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 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 main():
if len(sys.argv) != 6: # if no input
print ("ERORR:")
print ("syntex: distance_cal_no_precomput.py mol2_file(docked poses) mol2_file(find poses close to) threshold hname output ")
return
infilemol2_poses = sys.argv[1]
infilemol2_ref = sys.argv[2]
dist_threshold = float(sys.argv[3])
hname = sys.argv[4]
outfile = sys.argv[5]
print ("input file (poses) = ", infilemol2_poses)
print ("input file (reference) = ", infilemol2_ref)
print ("threshold =", dist_threshold)
print ("head_name =", hname)
print ("outputprefix =", outfile)
#mol2_vector = mol2.read_Mol2_file(infilemol2_poses)
mol2_vector = mol2.read_Mol2_file_head(infilemol2_poses)
mol2_ref = mol2.read_Mol2_file(infilemol2_ref)[0]
count = 0
for mol in mol2_vector:
min_dist = 100000
count_atom_lt_thes = 0
for atom in mol.atom_list:
if (atom.type == 'H'):
continue
#dist = cal_dist_closest_grid_point(grid_dist,gridscale,xn,yn,zn,origin,atom)
#dist = cal_dist_tri_linear(grid_dist,gridscale,xn,yn,zn,origin,atom)
dist = cal_min_dist_atom_mol(atom,mol2_ref)
if dist < min_dist:
min_dist = dist
if dist < dist_threshold:
count_atom_lt_thes = count_atom_lt_thes + 1
if min_dist < dist_threshold:
print("mol %d,dist=%f,num_atom_lt_threshold=%d"%(count,min_dist,count_atom_lt_thes))
#close_mol2.append(mol)
mol.header = mol.header+"########## %s_dist: %f\n"%(hname,min_dist)
mol.header = mol.header+"########## %s_num_atom_lt_threshold: %d\n"%(hname,count_atom_lt_thes)
mol2.append_mol2(mol, outfile+'.mol2')
count = count + 1
def multimol2_removeH(input, output):
#print "This file requires the mol2 library written by Trent Balius (AKA Xiaobo Wan) and sudipto mukherjee"
#print "syntex: multimol2_removeH.py input_file output_file"
infile = input
outfile = output
file = open(outfile, 'w') # overwrite
file.close()
mol_list = mol2.read_Mol2_file_head(infile)
#print len(mol_list)
for i in range(len(mol_list)):
#print "mol ", i
mol = mol2.remove_hydrogens(mol_list[i])
mol2.append_mol2(mol, outfile)
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)
import mol2
import sys
print "this file requiers the mol2 libary writen by trent balius and sudipto mukherjee"
print "syntex: multimol2_removeH.py input_file output_file"
infile = sys.argv[1]
outfile = sys.argv[2]
file = open(outfile, 'w') # overwrite
file.close()
mol_list = mol2.read_Mol2_file_head(infile)
print len(mol_list)
for i in range(len(mol_list)):
print "mol ", i
mol = mol2.remove_hydrogens(mol_list[i])
mol2.append_mol2(mol, outfile)