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Crystal-MET
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tcl file

This commit is contained in:
NehZio 2022-03-03 13:41:18 +01:00
parent eef1cf3d03
commit fda13b9553
1 changed files with 20 additions and 1 deletions
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21
crystal_mec.py
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@ -22,7 +22,8 @@ if __name__=='__main__':
elif sys.argv[2] == 'vvv':
verbose = 3
else:
print("Unknown argument -%s-"%sys.argv[3])
print("Unknown argument -%s-"%sys.argv[2])
sys.exit()
elif len(sys.argv) > 3:
print("Too much arguments, please provide an input file and a verbose level (v, vv, vvv)")
sys.exit()
@ -164,3 +165,21 @@ if __name__=='__main__':
print("The output has been written to %s \n"%outputFile)
out_interatomic_distances(coordinates)
with open("output.tcl",'w') as f:
tp = [atoms[i] for i in range(0, len(atoms), 4)]
f.write("mol new fragment.xyz\nmol delrep 0 0\nmol representation CPK\n")
for i in tp:
if i in ["Sc", "Ti", "V" , "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
"Y" , "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd",
"La", "Hf", "Ta", "W" , "Re", "Os", "Ir", "Pt", "Au", "Hg"]:
f.write('mol selection "type {:s}"\nmol color ColorID 3\nmol addrep 0\n'.format(i))
elif i in ["F", "Cl", "Br", "I"]:
f.write('mol selection "type {:s}"\nmol color ColorID 7\nmol addrep 0\n'.format(i))
else:
f.write('mol selection "type {:s}"\nmol color Name\nmol addrep 0\n'.format(i))
f.write("mol new bath_coloured.xyz\nmol delrep 0 1\nmol representation Points\n")
f.write('mol selection "type Cl"\nmol color colorID 17\nmol addrep 1\n')
f.write('mol selection "type C"\nmol color colorID 0\nmol addrep 1\n')