What I'm showing here is probably overkill -- there may be better ways of doing this with sed/awk*. However, since I had most of the code below ready as it was part of another script, doing this is python was quick and easy. Plus it's portable-ish.
*[ECCE, which I use for managing my calculations, is very, very particular about the format of the XYZ file, including the number of chars between coordinates. So simply doing e.g.
won't work. Not all pieces of software are that picky when it comes to xyz coordinates though -- jmol, for example, is very forgiving.]
Anyway, the script below flips a molecular structure by taking the geometry given as a (properly formatted) XYZ file, and changing the sign in front of the Z coordinates. It's that simple.
Save it, call it flip_xyz, make it executable and call it using e.g.
Script:
*[ECCE, which I use for managing my calculations, is very, very particular about the format of the XYZ file, including the number of chars between coordinates. So simply doing e.g.
cat molecule.xyz|gawk '{print $1,$2,$3,-$4}'won't work. Not all pieces of software are that picky when it comes to xyz coordinates though -- jmol, for example, is very forgiving.]
Anyway, the script below flips a molecular structure by taking the geometry given as a (properly formatted) XYZ file, and changing the sign in front of the Z coordinates. It's that simple.
Save it, call it flip_xyz, make it executable and call it using e.g.
flip_xyz molecule.xyz flipped_molecule.xyz
Script:
#!/usr/bin/python
import sys
def getrawdata(infile):
f=open(infile,'r')
n=0
preamble=[]
struct=[]
for line in f:
if n<2: data-blogger-escaped-if="" data-blogger-escaped-line.rstrip="" data-blogger-escaped-n="" data-blogger-escaped-preamble="">1:
line=line.rstrip()
struct+=[line]
n+=1
xyz=[struct]
return xyz, preamble
def genxyzstring(coords,elementnumber):
x_str='%10.5f'% coords[0]
y_str='%10.5f'% coords[1]
z_str='%10.5f'% -coords[2]
element=elementnumber
xyz_string=element+(3-len(element))*' '+10*' '+\
(8-len(x_str))*' '+x_str+10*' '+(8-len(y_str))*' '+y_str+10*' '+(8-len(z_str))*' '+z_str+'\n'
return xyz_string
def getstructures(rawdata,preamble,outfile):
n=0
for structure in rawdata:
n=n+1
num="%03d" % (n,)
g=open(outfile,'w')
cartesian=[]
for item in structure:
coordx=filter(None,item.split(' '))
coordy=filter(None,item.split('\t'))
if len(coordx)>len(coordy):
coords=coordx
else:
coords=coordy
coordinates=[float(coords[1]),float(coords[2]),float(coords[3])]
element=coords[0]
cartesian+=[genxyzstring(coordinates,element)]
g.write(str(preamble[0])+'\n')
g.write(str(preamble[1])+'\n')
for line in cartesian:
g.write(line)
g.close()
cartesian=[]
return 0
if __name__ == "__main__":
infile=sys.argv[1]
outfile=sys.argv[2]
xyz,preamble=getrawdata(infile)
structures=getstructures(xyz,preamble,outfile)
This is dummy text. It is not meant to be read. Accordingly, it is difficult to figure out when to end it. But then, this is dummy text. It is not meant to be read. Period.
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