def main():
if len(sys.argv) != 3: # if no input
print "This function takes as input two pdb files"
print "calculates distances and writes out a report"
print len(sys.argv)
return
pdb_file1 = sys.argv[1]
pdb_file2 = sys.argv[2]
#pdb_out = sys.argv[3]
print "center of voxal, file 1: " + pdb_file1
print "list of waters, file 2: " + pdb_file2
pdb1 = pdb_lib.read_pdb(pdb_file1)
pdb2 = pdb_lib.read_pdb(pdb_file2)
atomcount = [] # count how meny atoms are in each voxel
# intialize
for i in range(len(pdb1)):
atomcount.append(0)
i = 0
for voxelatom in pdb1:
for atom in pdb2:
#print atom.atomname
if atom.atomname.replace(" ","") != "O":
continue
if (in_voxel(voxelatom,atom,0.25)):
atomcount[i] = atomcount[i] + 1
i = i + 1
for i in range(len(pdb1)):
print "voxel%d, %d"%(i, atomcount[i])
print len(pdb2)/3
def readin_all_atoms_center_of_mass(fileinputpdb):
pdblist = pdb.read_pdb(fileinputpdb)
atoms =[]
for pdbatoms in pdblist:
for atom in pdbatoms:
atoms.append(atom)
return centre_of_mass(atoms)
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 readin_all_atoms_return_chains(fileinputpdb):
pdblist = pdb.read_pdb(fileinputpdb)
if (len(pdblist) > 1):
print("len(pdblist) = %d" % len(pdblist))
#print(pdblist[0])
print("pdblist is greater than 1. there is more than one model...")
pdblist_combined = []
for atoms in pdblist:
print(len(atoms))
for atom in atoms:
pdblist_combined.append(atom)
# exit()
atoms_list = []
chains = []
chains_dict = {}
#current_chain = pdblist_combined[0].chainid
for atom in pdblist_combined:
#for atom in pdbatoms:
if not (atom.chainid in chains_dict):
chains_dict[atom.chainid] = []
chains_dict[atom.chainid].append(atom)
for key in chains_dict:
chains.append(chains_dict[key])
return chains
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)
j = 0
crds = []
for i in range(size):
#print( "j=",j,"i=",i
x = pdb[i].X
y = pdb[i].Y
z = pdb[i].Z
crd = cord(x, y, z)
crds.append(crd)
mdcrd_writer(crdfilename, crds, "from " + pdbfilename)
return
def main():
if len(sys.argv) != 3: # if no input
print "This function takes as input two pdb files"
print "read in the xtal waters (pdb1) and the water positions predicted by GIST (pdb2)."
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)
pdb.cal_dists_TP_FP_FN(pdb1, pdb2)
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) != 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) != 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 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) != 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) != 6: # if no input
print "ERORR: there need to be 4 inputs: sph inputfilename, pdb inputfilename, res list outputfilename, distance."
return
fileinputsph = sys.argv[1]
fileinputpdb = sys.argv[2]
fileinputlist = sys.argv[3]
fileoutput = sys.argv[4]
distance = float(sys.argv[5])
print 'input_sph =' + fileinputsph
print 'input_pdb =' + fileinputpdb
print 'input_list =' + fileinputlist
print 'output =' + fileoutput
print 'distance = %6.3f'%distance
reslist = read_list(fileinputlist)
#exit(0)
sphlist = sph.read_sph(fileinputsph,"A","A")
pdblist = pdb.read_pdb(fileinputpdb)[0]
# make dictionary
dict_pdblist = make_dict_pdb_res(pdblist)
fhout = open(fileoutput,'w')
# for each residue find the spheres within a certian distance
for res in reslist:
print res
if not res in dict_pdblist:
print str(res) + " not in dict"
continue
list2 = distance_sph_pdb(sphlist, dict_pdblist[res], distance)
sphere_cluster = {}
for sphere in list2:
sphere_cluster[sphere.cluster] = ''
# sorted clusters contain all the sphere clusters that are close to the residue. note that the sphere cluster define a pocket.
