def main():
if len(sys.argv) != 3: # if no input
print "Syntax: python db2_to_mol2.py db2file.db2 outprefix ";
return
filename = sys.argv[1];
outfileprefix = sys.argv[2];
print "filename: " + filename
db2mols = read_Moldb2_file(filename)
allmol2s = convert_db2_to_mol2(db2mols)
filecount = 0
for mol2mols in allmol2s:
outfilename = outfileprefix + "." + str(filecount) + ".mol2"
print "writing "+ outfilename
count = 0
for mol2mol in mol2mols:
if count == 0:
mol2.write_mol2(mol2mol,outfilename)
else:
mol2.append_mol2(mol2mol,outfilename)
count = count + 1
filecount = filecount + 1
return;
def shift_mol2(fileprefix, ori_mol, xtran, ytran, ztran):
mol = copy.copy(ori_mol)
namemol2 = fileprefix + "_" + str(xtran) + "_" + str(ytran) + "_" + str(
ztran) + ".mol2"
for i in range(len(mol.atom_list)):
mol.atom_list[i].X = mol.atom_list[i].X + xtran
mol.atom_list[i].Y = mol.atom_list[i].Y + ytran
mol.atom_list[i].Z = mol.atom_list[i].Z + ztran
mol2.write_mol2(mol, namemol2)
return
def shift_mol2(fileprefix, ori_mol):
mol = copy.copy(ori_mol)
step = 0.03
name = 0.03
for i in range(10):
#outmol2 = open(fileprefix+"."+str(var)+".mol2",'w')
namemol2 = fileprefix + "." + str(name) + ".mol2"
print len(mol.atom_list)
for i in range(len(mol.atom_list)):
mol.atom_list[i].X = mol.atom_list[i].X + step
mol2.write_mol2(mol, namemol2)
name = name + 0.03
return
def main():
if len(sys.argv) != 6: # if no input
print(" This script needs the following:")
print(" (1) input mol2 file")
print(" (2) output mol2 file")
print(" (3-5) x, y, z rotation angles")
print(" rotation order: x, y, then z with be rotated in that order. ")
return
mol2file = sys.argv[1]
outputfile = sys.argv[2]
xangle = float(sys.argv[3])
yangle = float(sys.argv[4])
zangle = float(sys.argv[5])
cos_x = math.cos(xangle)
xsign = 1.0
if xangle < 0.0:
xsign = -1.0
cos_y = math.cos(yangle)
ysign = 1.0
if yangle < 0.0:
ysign = -1.0
cos_z = math.cos(zangle)
zsign = 1.0
if zangle < 0.0:
zsign = -1.0
mols = mol2.read_Mol2_file(mol2file)
first = True
for m in mols:
center = mol2.centre_of_mass(m)
translate(m, -center[0], -center[1], -center[2])
rotate_x(m.atom_list, cos_x, xsign)
rotate_y(m.atom_list, cos_y, ysign)
rotate_z(m.atom_list, cos_z, zsign)
translate(m, center[0], center[1], center[2])
if first:
mol2.write_mol2(m, outputfile)
first = False
else:
mol2.append_mol2(m, outputfile)
return
def modify_charges_mol2_file(mol2file, atom_list_hex, outputprefix):
## read in mol2 file
mol = mol2.read_Mol2_file(mol2file)[0]
n = len(atom_list_hex)
if n != len(mol.atom_list):
print "Error: n != len(mol.atom_list) : " + str(n) + " !=" + str(
len(mol.atom_list))
exit()
for i in range(n):
charge = atom_list_hex[i][2]
print mol.atom_list[i].Q, charge
mol.atom_list[i].Q = float(charge)
filename = outputprefix + '.mol2'
mol2.write_mol2(mol, filename)
return
def modify_mol2_file(mol2file, outputprefix):
## read in mol2 file
frist = True
mollist = mol2.read_Mol2_file(mol2file)
for mol in mollist:
ori_formal_charge = mol2.formal_charge(mol)
n = len(mol.atom_list)
Si_atoms_index = []
for i in range(n):
if mol.atom_list[i].name == 'CB' or mol.atom_list[i].name == 'SG':
print(mol.atom_list[i].type, mol.atom_list[i].name)
Si_atoms_index.append(i)
if len(Si_atoms_index) != 2:
print("error")
exit()
count_h = [0,
0] # remember how meny atoms are connected to the both Si
Hlist = [
] # remember which the atom index that are the connected bonds.
