def main():
if len(sys.argv) != 3: # if no input
print "ERORR"
return
namemol2 = sys.argv[1]
namesph = sys.argv[2]
mol = mol2.remove_hydrogens(mol2.read_Mol2_file(namemol2)[0])
write_sph(namesph, mol)
def main():
if len(sys.argv) != 3: # if no input
print "ERORR"
print "this script reads in a mol2 file and writes out a sph file."
print "this script takes 2 arguments: name.mol2 name.sph"
return
namemol2 = sys.argv[1]
namesph = sys.argv[2]
mol = mol2.remove_hydrogens(mol2.read_Mol2_file(namemol2)[0])
write_sph(namesph, mol)
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)
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)
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)
for mol_withH in mol_list:
mol = mol2.remove_hydrogens(mol_withH)
mol2.append_mol2(mol, outfile)
continue
# Atoms down here are always hydrogen
elif (a1.heavy_atom):
print bond.a1_num, bond.a1_num, m.atom_list[bond.a1_num-1].Q, m.atom_list[bond.a2_num-1].Q
m.atom_list[bond.a1_num-1].Q = m.atom_list[bond.a1_num-1].Q + m.atom_list[bond.a2_num-1].Q
m.atom_list[bond.a2_num-1].Q = 0
elif (a2.heavy_atom):
print bond.a1_num, bond.a1_num, m.atom_list[bond.a1_num-1].Q, m.atom_list[bond.a2_num-1].Q
m.atom_list[bond.a2_num-1].Q = m.atom_list[bond.a2_num-1].Q + m.atom_list[bond.a1_num-1].Q
m.atom_list[bond.a1_num-1].Q = 0
# Assuming that residue list does not change
#data = mol2.Mol(m.header,m.name,atom_list,bond_list,m.residue_list)
#return data
return m
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)
mol1 = combine_q_and_remove_hydrogens(mol_list[0])
mol = mol2.remove_hydrogens( mol1 )
mol2.write_mol2(mol,outfile)