Hi all,
I'm trying to write a script to data mine the pdb. I'm want to look at the
ligands in a pdb file and fish out those that meet a certain criteria. I've
got a script that can look at the ligands all at once but I need to assess
each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
define them individually. I've tried variations on "%s' % (resi)" and
"bymolec" but I can't seem to figure out how to get them parsed separately
without specifying a number. I've also tried using index to create a tuples
list and iterating from that but I keep hitting the same issue. I've
attached a couple of the attempted scripts so you can laugh at my google
derived python skills.
I've been trying to figure this out for a week now and I'm completely
stumped. If anyone could nudge me in the right direction, even if it's some
Pymolwiki article I missed, I would appreciate it immensely.
Thanks for your time,
Katherine
--
"Nil illegitimo carborundum"* - *Didactylos
from pymol import cmd
from glob import glob
for file in glob("*.pdb"):
cmd.load(file,'prot')
#some selection criteria. I've tried 'het and (not solvent) and %s' % (resi)
while cmd.count_atoms("solvent within 3.5 of sele") != 0
if cmd.count_atoms("solvent within 3.5 of het") == 0:
print file
break
cmd.delete("prot")
from pymol import cmd
from glob import glob
for file in glob("*.pdb"):
cmd.load(file,'prot')
for a in cmd.index('het and (not solvent) and %s' % (resi)):
solvent.name = []
cmd.iterate('%a', count_atoms('solvent within 3.5 of %a'))
if cmd.count_atoms("solvent within 3.5 of %a") == 0:
print file
cmd.delete("prot")
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