Si1 = Si_atoms_index[0]
Si2 = Si_atoms_index[1]
for bond in mol.bond_list:
if bond.a1_num - 1 == Si1:
if (mol.atom_list[bond.a2_num - 1].type == 'H'):
count_h[0] = count_h[0] + 1
Hlist.append(bond.a2_num)
if bond.a2_num - 1 == Si1:
if (mol.atom_list[bond.a1_num - 1].type == 'H'):
count_h[0] = count_h[0] + 1
Hlist.append(bond.a1_num)
if bond.a1_num - 1 == Si2:
if (mol.atom_list[bond.a2_num - 1].type == 'H'):
count_h[1] = count_h[1] + 1
Hlist.append(bond.a2_num)
if bond.a2_num - 1 == Si2:
if (mol.atom_list[bond.a1_num - 1].type == 'H'):
count_h[1] = count_h[1] + 1
Hlist.append(bond.a1_num)
print(Hlist)
print(count_h)
# (1) remove 5 hydrogen atoms,
# (2) change Si to Du and the atom name,
new_atomlist = []
for i, atom in enumerate(mol.atom_list):
print(i, atom.num)
#exit()
if atom.num in Hlist:
continue
if atom.num - 1 == Si1:
atom.type = 'Du'
atom.Q = 0.0
print("Hcount ==", count_h[0])
if count_h[0] == 3:
atom.name = 'D2'
elif count_h[0] == 0: # SG will just have no H
#elif count_h[0] == 2:
atom.name = 'D1'
if atom.num - 1 == Si2:
atom.type = 'Du'
atom.Q = 0.0
print("Hcount ==", count_h[1])
if count_h[1] == 3:
atom.name = 'D2'
#elif count_h[1] == 2: #
elif count_h[1] == 0: # SG will just have no H
atom.name = 'D1'
new_atomlist.append(copy.copy(atom))
# (3) generate mapping from old to new atom numbering to be used in the bond modification.
atom_num_map = {}
for i, atom in enumerate(new_atomlist):
atom_num_map[atom.num] = i + 1
atom.num = i + 1
# (4) remove bonds that contain any of the removed hydrogens.
new_bondlist = []
for i, bond in enumerate(mol.bond_list):
if bond.a1_num in Hlist or bond.a2_num in Hlist:
continue
new_bondlist.append(copy.copy(bond))
# (5) renumber the bonds, map old atom numbering to new atom number for bonds
i = 1
for bond in new_bondlist:
bond.num = i
bond.a1_num = atom_num_map[bond.a1_num]
bond.a2_num = atom_num_map[bond.a2_num]
i = i + 1
mol.atom_list = new_atomlist
mol.bond_list = new_bondlist
# ajust Si-Si-C bond angle. Looks like it is 90 deg.
#ajust_angle(mol,ang)
