Vitor Hideyoshi Nakazone Batista
2899031b71
Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
65 lines
1.7 KiB
Python
65 lines
1.7 KiB
Python
#!/opt/local/bin/python3
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import sys, math
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from math import pi
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import numpy as np
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from numpy import linalg
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from numpy.random import rand, random
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from copy import deepcopy
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from DPpack.MolHandling import *
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from DPpack.PTable import *
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natoms = input("# of atoms: ")
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natoms = int(natoms)
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file = input("xyz file: ")
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molecules=[]
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with open(file) as fh:
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xyzfile = fh.readlines()
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file += ".new"
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file2 = file + "2"
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fh = open(file, "w")
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fh2 = open(file2, "w")
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total_atoms = int(xyzfile.pop(0).split()[0])
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fh.write("{}\n".format(total_atoms))
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comment = xyzfile.pop(0)
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fh.write("{}".format(comment))
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nmols = round(total_atoms/natoms)
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for i in range(nmols):
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molecules.append([])
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for j in range(natoms):
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molecules[i].append({})
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line = xyzfile.pop(0).split()
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molecules[i][j]['na'] = int(line[0])
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molecules[i][j]['rx'] = float(line[1])
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molecules[i][j]['ry'] = float(line[2])
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molecules[i][j]['rz'] = float(line[3])
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molecules[i][j]['mass'] = atommass[molecules[0][j]['na']]
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for atom in molecules[0]:
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fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
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atom['rx'], atom['ry'], atom['rz']))
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fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
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atom['rx'], atom['ry'], atom['rz']))
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for i in range(1, nmols):
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fh2.write("{}\n".format(natoms))
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fh2.write("{}".format(comment))
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rmsd, projected_mol = rmsd_fit(molecules[i], molecules[0])
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print("{:>9.5f}".format(rmsd))
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for atom in projected_mol:
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fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
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atom['rx'], atom['ry'], atom['rz']))
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fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']],
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atom['rx'], atom['ry'], atom['rz']))
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fh.close()
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fh2.close()
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