I'm writing a function script in Python for PyMOL and I need to convert an
atoms number to its location, or somehow gain a list of atom locations form
a group location.
When the script is ran and the function is used the atom locations are
entered :
GKDistance("////GLY`730/*","////LYS`115/N*")
If I could somehow turn those two group locations into two lists or atom
names in those groups then I could finish writing this program. But I am
having no luck of converting the group location or the atom number to the
atom locations in that group.
I do also understand the cmd.distance command is being used with atom
numbers instead of locations, I just left it that way but I do understand
that the command does no work this way. Everything else in my program
outputs the way I want it to too.
Here is a copy of my script:
def GKDistance(group1, group2 ):
from pymol import stored
f=open('DistanceResults.txt','w')
group_distance=cmd.distance(group1,group2)
f.write("Distance of group 1 to group 2 is:")
f.write("\n")
group_average="%f" %group_distance
f.write(group_average)
f.write("\n")
list1=cmd.index(group1)
list2=cmd.index(group2)
for i in range(0,len(list1)):
location=list1[i]
header="Group1 atom %s distance to:" %(location[1])
f.write(header)
f.write("\n")
for j in range(0,len(list2)):
statement=list2[j]
distance=cmd.distance('%d','%d') %(location[1],statement[1])
fullstatement="atom %s is %d \n" %(statement[1], 50)
f.write(fullstatement)
from pymol import cmd, stored
cmd.extend( "GKDistance", GKDistance );
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