def main():
if len(sys.argv) != 6: # if no input
print("ERORR:")
print(
"syntex: mol2_energy_filter mol2_file(docked poses) energy_threshold energyname cnum output "
)
print(
" energyname is the name of the energy term and cnum is the column, eg 'Total Energy' where cnum is 4 or 'Footprint_Similarity_Score:' where cnum is 3"
)
return
infilemol2_poses = sys.argv[1]
val = float(sys.argv[2])
ename = sys.argv[3]
cnum = int(sys.argv[4])
outfile = sys.argv[5]
print("input file (poses) = %s" % infilemol2_poses)
print("energy threshold = %f" % val)
print("outputprefix = %s" % outfile)
if infilemol2_poses.split('.')[-1] == 'mol2':
print("reading in mol2")
#mol2_vector = mol2.read_Mol2_file(infilemol2_poses)
mol2_vector = mol2.read_Mol2_file_head(infilemol2_poses)
if infilemol2_poses.split('.')[-1] == 'gz':
print("reading in gz mol2 file")
mol2_vector = mol2.read_Mol2_file_head_gz(infilemol2_poses)
count = 0
for mol in mol2_vector:
#print(mol.header)
lines = mol.header.split('\n') #file1.close()
for line in lines:
#print(line)
if ename in line:
#print(line)
splitline = line.split()
energy = float(splitline[cnum - 1])
#print(energy)
if energy < val:
print(energy)
mol2.append_mol2(mol, outfile + '.mol2')
def main():
if len(sys.argv) != 4: # if no input
print("ERORR:")
print(
"syntex: mol2_energy_filter mol2_file(docked poses) energy_threshold output "
)
return
infilemol2_poses = sys.argv[1]
val = float(sys.argv[2])
outfile = sys.argv[3]
print("input file (poses) = %s" % infilemol2_poses)
print("energy threshold = %f" % val)
print("outputprefix = %s" % outfile)
if infilemol2_poses.split('.')[-1] == 'mol2':
print("reading in mol2")
#mol2_vector = mol2.read_Mol2_file(infilemol2_poses)
mol2_vector = mol2.read_Mol2_file_head(infilemol2_poses)
if infilemol2_poses.split('.')[-1] == 'gz':
print("reading in gz mol2 file")
mol2_vector = mol2.read_Mol2_file_head_gz(infilemol2_poses)
count = 0
for mol in mol2_vector:
#print(mol.header)
lines = mol.header.split('\n') #file1.close()
for line in lines:
#print(line)
if 'Total' in line:
#print(line)
splitline = line.split()
energy = float(splitline[3])
#print(energy)
if energy < val:
print(energy)
mol2.append_mol2(mol, outfile + '.mol2')
def main():
if len(sys.argv) != 3: # if no input
print("ERORR:")
print("syntex: mol2_energy_sort mol2_file(docked poses) output ")
return
infilemol2_poses = sys.argv[1]
outfile = sys.argv[2]
print("input file (poses) = %s" % infilemol2_poses)
print("outputprefix = %s" % outfile)
if infilemol2_poses.split('.')[-1] == 'mol2':
print("reading in mol2")
#mol2_vector = mol2.read_Mol2_file(infilemol2_poses)
mol2_vector = mol2.read_Mol2_file_head(infilemol2_poses)
if infilemol2_poses.split('.')[-1] == 'gz':
print("reading in gz mol2 file")
mol2_vector = mol2.read_Mol2_file_head_gz(infilemol2_poses)
count = 0
energy_vec = []
for mol in mol2_vector:
lines = mol.header.split('\n') #file1.close()
for line in lines:
if 'Total' in line:
splitline = line.split()
energy = float(splitline[3])
energy_vec.append(energy)
energy_vec_sort = sorted(enumerate(energy_vec), key=lambda x: x[1])
#energy_vec_sort = sorted(enumerate(energy_vec), key=lambda x: -x[1])
for entry in energy_vec_sort:
print(entry)
print(entry[0])
mol2.append_mol2(mol2_vector[entry[0]], outfile + '.mol2')
print("wrong number of arguments. there must be 5 or 6, not %d. " %
len(sys.argv))
exit()
infile = sys.argv[1]
outfile = sys.argv[2]
a1_ori = sys.argv[3] # ori
a2_rep = sys.argv[4]
a3_search = sys.argv[5]
if (len(sys.argv) == 7):
a2_name = sys.argv[6] #new atom name
else:
a2_name = "NONE"
print(
'infile=%s,\noutfile=%s,\na1_ori=%s,\na2_rep=%s,\na3_search=%s\na2_name=%s\n'
% (infile, outfile, a1_ori, a2_rep, a3_search, a2_name))
mol_list = mol2.read_Mol2_file(infile)
print(len(mol_list))
count = 0
for mol in mol_list:
moln = loop_bonds(a1_ori, a2_rep, a3_search, a2_name, mol)
if (count == 0):
mol2.write_mol2(moln, outfile)
else:
mol2.append_mol2(moln, outfile)
count = count + 1
print("processed %d mol2 entries" % count)
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].type == 'Si':
print (mol.atom_list[i].type, mol.atom_list[i].name)
Si_atoms_index.append(i)
#if len(Si_atoms_index) != 2:
if len(Si_atoms_index) != 1:
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
if count_h[0] == 3:
#atom.name = 'D2'
atom.name = 'D1'
elif count_h[0] == 2:
#atom.name = 'D1'
print ("error")
exit()
# if atom.num-1 == Si2:
# atom.type = 'Du'
# atom.Q = 0.0
# if count_h[1] == 3:
# atom.name = 'D2'
# elif count_h[1] == 2: #
# 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 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