def main():
if (len(sys.argv) != 4): # if no input
print " (1) pdb file name,"
print " (1) crd file name,"
print " (2) output file "
return
pdbfilename = sys.argv[1]
crdfilename = sys.argv[2]
output = sys.argv[3]
#cl = pdb_lib.read_pdb(pdb_file)
pdb = pdb_lib.read_pdb(pdbfilename)[0]
size = len(pdb)
frames = coord_reader(crdfilename, size)
j = 0
for f in frames:
i = 0
for c in f.cords:
print "j=", j, "i=", i
pdb[i].X = c.x
pdb[i].Y = c.y
pdb[i].Z = c.z
i = i + 1
pdb_lib.output_pdb(pdb, output + "." + str(j) + ".pdb")
j = j + 1
return
def main():
if len(sys.argv) != 5: # if no input
print "ERORR: there need to be 4 inputs: pdb inputfilename, bfactorfilename(2 colomn:resname,value) residuelist, outputfileprefix."
return
fileinputpdb = sys.argv[1]
filebfactor = sys.argv[2]
res_string = sys.argv[3]
fileoutput = sys.argv[4]
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()
pdblist_chains = pdb.read_pdb(fileinputpdb)
pdblist = []
for chain in pdblist_chains:
pdblist = pdblist + chain
pdblist_mod = add_bfactors(pdblist, residlist, filebfactor)
pdb.output_pdb(pdblist_mod, fileoutput + '.pdb')
def main():
filename = sys.argv[1]
intval = int(sys.argv[2])
fileprefix = sys.argv[3]
pdbchains = pdb_lib.read_pdb(filename)
count = 1
for pdbmol in pdbchains:
renumber_residue_continuous(pdbmol, intval)
pdb_lib.output_pdb(pdbmol, '%s_%i.pdb' % (fileprefix, count))
count = count + 1
def main():
if len(sys.argv) != 4: # if no input
print "This function takes as input two pdb files"
print "read in the low dielectric spheres (pdb1) and the water positions (pdb2)."
print "calculates distances and writes out a the overlaping atoms from the second file (water positions)"
print len(sys.argv)
return
pdb_file1 = sys.argv[1]
pdb_file2 = sys.argv[2]
pdb_out = sys.argv[3]
print "file 1: " + pdb_file1
print "file 2: " + pdb_file2
pdb1 = pdb.read_pdb(pdb_file1)
pdb2 = pdb.read_pdb(pdb_file2)
pdb2_close = pdb.cal_dists_close(pdb1, pdb2)
pdb.output_pdb(pdb2_close, pdb_out)
def main():
if len(sys.argv) != 4: # if no input
print(
"ERORR: there need to be 3 inputs: pdb inputfilename, residue:atom_list, outputfileprefix."
)
print(
"list is resnum1:atomname1,...,resnum1:atomnamei,...,resnumk,atomnamej,..."
)
return
fileinputpdb = sys.argv[1]
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(',')
residlist = res_string_split
print res_string_split
pdblist = pdb.read_pdb(fileinputpdb)[0]
center = centre_of_mass(pdblist, residlist)
#print ("%6.4f %6.4f %6.4f"%(center[0],center[1],center[2]))
print(
"HETATM 1 ZN ZN A 1 %8.3f%8.3f%8.3f 1.00 0.00 ZN"
% (center[0], center[1], center[2]))
fh = open(fileoutput + '_zinc.pdb', 'w')
fh.write(
"HETATM 1 ZN ZN A 1 %8.3f%8.3f%8.3f 1.00 0.00 ZN\n"
% (center[0], center[1], center[2]))
fh.close()
change_name(pdblist, residlist)
pdb.output_pdb(pdblist, fileoutput + '.pdb')
def main():
if len(sys.argv) != 5: # if no input
print "This function takes as input two pdb files, output file name and the value"
print "read in the ligand (pdb1) and the water positions (pdb2)."
