
if len(sys.argv) != 4: # if no input
print "ERORR: there needs to be 3 inputs: sph inputfilename, max random value, outputfilename."
return
fileinputsph = sys.argv[1]
maxval = float(sys.argv[2])
fileoutput = sys.argv[3]
print 'input_sph =' + fileinputsph
print 'output =' + fileoutput
list = sph.read_sph(fileinputsph, 'A', 'A')
list2 = randomomize_sph(list, maxval)
sph.write_sph(fileoutput, list2)
def main():
if len(sys.argv) != 4: # if no input
print "ERORR: there needs to be 3 inputs: sph inputfilename, max random value, outputfilename."
print "spheres with radius of 0.5 (0.0 are changed to 0.5) (ligand atoms) will not be perturbed. Change radius to zero or 0.5 to not move. "
return
fileinputsph = sys.argv[1]
maxval = float(sys.argv[2])
fileoutput = sys.argv[3]
print 'input_sph =' + fileinputsph
print 'output =' + fileoutput
list = sph.read_sph(fileinputsph, 'A', 'A') # when we read in the
list2 = randomomize_sph(list, maxval)
sph.write_sph(fileoutput, list2)
def main():
if len(sys.argv) != 4: # if no input
print "ERORR: there need to be 3 inputs: sph inputfilename, pdb inputfilename, outputfilename."
return
fileinputsph = sys.argv[1]
fileinputpdb = sys.argv[2]
fileoutput = sys.argv[3]
print 'input_sph =' + fileinputsph
print 'input_pdb =' + fileinputpdb
print 'output =' + fileoutput
list = sph.read_sph(fileinputsph, "A", "A")
pdblist = pdb.read_pdb(fileinputpdb)[0]
list2 = distance_sph_pdb(list, pdblist, 5)
sph.write_sph(fileoutput, list2)
def main():
if len(sys.argv) != 5: # if no input
print "ERORR: there need to be 4 inputs: sph inputfilename, pdb inputfilename, outputfilename, distance."
return
fileinputsph = sys.argv[1]
fileinputpdb = sys.argv[2]
fileoutput = sys.argv[3]
distance = float(sys.argv[4])
print 'input_sph =' + fileinputsph
print 'input_pdb =' + fileinputpdb
print 'output =' + fileoutput
print 'distance = %6.3f'%distance
list = sph.read_sph(fileinputsph,"A","A")
pdblist = pdb.read_pdb(fileinputpdb)[0]
list2 = distance_sph_pdb(list, pdblist,distance)
sph.write_sph(fileoutput,list2)
def main():
#if len(sys.argv) != 5: # if no input
# print "ERORR: there need to be 4 inputs: sph inputfilename, pdb inputfilename, outputfilename, distance."
# return
if len(sys.argv) != 4: # if no input
print "ERORR: there need to be 3 inputs: sph inputfilename, pdb inputfilename, outputfilename"
return
fileinputsph = sys.argv[1]
fileinputpdb = sys.argv[2]
fileoutput = sys.argv[3]
#distance = float(sys.argv[4])
print 'input_sph =' + fileinputsph
print 'input_pdb =' + fileinputpdb
print 'output =' + fileoutput
#print 'distance = %6.3f'%distance
sph_cluster_list = sph.read_sph_cluster_list(fileinputsph)
pdblist = pdb.read_pdb(fileinputpdb)[0]
#list2 = distance_sph_pdb(sph_cluster_list, pdblist, distance)
list2 = distance_sph_pdb(sph_cluster_list, pdblist)
sph.write_sph(fileoutput, list2)
def main():
if len(sys.argv) != 4: # if no input
print "ERORR: there need to be 3 inputs: pdb inputfilename, residuelist, outputfileprefix."
return
fileinputpdb = sys.argv[1]
#fileinputsph = sys.argv[2]
#res_string = sys.argv[3]
#fileoutput = sys.argv[4]
res_string = sys.argv[2]
fileoutput = sys.argv[3]
splitname = fileinputpdb.split('\\')[-1].split('.')
if len(splitname) != 2:
print "error pdb file is weird. "
exit()
prefix = splitname[0]
print 'input_pdb =' + fileinputpdb
print 'sph prefix =' + prefix
print 'residue string =' + res_string
print 'output =' + fileoutput
residlist = []
res_string_split = res_string.split(',')
print res_string_split
# if len(res_string_split) == 1:
# residlist.append(int(res_string_split[0]))
# else:
#print res_string_split
for s in res_string_split:
if ('-' in s):
s_split = s.split('-')
if (len(s_split) != 2):
print "something is wrong with residue string."
