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)
print "syntex: mol2_shuffle.py input_file1 input_file2 input_file3 output_file"
print "this file takes in 3 mol2 input files 2 of the files are the same but a different order. "
print "The 3 input is a file that you want to suffle for the order of 1 to 2"
print "(1) origenal order."
print "(2) the new order."
print "(3) mol2 to file to change the order (can be multi mol2)"
print "(4) name to which to write newly reordered mol2."
infile1 = sys.argv[1]
infile2 = sys.argv[2]
infile3 = sys.argv[3]
outfile = sys.argv[4]
mol_1 = mol2.read_Mol2_file(infile1)[0] # ori order
mol_2 = mol2.read_Mol2_file(infile2)[0] # new order
mol_3list = mol2.read_Mol2_file_head(infile3)
maping = maping_by_cord(mol_1, mol_2)
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)
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)