*[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)
