def main():
if len(sys.argv) != 3: # if no input
print "ERORR"
return
namemol2 = sys.argv[1]
namedocktype = sys.argv[2]
fh = open(namedocktype, 'w')
fh1 = open(namedocktype + '.amb.crg.oxt', 'w')
fh2 = open(namedocktype + '.prot.table.ambcrg.ambH', 'w')
mol = mol2.read_Mol2_file(namemol2)[0]
dt = mol2.convert_sybyl_to_dock(mol)
for i in range(len(mol.atom_list)):
print i + 1, mol.atom_list[i].type, dt[i]
fh.write('%2d %4s %4s %4s %-6s %2s\n' %
(i + 1, mol.atom_list[i].name, mol.atom_list[i].resname,
upper_to_lower(
mol.atom_list[i].resname), mol.atom_list[i].type, dt[i]))
fh1.write(
'%-4s %4s %6.3f\n' %
(mol.atom_list[i].name, upper_to_lower(
mol.atom_list[i].resname), mol.atom_list[i].Q))
fh2.write('%4s %4s %6.3f %2s\n' %
(pad_string(mol.atom_list[i].name), mol.atom_list[i].resname,
mol.atom_list[i].Q, dt[i]))
fh.close()
fh1.close()
fh2.close()
def write_sph(filename, mol):
dt = mol2.convert_sybyl_to_dock(mol) # get dock atom types.
dockbase = os.environ.get('DOCKBASE')
vdw_dict = intialize_vdw_parm(dockbase +
'/proteins/defaults/vdw.parms.amb.mindock')
outsph = open(filename, 'w')
print len(mol.atom_list)
outsph.write("DOCK spheres generated from ligand heavy atoms\n")
outsph.write("cluster 1 number of spheres in cluster %d\n" %
len(mol.atom_list))
for i in range(len(mol.atom_list)):
radius = vdw_dict[dt[i]]
#outsph.write("%5d%10.5f%10.5f%10.5f%8.3f%5d \n" %
outsph.write(
"%5d%10.5f%10.5f%10.5f%8.3f%5d 0 0\n" %
(i + 1, round(mol.atom_list[i].X, 3), round(mol.atom_list[i].Y, 3),
round(mol.atom_list[i].Z, 3), radius, i + 1))
outsph.close()
return
def calc_score(fileprefix, values, gridscale, xn, yn, zn, origin, mol,
vdw_dict, fileh, return_vals, Hchoice):
# file - log file
# values gist values
# gridscale - the grid spacing
if Hchoice != 0 and Hchoice != 1 and Hchoice != 2:
print "Hchoice must be 0(use standard radius), 1 (use 0.8 for nonpolar H, instead of 1.540), or 2 (ignore H)"
exit()
dt = mol2.convert_sybyl_to_dock(mol) # get dock atom types.