print "calculates distances and writes out a the overlaping atoms from the second file (water positions)"
print len(sys.argv)
return
pdb_file1 = sys.argv[1]
pdb_file2 = sys.argv[2]
pdb_out = sys.argv[3]
val = float(sys.argv[4])
print "file 1: " + pdb_file1
print "file 2: " + pdb_file2
print "file out: " + pdb_out
print "value: " + str(val)
pdb1 = pdb.read_pdb(pdb_file1)[0]
pdb2 = pdb.read_pdb(pdb_file2)[0]
pdb2_close = pdb.cal_dists_close_val(pdb1,pdb2,val**2)
pdb.output_pdb( pdb2_close, pdb_out)
def convert_sph_to_pdb_and_write(sphs,energies,pdbfilename):
molname = "CLU"
chainid = "A"
resname = "CLU"
resnum = 1
atomname = "O"
i = 0
atoms = []
for sph in sphs:
atomnum = sph.atomnum
X = sph.X
Y = sph.Y
Z = sph.Z
bfact = energies[i]
boolhet = False
atom = pdb_lib.PDB_atom_info(molname, chainid, resname, resnum, atomname, atomnum, X, Y, Z, bfact, boolhet)
atoms.append(atom)
i=i+1
pdb_lib.output_pdb(atoms,pdbfilename)
def run_energy_cal():
# this function will run amber.
# cluster. we start with the frist water. find everything close, then go to the next water not alreay assigned. find everything close, repeat until all are assigned.
wats = pdb_lib.read_pdb("waters.pdb")
wat_clus = []
for i in range(len(wats)):
wat_clus.append(0)
clusterheads = []
cluster = 1
for i, wat1 in enumerate(wats):
if wat_clus[
i] != 0: # if cluster is already asigned then continue to next water
continue
print "water" + str(i) + " is a clusterhead. "
clusterheads.append(wat1)
for j, wat2 in enumerate(wats):
if wat_clus[
j] != 0: # if cluster is already asigned then continue to next water
continue
dist = dist_wat(wat1, wat2)
#if dist < 3.0:
if dist < 2.8:
wat_clus[j] = cluster
cluster = cluster + 1
pdb_lib.output_pdb(clusterheads, "waterclusters.pdb")
# check if there is a tleap input file:
# if there is not then write a defualt file, if one already exist then use that one.
# This way someone can perpare the receptor the way they want.
if not (os.path.isfile("./tleap.in")):
#os.system('cp rec.pdb rec_ori.pdb'
file1 = open("tleap.in", 'w')
file1.write(
" set default PBradii mbondi2 \n source leaprc.ff14SB \n \n REC = loadpdb rec_ori.pdb \n WAT = loadpdb water1.pdb \n COM = combine {REC WAT} \n saveamberparm REC rec.leap.prm7 rec.leap.rst7 \n saveamberparm COM rec.1wat.leap.prm7 rec.1wat.leap.rst7 \n charge REC \n quit \n"
)
file1.close()
else:
print "using pre-existing tleap.in"
# cut -c 24-28 rec_ori.pdb | sort -u | wc -l
numres = 290
if not (os.path.isfile("./min.in")):
file2 = open("min.in", 'w')
#file2.write(" 01mi.in: equil minimization with Cartesian restraints /n &cntrl /n imin=1, maxcyc=3000, ncyc = 1500, /n ntpr=100, /n ntwr=100000000, /n ntr=1, /n restraint_wt=100.0, /n restraintmask= ':1-%d & !@H' /n / /n "%(numres))
file2.write(
" min.in: minimization with GB \n &cntrl \n imin = 1, maxcyc = 100, ncyc = 50, ntmin = 1, \n igb=1, \n ntx = 1, ntc = 1, ntf = 1, \n ntb = 0, ntp = 0, \n ntwx = 1000, ntwe = 0, ntpr = 1000, \n cut = 999.9, \n ntr = 1, \n restraintmask = '!@H=', \n restraint_wt = 0.1, \n / \n "
)
file2.close()
#fh = open('waters.pdb','r')
fh = open('waterclusters.pdb', 'r')
lines = fh.readlines()
fh.close()
fh = open('water1.pdb', 'w')
fh.write(lines[0])
fh.close()
os.system("setenv AMBERHOME = /nfs/soft/amber/amber14")
os.system("$AMBERHOME/bin/tleap -s -f tleap.in > ! tleap.out")
# minimize the receptor alone.
os.system(
"$AMBERHOME/bin/sander -O -i min.in -o min.out -p rec.leap.prm7 -c rec.leap.rst7 -ref min.rst7 -x min.mdcrd -inf min.info -r min.rst7"
)