else:
start = int(s_split[0])
stop = int(s_split[1]) + 1
for i in range(start, stop):
residlist.append(i)
else:
residlist.append(int(s))
for i in range(1, len(residlist)):
if residlist[i - 1] > residlist[i]:
print "uhoh. list is not monotonic"
exit()
print residlist
#exit()
run_dms_sph(fileinputpdb, prefix)
list1 = sph.read_sph(prefix + ".sph", "A", "A")
pdblist = pdb.read_pdb(fileinputpdb)
center = centre_of_mass(pdblist, residlist)
print center
list2 = closest_sphs_to_center(list1, center, 4)
sph.write_sph(fileoutput + ".sph", list2)
# add center to list and write agian to new file
#tmp_sphere = sphere(index,x,y,z,r,atomnum,clust,col)
tmp_sphere = sph.sphere(2, center[0], center[1], center[2], 0.7, 2, 0, 0)
list2.append(tmp_sphere)
sph.write_sph(fileoutput + "_and_center.sph", list2)
convert_sph_to_pdb(fileoutput + ".sph", fileoutput)
def run_spheregen(num, maxradius, minradius, proberadius):
#DOCKPATH = "/nfs/home/tbalius/zzz.github/DOCK"
DOCKPATH = "/home/baliuste/zzz.github/DOCK"
ligfile = "xtal-lig.mol2"
recdms = "rec.dms"
recpdb = "rec.pdb"
recsph = "rec.sph"
recsphp = "rec_mod.sph"
#recsphpdb = "rec.sph.pdb"
recsphpdb = "rec.sph"
name = "rec"
if not (os.path.isfile("./rec_ori.pdb")):
os.system('cp rec.pdb rec_ori.pdb')
#step one generate molecular surface.
#DMS = DOCKPATH+"/proteins/dms/bin/dms"
#flags = " "+recpdb+" -a -n -w 1.0 -v -o "+recdms
#dmscmd = DMS + flags
# -w is the probe radius
#proberadius = 1.2
dmscmd = DOCKPATH + "/proteins/dms/bin/dms " + recpdb + " -a -d 0.2 -g dms.log -p -n -w " + str(
proberadius) + " -o " + recdms
print "Run dms \n " + dmscmd
os.system(dmscmd)
# step one generate spheres.
os.system(
"rm -rf OUTSPH temp1.ms temp2* temp3.atc rec.sph rec.sph.pdb* showshere.in"
)
SPH = DOCKPATH + "/proteins/sphgen/bin/sphgen"
#maxradius = 1.8
#minradius = 1.2
file1 = open('INSPH', 'w')
#file1.write("%s\nR\nX\n0.0\n%3.1f\n%3.1f\n%s\n"%(recdms,maxradius,minradius,recsph))
file1.write("%s\nR\nX\n-0.1\n%3.1f\n%3.1f\n%s\n" %
(recdms, maxradius, minradius, recsph))
file1.close()
print "Run Sphgen"
os.system(SPH)
print "Process Spheres"
sphlist = sph_lib.read_sph(recsph, 'A', 'A')
sphlist_processed = []
for sph in sphlist:
if sph.radius < maxradius and sph.radius > minradius:
sphlist_processed.append(sph)
sph_lib.write_sph(recsphp, sphlist_processed)
file2 = open("showshere.in", 'w')
file2.write(recsphp + "\n-1\nN \n" + recsphpdb + '\nN \n')
file2.close()
# Enter name of sphere cluster file: adfds
# Enter cluster number to process (<0 = all): -1
# Generate surfaces as well as pdb files (<N>/Y)? N
# Enter name for output file prefix: adafdsf
# Process clu0 (ALL spheres) (<N>/Y)? N
ShSPH = DOCKPATH + "/proteins/showsphere/bin/showsphere < showshere.in"
os.system(ShSPH)
os.system("cp rec.pdb rec.pdb_num" + str(num))
#os.system("cat "+recsphpdb+"_1.pdb | sed -e 's/C/O/g' -e 's/SPH/HOH/g' | grep -v 'TER' >> rec.pdb")
num_waters = int(
os.popen(
"cat " + recsphpdb +
"_1.pdb | sed -e 's/C/O/g' -e 's/SPH/HOH/g' | grep -v 'TER' | wc -l "
).readlines()[0])
#print num_waters
os.system("touch waters.pdb")
os.system(
"cat " + recsphpdb +
"_1.pdb | sed -e 's/C/O/g' -e 's/SPH/HOH/g' | grep -v 'TER' >> waters.pdb"
)
os.system("cat waters.pdb >> rec.pdb")
os.system("mkdir dir%d ; mv %s*.pdb dir%d/;cp rec* dir%d/" %
(num, recsphpdb, num, num))
os.system("mv INSPH OUTSPH dir%d" % (num))
#SPHSEL = DOCKPATH+"/bin/sphere_selector"
#os.system(SPHSEL + " "+recsph+" " +ligfile+" 5.0")
#shutil.copyfile("selected_spheres.sph", "rec.5.0.sph")
return num_waters