print strerror
sys.exit()
else:
print "Please add hydrogens to the file using pdb_addH.py"
sys.exit()
# Calculate the dipole moment and write out
try:
moment = pdbMoment(pdb)
except PdbMomentError, (strerror):
print "Problem with %s" % pdb_file
print strerror
sys.exit()
out.append("%30s" % short_pdb)
out.append("%10.3F%10.3F%10.3F" % tuple(moment))
out.append("%10.3F\n" % geometry.dist(moment))
# Combine output, split only on line breaks, remove blank lines
out = "".join(out)
out = out.split("\n")
out = [x for x in out if x.strip() != ""]
# Add line numbers and header
out = ["%10i%s\n" % (i,x) for i, x in enumerate(out)]
out.insert(0,"%10s%30s%10s%10s%10s%10s\n" %
(" ","pdb","x","y","z","length"))
print "".join(out)
# If run from command line...
def pdbNeighbors(pdb,
distance_cutoff=10,
sequence_cutoff=4,
residue=None,
atom=None,
calc_everything=False):
"""
Finds number of neighbors for each residue in a pdb and returns a list of
residues and a list of number of neighbors.
"""
pdb = [l for l in pdb if l[0:6] == "ATOM "]
cb_atoms = []
cb_coord = []
for line_counter, line in enumerate(pdb):
# Look for Gly CA and use to create fake CB
if line[17:20] == "GLY" and line[13:16] == "CA ":
cb_atoms.append("\"CB%s\"" % line[15:26])
n = []
ca = []
co = []
for i in range(3):
n.append(float(pdb[line_counter - 1][30 + i * 8:38 + i * 8]))
ca.append(float(pdb[line_counter][30 + i * 8:38 + i * 8]))
co.append(float(pdb[line_counter + 1][30 + i * 8:38 + i * 8]))
#cb_coord.append(ca)
cb_coord.append(geometry.calcGlyCbeta(n, ca, co))
# For all other residues, append a CB
#elif line[13:16] == "CA ":
elif line[13:16] == "CB ":
cb_atoms.append("\"%s\"" % line[13:26])
cb_coord.append(
[float(line[31 + i * 8:38 + i * 8]) for i in range(3)])
else:
continue
# Create list of atoms for which to find number of cb atom neighbors.
if calc_everything:
compare_atoms = ["\"%s\"" % l[13:26] for l in pdb]
compare_coord = [[float(l[30 + i * 8:38 + i * 8]) for i in range(3)]
for l in pdb]
elif residue == None and atom == None:
compare_atoms = cb_atoms[:]
compare_coord = cb_coord[:]
else:
if residue != None:
compare_list = [l for l in pdb if l[17:20] == residue]
else:
compare_list = pdb[:]
if atom != None:
compare_list = [
l for l in compare_list if l[13:16].strip() == atom
]
compare_atoms = ["\"%s\"" % l[13:26] for l in compare_list]
compare_coord = [[float(l[30 + i * 8:38 + i * 8]) for i in range(3)]
for l in compare_list]
# Calculate array of distances between each coordinate
num_compare = len(compare_coord)
num_cb = len(cb_coord)
dist_array = [[0. for j in range(num_cb)] for i in range(num_compare)]
for i in range(num_compare):
for j in range(num_cb):
dist_array[i][j] = geometry.dist(compare_coord[i], cb_coord[j])
# Count number of neighbors within distance_cutoff angstroms
# for each position
num_neighbors = [0 for x in compare_atoms]
for i in range(num_compare):
neighbors = 0
for j in range(num_cb):
# Skip neighbors that are simply close in sequence
if compare_atoms[i][9] == cb_atoms[j][9]:
seq_dist = int(compare_atoms[i][10:14]) - int(
cb_atoms[j][10:14])
if abs(seq_dist) < sequence_cutoff:
continue
# If the neighboring atom is close in space, add to counter
if dist_array[i][j] <= distance_cutoff:
num_neighbors[i] += 1
return compare_atoms, num_neighbors
def pdbNeighbors(pdb,distance_cutoff=10,sequence_cutoff=4,residue=None,
atom=None,calc_everything=False):
"""
Finds number of neighbors for each residue in a pdb and returns a list of
residues and a list of number of neighbors.