# loop over all waters, run a minimization on each water in the context of the receptor.
count = 1
for line in lines:
name = "water_" + str(count)
print "we are minimzing " + name
fh = open(name + ".pdb", 'w')
fh.write(line)
fh.close()
os.system("python /nfs/home/tbalius/zzz.scripts/add_h_to_wat.py " +
name + ".pdb")
#print "cat rec.leap.rst7 "+name+".pdb.rst7 > "+name+".rst7"
#os.system("cat rec.leap.rst7 "+name+".pdb.rst7 > "+name+".rst7")
fh = open('rec.leap.rst7', 'r')
fh2 = open(name + '.rst7', 'w')
linecount = 0
for line in fh:
if linecount == 1:
num = int(line.split()[0])
num = num + 3
fh2.write('%d\n' % num)
else:
fh2.write(line)
linecount = linecount + 1
fh.close()
fh = open(name + ".pdb.rst7", 'r')
for line in fh:
fh2.write(line)
fh.close()
fh2.close()
#exit()
os.system("$AMBERHOME/bin/ambpdb -p rec.1wat.leap.prm7 < " + name +
".rst7 > before_min_" + name + ".pdb")
os.system("$AMBERHOME/bin/sander -O -i min.in -o min." + name +
".out -p rec.1wat.leap.prm7 -c " + name + ".rst7 -ref " +
name + ".rst7 -x min." + name + ".mdcrd -inf min." + name +
".info -r min." + name + ".rst7")
os.system("$AMBERHOME/bin/ambpdb -p rec.1wat.leap.prm7 < min." + name +
".rst7 > min." + name + ".pdb")
count = count + 1
def cluster_water_pdb(inputfilename, cutoff, outputfilename, denominator):
bonds = []
bond_dic = {}
duplicate = {}
pdb_ori = pdb_lib.read_pdb(inputfilename)
pdb_water = []
pdb_other = []
for atom in pdb_ori:
#print atom.resname
if atom.resname == "HOH":
pdb_water.append(atom)
else:
pdb_other.append(atom)
numwat = len(pdb_water)
for i in range(numwat):
for j in range(i + 1, numwat):
dist = dist_wat(pdb_water[i], pdb_water[j])
#print i, j, pdb_water[i].resnum, pdb_water[j].resnum, dist
if (dist == 0.0): # discard duplicates
duplicate[j] = i
elif (dist < cutoff):
#bonds.append([i,j, dist])
bonds.append([i, j])
print "bond: %d %d %f" % (i, j, dist)
bond_dic[i] = 1
bond_dic[j] = 1
clusters = {} # what cluster belongs to each atom
count = 0
#
for bond in bonds:
if bond[0] in clusters: # if the starting point is in a cluster then put the ending point in that same cluster
clusters[bond[1]] = clusters[bond[0]]
elif bond[
1] in clusters: # if the ending point is in a cluster then put the starting point in that same cluster
clusters[bond[0]] = clusters[bond[1]]
else: # nether point is in a cluster
clusters[bond[0]] = count
clusters[bond[1]] = count
count = count + 1
for i in range(numwat):
if not i in bond_dic and not i in duplicate:
# then singlton.
clusters[i] = count
count = count + 1
cluster_lists = {} # list of atoms in each cluster
print clusters
for key in clusters.keys(): # key is atom
print key, clusters[key]
cluster_lists[clusters[key]] = [] # intialize
for key in clusters.keys():
cluster_lists[clusters[key]].append(key)
cluster_centers = []
cluster_median = []
for cluster in cluster_lists:
X = 0.0
Y = 0.0
Z = 0.0
count = 0
for atom in cluster_lists[cluster]:
X = X + pdb_water[atom].X
Y = Y + pdb_water[atom].Y
Z = Z + pdb_water[atom].Z
count = count + 1
X = X / count
Y = Y / count
Z = Z / count
#alpha = float(count)/float(numwat)
alpha = float(count) / denominator
temp_atom_info = pdb_lib.PDB_atom_info('', "A", "HOH", cluster, " O ",
cluster, X, Y, Z, alpha, False)
# find median water
min_val = [-1, 1000]
for i in range(len(cluster_lists[cluster])):
dist = dist_wat(temp_atom_info,
pdb_water[cluster_lists[cluster][i]])
if dist < min_val[1]:
min_val[0] = i
min_val[1] = dist
cluster_centers.append(temp_atom_info)
cluster_median.append(
pdb_water[cluster_lists[cluster][min_val[0]]]) # g
pdb_lib.output_pdb(cluster_centers, outputfilename + "_center.pdb")
pdb_lib.output_pdb(cluster_median, outputfilename + "_median.pdb")
print c.X
print c.Y
print c.Z
new_wat.append(c)
#count = count+1
c1 = copy.copy(c)
new_wat.append(c1)
count = count + 1