# loop over each atom.
dict_gridpoint = {} # for each grid point have a list of atoms it is in
sum_per_atom = []
for atom_i, atom in enumerate(mol.atom_list):
sum_per_atom.append(0.0)
#if (Hchoice == 1 and dt[atom_i] == 6):
if (Hchoice == 1 and dt[atom_i] == 7):
radius = 0.8
elif (Hchoice == 2 and (dt[atom_i] == 6 or dt[atom_i] == 7)):
continue # go to nexed atom
else:
radius = vdw_dict[dt[atom_i]]
#print atom.type, atom.X, atom.Y, atom.Z, atom.type, dt[atom_i], radius
grid_i = round((atom.X - origin[0]) / gridscale)
grid_j = round((atom.Y - origin[1]) / gridscale)
grid_k = round((atom.Z - origin[2]) / gridscale)
if (grid_i < 0.0 or grid_j < 0.0 or grid_k < 0.0):
print "ERROR. . . "
exit()
radius_gridpoint = math.ceil(radius / gridscale) + 1
#print radius, gridscale, radius_gridpoint
#print grid_i,grid_j, grid_k
start_i = max([(grid_i - radius_gridpoint), 0.0])
stop_i = min([(grid_i + radius_gridpoint), xn])
start_j = max([(grid_j - radius_gridpoint), 0.0])
stop_j = min([(grid_j + radius_gridpoint), yn])
start_k = max([(grid_k - radius_gridpoint), 0.0])
stop_k = min([(grid_k + radius_gridpoint), zn])
'''
print "centerpoint:",grid_i, grid_j, grid_k
print "i", start_i, stop_i
print "j", start_i, stop_i
print "k", start_i, stop_i
'''
'''
count = 0
for i in range(xn):
x = (i * gridscale) + origin[0]
for j in range(yn):
y = (j * gridscale) + origin[1]
for k in range(zn):
z = (k * gridscale) + origin[2]
dist = distance([x,y,z],[atom.X,atom.Y,atom.Z])
if (dist <= radius):
if not (count in dict_gridpoint):
dict_gridpoint[count] = [atom_i]
else:
dict_gridpoint[count].append(atom_i)
count = count+1
'''
for i in range(int(start_i), int(
stop_i)): # looping over the cube about the center of the atom
x = (i * gridscale) + origin[0]
for j in range(int(start_j), int(stop_j)):
y = (j * gridscale) + origin[1]
for k in range(int(start_k), int(stop_k)):
z = (k * gridscale) + origin[2]
dist = distance([x, y, z], [atom.X, atom.Y, atom.Z])
if (dist <= radius):
#count = i*((xn)**2)+j*(xn) + k
count = i * (yn * zn) + j * (zn) + k
if not (count in dict_gridpoint):
dict_gridpoint[count] = [atom_i]
else:
dict_gridpoint[count].append(atom_i)
sum_val = 0
sum_val_positive = 0
sum_val_negative = 0
voxel_vol = gridscale**3.0
# loop over all displaced grid points.
for key in dict_gridpoint.keys():
# sum up total value as well as positive, and negative contrabutions.
sum_val = sum_val + values[key]
if values[key] > 0:
sum_val_positive = sum_val_positive + values[key]
else:
sum_val_negative = sum_val_negative + values[key]
# also calculate the per-atom gist decomposition.
# if a point is shared by multiple atoms, divied the value by the
# number of atoms that share that point and asign that fractional
# value to each atom
N = len(dict_gridpoint[key])
for atom_i in dict_gridpoint[key]:
#print atom_i
sum_per_atom[atom_i] = sum_per_atom[atom_i] + (values[key] / N)
molN = len(dict_gridpoint.keys())
boxN = len(values)
boxV = xn * gridscale * yn * gridscale * zn * gridscale
molV = float(molN) / float(boxN) * boxV
print "gist_val:", sum_val * voxel_vol
print "gist_val_positive:", sum_val_positive * voxel_vol
print "gist_val_negative:", sum_val_negative * voxel_vol
print "molN=", molN, " boxN=", boxN, " boxV=", boxV
print "molV=", molV
fileh.write('%s,%f\n' % ("gist_val", sum_val * voxel_vol))
fileh.write('%s,%f\n' %
("gist_val_positive", sum_val_positive * voxel_vol))
fileh.write('%s,%f\n' %
("gist_val_negative", sum_val_negative * voxel_vol))
fileh.write('%s,%f\n' % ("molN", molN))
fileh.write('%s,%f\n' % ("boxN", boxN))
fileh.write('%s,%f\n' % ("boxV", boxV))
fileh.write('%s,%f\n' % ("molV", molV))
for i, atom in enumerate(mol.atom_list):
print i, ":", sum_per_atom[i] * voxel_vol
fileh.write('atom%d,%f\n' % (i + 1, sum_per_atom[i] * voxel_vol))
new_values = []
# make a new grid with only the voxels in the ligand are non-zerro
if (return_vals):
new_values = []
for i, val in enumerate(values):
#if i in dict_gridpoint.keys():
if i in dict_gridpoint:
new_values.append(val)
else:
new_values.append(0.0)
return new_values
def calc_score(fileprefix, values, gridscale, xn, yn, zn, origin, mol,
vdw_dict, fileh, return_vals, Hchoice):
# file - log file
# values gist values
# gridscale - the grid spacing
mol_name = mol.name
if Hchoice != 0 and Hchoice != 1 and Hchoice != 2:
print "Hchoice must be 0(use standard radius), 1 (use 0.8 for nonpolar H, instead of 1.540), or 2 (ignore H)"
exit()
dt = mol2.convert_sybyl_to_dock(mol) # get dock atom types.
