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 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")
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")