new_wat[count].atomname = " H1 " #= line[12:16
new_wat[count].X = new_wat[count].X + H1[0] - O[0] #
new_wat[count].Y = new_wat[count].Y + H1[1] - O[1] #
new_wat[count].Z = new_wat[count].Z + H1[2] - O[2] #
c2 = copy.copy(c)
new_wat.append(c2)
count = count + 1
new_wat[count].atomname = " H2 " #= line[12:16
new_wat[count].X = new_wat[count].X + H2[0] - O[0] #
new_wat[count].Y = new_wat[count].Y + H2[1] - O[1] #
new_wat[count].Z = new_wat[count].Z + H2[2] - O[2] #
fh.write(
" %11.7f %11.7f %11.7f %11.7f %11.7f %11.7f\n %11.7f %11.7f %11.7f\n" %
(new_wat[0].X, new_wat[0].Y, new_wat[0].Z, new_wat[1].X, new_wat[1].Y,
new_wat[1].Z, new_wat[2].X, new_wat[2].Y, new_wat[2].Z))
fh.close()
pdb_lib.output_pdb(new_wat, pdb_file + "_new")
# len(c)
# for a in c:
# print a
def cluster_water_pdb(inputfilename, cutoff, outputfilename, denominator):
bonds = []
bond_dic = {}
duplicate = {}
pdb_ori = pdb_lib.read_pdb(inputfilename)[0]
pdb_water = []
pdb_other = []
#print inputfilename
for atom in pdb_ori:
#print atom.resname
if atom.resname == "HOH":
pdb_water.append(atom)
else:
pdb_other.append(atom)
numwat = len(pdb_water)
print "%s contains %d waters" % (inputfilename, numwat)
if numwat == 0:
print "There are zero waters in the file. If this is not right make sure that there are no TER in the file and re-run. "
for i in range(numwat):
for j in range(i + 1, numwat):
dist = dist_wat(pdb_water[i], pdb_water[j])
#print i, j, pdb_water[i].resnum, pdb_water[j].resnum, dist
if (dist == 0.0): # discard duplicates
duplicate[j] = i
elif (dist < cutoff):
#bonds.append([i,j, dist])
bonds.append([i, j])
print "bond: %d %d %f" % (i, j, dist)
bond_dic[i] = 1
bond_dic[j] = 1
clusters = {} # what cluster belongs to each atom
count = 0
#
for bond in bonds:
if bond[0] in clusters: # if the starting point is in a cluster then put the ending point in that same cluster
clusters[bond[1]] = clusters[bond[0]]
elif bond[
1] in clusters: # if the ending point is in a cluster then put the starting point in that same cluster
clusters[bond[0]] = clusters[bond[1]]
else: # nether point is in a cluster
clusters[bond[0]] = count
clusters[bond[1]] = count
count = count + 1
for i in range(numwat):
if not i in bond_dic and not i in duplicate:
# then singlton.
clusters[i] = count
count = count + 1
cluster_lists = {} # list of atoms in each cluster
print clusters
for key in clusters.keys(): # key is atom
print key, clusters[key]
cluster_lists[clusters[key]] = [] # intialize
for key in clusters.keys():
cluster_lists[clusters[key]].append(key)
cluster_centers = []
cluster_median = []
for cluster in cluster_lists:
X = 0.0
Y = 0.0
Z = 0.0
count = 0
for atom in cluster_lists[cluster]:
X = X + pdb_water[atom].X
Y = Y + pdb_water[atom].Y
Z = Z + pdb_water[atom].Z
count = count + 1
X = X / count
Y = Y / count
Z = Z / count
#alpha = float(count)/float(numwat)
alpha = float(count) / denominator
temp_atom_info = pdb_lib.PDB_atom_info('', "A", "HOH", cluster, " O ",
cluster, X, Y, Z, 0.0, alpha,
False)
# find median water
min_val = [-1, 1000]
for i in range(len(cluster_lists[cluster])):
dist = dist_wat(temp_atom_info,
pdb_water[cluster_lists[cluster][i]])
if dist < min_val[1]:
#min_val[0] = i # this index of the cluster member
min_val[0] = cluster_lists[cluster][
i] # index of the water, simplifies call
min_val[1] = dist
pdb_water[cluster_lists[cluster][
i]].bfact = temp_atom_info.bfact # make both report the number of waters/ dem in b column
cluster_centers.append(temp_atom_info)
#cluster_median.append(pdb_water[cluster_lists[cluster][min_val[0]]]) # when we saved the index of the cluster instead of index of water
cluster_median.append(pdb_water[min_val[0]]) #
pdb_lib.output_pdb(cluster_centers, outputfilename + "_center.pdb")
pdb_lib.output_pdb(cluster_median, outputfilename + "_median.pdb")