519. Formatting an XYZ molecular geometry file using python

This is a silly little script -- ECCE, which I use to manage all my computations, is very particular about what XYZ files it can and cannot read -- if the number of spaces between the coordinates are wrong, it will fail to read the structure. So here's a python script, based on parts I've cannibalised from other scripts that I've written in the past (i.e. it could be made more elegant, but I had the parts ready and just wanted something that works) which takes a somewhat ugly XYZ file and turns it into something beautiful. At least in the eyes of ECCE.

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)

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About Admin MC3

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