"""
pdb = [l for l in pdb if l[0:6] == "ATOM "]
cb_atoms = []
cb_coord = []
for line_counter, line in enumerate(pdb):
# Look for Gly CA and use to create fake CB
if line[17:20] == "GLY" and line[13:16] == "CA ":
cb_atoms.append("\"CB%s\"" % line[15:26])
n = []; ca = []; co = []
for i in range(3):
n.append(float(pdb[line_counter-1][30+i*8:38+i*8]))
ca.append(float(pdb[line_counter][30+i*8:38+i*8]))
co.append(float(pdb[line_counter + 1][30+i*8:38+i*8]))
#cb_coord.append(ca)
cb_coord.append(geometry.calcGlyCbeta(n,ca,co))
# For all other residues, append a CB
#elif line[13:16] == "CA ":
elif line[13:16] == "CB ":
cb_atoms.append("\"%s\"" % line[13:26])
cb_coord.append([float(line[31+i*8:38+i*8]) for i in range(3)])
else:
continue
# Create list of atoms for which to find number of cb atom neighbors.
if calc_everything:
compare_atoms = ["\"%s\"" % l[13:26] for l in pdb]
compare_coord = [[float(l[30+i*8:38+i*8]) for i in range(3)]
for l in pdb]
elif residue == None and atom == None:
compare_atoms = cb_atoms[:]
compare_coord = cb_coord[:]
else:
if residue != None:
compare_list = [l for l in pdb if l[17:20] == residue]
else:
compare_list = pdb[:]
if atom != None:
compare_list = [l for l in compare_list if l[13:16].strip() == atom]
compare_atoms = ["\"%s\"" % l[13:26] for l in compare_list]
compare_coord = [[float(l[30+i*8:38+i*8]) for i in range(3)]
for l in compare_list]
# Calculate array of distances between each coordinate
num_compare = len(compare_coord)
num_cb = len(cb_coord)
dist_array = [[0. for j in range(num_cb)]
for i in range(num_compare)]
for i in range(num_compare):
for j in range(num_cb):
dist_array[i][j] = geometry.dist(compare_coord[i],cb_coord[j])
# Count number of neighbors within distance_cutoff angstroms
# for each position
num_neighbors = [0 for x in compare_atoms]
for i in range(num_compare):
neighbors = 0
for j in range(num_cb):
# Skip neighbors that are simply close in sequence
if compare_atoms[i][9] == cb_atoms[j][9]:
seq_dist = int(compare_atoms[i][10:14])-int(cb_atoms[j][10:14])
if abs(seq_dist) < sequence_cutoff:
continue
# If the neighboring atom is close in space, add to counter
if dist_array[i][j] <= distance_cutoff:
num_neighbors[i] += 1
return compare_atoms, num_neighbors
print strerror
sys.exit()
else:
print "Please add hydrogens to the file using pdb_addH.py"
sys.exit()
# Calculate the dipole moment and write out
try:
moment = pdbMoment(pdb)
except PdbMomentError, (strerror):
print "Problem with %s" % pdb_file
print strerror
sys.exit()
out.append("%30s" % short_pdb)
out.append("%10.3F%10.3F%10.3F" % tuple(moment))
out.append("%10.3F\n" % geometry.dist(moment))
# Combine output, split only on line breaks, remove blank lines
out = "".join(out)
out = out.split("\n")
out = [x for x in out if x.strip() != ""]
# Add line numbers and header
out = ["%10i%s\n" % (i, x) for i, x in enumerate(out)]
out.insert(
0,
"%10s%30s%10s%10s%10s%10s\n" % (" ", "pdb", "x", "y", "z", "length"))
print "".join(out)