sorted_clusters = sorted(sphere_cluster.keys())
print "sphere clusters close to residue %d:"%(res), sorted_clusters
if len(sorted_clusters) != 0:
fhout.write("sphere clusters close to residue %d: %s\n"%(res,int_list_to_string(sorted_clusters)))
print "I AM HERE"
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 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")
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 main():
if len(sys.argv) != 5: # if no input
print(
"ERORR: there need to be 4 inputs: pdb file_pdb_list lig_resid dcutoff (center of ligand to center of model)"
)
return
fileinputpdb1 = sys.argv[1]
file_pdb_list = sys.argv[2]
ligand_name = sys.argv[3]
ligand_dist = float(sys.argv[4])
prefix = check_filename(fileinputpdb1)
print('input_pdb1 =' + fileinputpdb1)
print('sph prefix =' + prefix)
print('pdb list file =' + file_pdb_list)
print('lig_name =' + ligand_name)
print('lig_dist = %d' % ligand_dist)
#center = centre_of_mass(pdblist)
# calculate the center of mass of the full file that contains all molecles
center1 = readin_all_atoms_center_of_mass(fileinputpdb1)
fh = open(file_pdb_list, 'r')
dist_list = []
pdb_f_list = []
center_list = []
# loop over the list of pdb files. one file contains one model
for line in fh:
fileinputpdb2 = line.split()[0]
print('input_pdb2 =' + fileinputpdb2)
check_filename(fileinputpdb2)
center2 = readin_all_atoms_center_of_mass(fileinputpdb2)
d = distance(center1, center2)
dist_list.append(d)
pdb_f_list.append(fileinputpdb2)
center_list.append(center2)
distmin_id = 0
distmin = dist_list[distmin_id]
for i in range(0, len(dist_list)):
if (dist_list[i] < distmin):
#if dist_list[i] < dist_list[distmin_id]:
distmin_id = i
distmin = dist_list[distmin_id]
print("The model closest (dist = %f) to center is %s" %
(dist_list[distmin_id], pdb_f_list[distmin_id]))
# lets get the ligand
pdblist = pdb.read_pdb(
pdb_f_list[distmin_id]
) # read in the model that is closest to the center (this one should be completely suronded by neibors).
# get the subset of atoms of just the ligand
atom_lig_list = []
for pdbatoms in pdblist:
for atom in pdbatoms:
#print(atom.resname)
if (atom.resname == ligand_name):
atom_lig_list.append(atom)
lig_center = centre_of_mass(atom_lig_list)
filelist = [] # remember wich models are close by center of position.
for i, center in enumerate(center_list):
d = distance(center, lig_center)
if d < ligand_dist:
print(
"The model within cutoff (dist = %f) to center of ligand is %s"
% (d, pdb_f_list[i]))
filelist.append(pdb_f_list[i])
cat_string = " files to cat "
cat_cmd = " cat "
for filename in filelist:
print(filename)
pdblist = pdb.read_pdb(
filename
) # read in the model that is closest to the center (this one should be completely suronded by neibors).
atom_list = []
for pdbatoms in pdblist:
for atom in pdbatoms:
#print(atom.resname)
atom_list.append(atom)
flag_write = min_dist_between_two_sets_of_atoms(
atom_lig_list, atom_list, filename, 5)
if flag_write:
cat_string = cat_string + " " + filename
cat_cmd = cat_cmd + " " + filename
print(cat_string)
os.system(cat_cmd + " > complex.pdb")
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
import pdb_lib
import sys, copy
# Written by Trent E. Balius, B. Shoichet Lab
O = [28.781, 50.284, 29.051]
H1 = [29.738, 50.284, 29.051]
H2 = [28.541, 51.210, 29.051]
pdb_file = sys.argv[1]
wat_o = pdb_lib.read_pdb(pdb_file)
print len(wat_o)
fh = open(pdb_file + ".rst7", 'w')
new_wat = []
count = 0
for c in wat_o:
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] #
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")