# loop over each atom.
dict_gridpoint = {} # for each grid point have a list of atoms it is in
sum_per_atom = []
for atom_i, atom in enumerate(mol.atom_list):
sum_per_atom.append(0.0)
#if (Hchoice == 1 and dt[atom_i] == 6):
if (Hchoice == 1 and dt[atom_i] == 7):
radius = 0.8
elif (Hchoice == 2 and (dt[atom_i] == 6 or dt[atom_i] == 7)):
continue # go to nexed atom
else:
radius = vdw_dict[dt[atom_i]]
#print atom.type, atom.X, atom.Y, atom.Z, atom.type, dt[atom_i], radius
grid_i = round((atom.X - origin[0]) / gridscale)
grid_j = round((atom.Y - origin[1]) / gridscale)
grid_k = round((atom.Z - origin[2]) / gridscale)
if (grid_i < 0.0 or grid_j < 0.0 or grid_k < 0.0):
print "ERROR. . . "
exit()
radius_gridpoint = math.ceil(radius / gridscale) + 1
#print radius, gridscale, radius_gridpoint
#print grid_i,grid_j, grid_k
start_i = max([(grid_i - radius_gridpoint), 0.0])
stop_i = min([(grid_i + radius_gridpoint), xn])
start_j = max([(grid_j - radius_gridpoint), 0.0])
stop_j = min([(grid_j + radius_gridpoint), yn])
start_k = max([(grid_k - radius_gridpoint), 0.0])
stop_k = min([(grid_k + radius_gridpoint), zn])
'''
print "centerpoint:",grid_i, grid_j, grid_k
print "i", start_i, stop_i
print "j", start_i, stop_i
print "k", start_i, stop_i
'''
'''
count = 0
for i in range(xn):
x = (i * gridscale) + origin[0]
for j in range(yn):
y = (j * gridscale) + origin[1]
for k in range(zn):
z = (k * gridscale) + origin[2]
dist = distance([x,y,z],[atom.X,atom.Y,atom.Z])
if (dist <= radius):
if not (count in dict_gridpoint):
dict_gridpoint[count] = [atom_i]
else:
dict_gridpoint[count].append(atom_i)
count = count+1
'''
for i in range(int(start_i), int(
stop_i)): # looping over the cube about the center of the atom
x = (i * gridscale) + origin[0]
for j in range(int(start_j), int(stop_j)):
y = (j * gridscale) + origin[1]
for k in range(int(start_k), int(stop_k)):
z = (k * gridscale) + origin[2]
dist = distance([x, y, z], [atom.X, atom.Y, atom.Z])
if (dist <= radius):
#count = i*((xn)**2)+j*(xn) + k
scale = cal_gausian(dist, radius / 2.0)
count = i * (yn * zn) + j * (zn) + k
if not (count in dict_gridpoint):
dict_gridpoint[count] = [[atom_i, scale]]
else:
dict_gridpoint[count].append([atom_i, scale])
