The impetus for this was that someone gave me an XYZ file the had generated by copying columns from Excel. On Mac. mac2unix took care of the line endings, but there were tabs (\t) all over the place.
Usage:
polish_xyz ugly.xyz pretty.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="">3:
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')
itson=False
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)