# ajust the partial charge to make it an integer.
make_integer_charge(mol, ori_formal_charge)
#exit()
filename = outputprefix + '.mol2'
if frist:
mol2.write_mol2(mol, filename)
frist = False
else:
mol2.append_mol2(mol, filename)
return
for j, mol_3 in enumerate(mol_3list):
print "molecule %d" % (j)
#mol_3_new = copy.deepcopy(mol_3)
atomlist = []
for i, move in enumerate(maping):
#print i,move,maping[i]
atom = mol_3.atom_list[move]
atom.num = i + 1
atomlist.append(atom)
#mol_3_new.atom_list = atomlist
#bondlist = copy.deepcopy(mol_2.bond_list)
bondlist = mol_2.bond_list
header = mol_3.header
name = mol_3.name
residuelist = mol_3.residue_list
mol_3_new = mol2.Mol(header, name, atomlist, bondlist, residuelist)
print mol_3.header, mol_3_new.header
# for bond in mol_3_new.bond_list:
# print bond.a1_num, bond.a2_num, bond.num, bond.type
# print atomlist[bond.a1_num-1].num, atomlist[bond.a2_num-1].num, bond.num, bond.type
if j == 0:
mol2.write_mol2(mol_3_new, outfile)
else:
mol2.append_mol2(mol_3_new, outfile)
#print len(mol_list)
#mol = mol2.remove_hydrogens( mol_list[0] )
#mol2.write_mol2(mol,outfile)
def zernike_moments(mol2_file, nmax=20, np=50, uniform=True, fix_dx=False, np_on_grid=20, shift=False, buildmap=False, coef_out=True, calc_intensity=True, external_rmax=-1):
base = mol2_file.split('.')[0]
splat_range = 0
fraction = 0.9
default_dx = 0.5
models = mol2.read_Mol2_file( mol2_file )
if(len( models )== 0):
return None,None,None
## for testing purpose, here only the first model in the mol2 file is converted ##
this_molecule = models[0]
## models should be a list of molecules, same ligand at different conformations ##
all_atoms = this_molecule.atom_list
if(len( all_atoms )== 0):
return None,None,None
# predefine some arrays we will need
xyz = flex.vec3_double()
charges = flex.double()
# keep track of the atom types we have encountered
for atom in all_atoms:
xyz.append( ( atom.X, atom.Y, atom.Z ) )
charges.append( atom.Q )
if(xyz.size() == 0):
return None,None,None
if (uniform):
density=flex.double(xyz.size(),1.0)
else: # use charges
density=charges
voxel_obj = math.sphere_voxel(np,splat_range,uniform,fix_dx,external_rmax, default_dx, fraction,xyz,density)
np = voxel_obj.np()
rmax=voxel_obj.rmax()/fraction
#print base, "RMAX: ", voxel_obj.rmax()
#print time.time()
grid_obj = math.sphere_grid(np, nmax)
pdb_out = False
grid_obj.clean_space(voxel_obj, pdb_out)
#print time.time(), "END GRID CONST"
grid_obj.construct_space_sum()
#print time.time(), "SS CALC"
mom_obj = math.zernike_moments(grid_obj, nmax)
#print time.time(), "END MOM CALC"
moments = mom_obj.moments()
if(coef_out):
nn = mom_obj.fnn()
easy_pickle.dump(base+'.nlm.pickle', moments.coefs() )
easy_pickle.dump(base+'.nn.pickle', nn.coefs() )
#
####### The following will be optional ###
if(shift):
shift = [rmax, rmax, rmax]
centered_xyz = voxel_obj.xyz() + shift
out_mol2_filename =base+'_centered.mol2'
for a,xyz in zip( all_atoms, centered_xyz):
a.X = xyz[0]
a.Y = xyz[1]
a.Z = xyz[2]
mol2.write_mol2( this_molecule, out_mol2_filename )
original_map = voxel_obj.map()
xplor_map_type( original_map, np, rmax, file_name=base+'_pdb.xplor')
######## Calculate Intnesity Profile ############
if(calc_intensity):
q_array = flex.double( range(51) )/100.0
z_model = zm.zernike_model( moments, q_array, rmax, nmax)
nn = mom_obj.fnn()
intensity = z_model.calc_intensity(nn)
#iq_file = open(base+"_"+str(nmax)+"_"+str(int(rmax*fraction))+".zi", 'w')
iq_file = open(base+"_"+str(nmax)+".zi", 'w')
for qq, ii in zip(q_array, intensity):
print>>iq_file, qq,ii
iq_file.close()
####### END of Intensity Calculation ###########
if(buildmap):
print "grid setting up..."
zga = math.zernike_grid(np_on_grid, nmax, False)
print "grid setting up...Done"
zga.load_coefs(moments.nlm(), moments.coefs() )
print "start reconstruction"
map=flex.abs(zga.f() )
print "finished reconstruction"
xplor_map_type( map, np_on_grid, rmax, file_name=base+'.xplor')
ccp4_map_type( map, np_on_grid, rmax, file_name=base+'.ccp4' )
return mom_obj, voxel_obj, models
import mol2 import sys print "this file requiers the mol2 libary writen by trent balius and sudipto mukherjee" print "syntex: mol2_removeH.py input_file output_file" infile = sys.argv[1] outfile = sys.argv[2] mol_list = mol2.read_Mol2_file(infile) print len(mol_list) mol = mol2.remove_hydrogens( mol_list[0] ) mol2.write_mol2(mol,outfile)