sum_val = 0
sum_val_positive = 0
sum_val_negative = 0
voxel_vol = gridscale**3.0
# loop over all displaced grid points.
for key in dict_gridpoint.keys():
key_sum = 0
for atom_i, scale in dict_gridpoint[key]:
key_sum += -voxel_vol * values[key] * scale
sum_val = sum_val + -1. * values[key] * scale
print "gist_val:", sum_val * voxel_vol
fileh.write('%f\n' % (sum_val * voxel_vol))
new_values = []
# make a new grid with only the voxels in the ligand are non-zerro
if (return_vals):
new_values = []
for i, val in enumerate(values):
#if i in dict_gridpoint.keys():
if i in dict_gridpoint:
new_values.append(val)
else:
new_values.append(0.0)
return new_values
def calc_score(fileprefix, values, gridscale, xn, yn, zn, origin, mol,
vdw_dict, fileh):
# file - log file
# values gist values
# gridscale - the grid spacing
# here the vector of values is transformed to a multidemitional array (grid)
grid_old = []
count = 0
for i in range(xn):
ydim = []
for j in range(yn):
zdem = []
for k in range(zn):
zdem.append(values[count])
count = count + 1
ydim.append(zdem)
grid_old.append(ydim)
dt = mol2.convert_sybyl_to_dock(mol) # get dock atom types.
# loop over each atom.
dict_gridpoint = {} # for each grid point have a list of atoms it is in
sum_per_atom = []
for atom_i, atom in enumerate(mol.atom_list):
sum_per_atom.append(0.0)
radius = vdw_dict[dt[atom_i]]
#print atom.type, atom.X, atom.Y, atom.Z, atom.type, dt[atom_i], radius
grid_i = (atom.X - origin[0]) / gridscale
grid_j = (atom.Y - origin[0]) / gridscale
grid_k = (atom.Z - origin[0]) / gridscale
#print grid_i,grid_j, grid_k
count = 0
for i in range(xn):
x = (i * gridscale) + origin[0]
for j in range(yn):
y = (j * gridscale) + origin[1]
for k in range(zn):
z = (k * gridscale) + origin[2]
dist = distance([x, y, z], [atom.X, atom.Y, atom.Z])
if (dist <= radius):
if not (count in dict_gridpoint):
dict_gridpoint[count] = [atom_i]
else:
dict_gridpoint[count].append(atom_i)
count = count + 1
sum_val = 0
sum_val_positive = 0
sum_val_negative = 0
voxel_vol = gridscale**3.0
# loop over all displaced grid points.
for key in dict_gridpoint.keys():
# sum up total value as well as positive, and negative contrabutions.
sum_val = sum_val + values[key]
if values[key] > 0:
sum_val_positive = sum_val_positive + values[key]
else:
sum_val_negative = sum_val_negative + values[key]
# also calculate the per-atom gist decomposition.
# if a point is shared by multiple atoms, divied the value by the
# number of atoms that share that point and asign that fractional
# value to each atom
N = len(dict_gridpoint[key])
for atom_i in dict_gridpoint[key]:
#print atom_i
sum_per_atom[atom_i] = sum_per_atom[atom_i] + (values[key] / N)
molN = len(dict_gridpoint.keys())
boxN = len(values)
boxV = xn * gridscale * yn * gridscale * zn * gridscale
molV = float(molN) / float(boxN) * boxV
print "gist_val:", sum_val * voxel_vol
print "gist_val_positive:", sum_val_positive * voxel_vol
print "gist_val_negative:", sum_val_negative * voxel_vol
print "molN=", molN, " boxN=", boxN, " boxV=", boxV
print "molV=", molV
fileh.write('%s,%f\n' % ("gist_val", sum_val * voxel_vol))
fileh.write('%s,%f\n' %
("gist_val_positive", sum_val_positive * voxel_vol))
fileh.write('%s,%f\n' %
("gist_val_negative", sum_val_negative * voxel_vol))
fileh.write('%s,%f\n' % ("molN", molN))
fileh.write('%s,%f\n' % ("boxN", boxN))
fileh.write('%s,%f\n' % ("boxV", boxV))
fileh.write('%s,%f\n' % ("molV", molV))
for i, atom in enumerate(mol.atom_list):
print i, ":", sum_per_atom[i] * voxel_vol
fileh.write('atom%d,%f\n' % (i + 1, sum_per_atom[i] * voxel_vol))
# make a new grid with only the voxels in the ligand are non-zerro
new_values = []
for i, val in enumerate(values):
if i in dict_gridpoint.keys():
new_values.append(val)
else:
new_values.append(0.0)
return new_values