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2024-05-02T18:11:53Z

asdf

← Older revision		Revision as of 18:11, 2 May 2024
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	category_file.write('{0}'.format(entry))		category_file.write('{0}'.format(entry))
	</pre>		</pre>

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Jyoung at 19:15, 15 April 2020

2020-04-15T19:15:41Z

← Older revision		Revision as of 19:15, 15 April 2020
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	<pre>from __future__ import print_function		<pre>
			###########################
			# Written by Jennifer Young
			# Last revised April 2020
			# Version 1.0
			###########################

			from __future__ import print_function
	import pdb		import pdb
	import itertools		import itertools

Frodo: asdf

2020-04-15T16:58:46Z

asdf

New page

<pre>from __future__ import print_function
import pdb
import itertools
import sys
import shlex
import subprocess

from rdkit.Chem import (
MolFromSmiles,
MolToSmiles,
AddHs,
)

from rdkit.Chem.SaltRemover import (
SaltRemover
)

from rdkit.Chem.Descriptors import MolLogP, MolWt

def scale_logp_value(logp):
if logp < -9.0:
logp = -9.0
elif logp > 9.0:
logp = 9.0
elif logp < 0 or logp >= 5.0:
logp = 100*int(logp)
elif logp >= 0.0 or logp < 1:
logp = 10*int(10*logp)
elif logp >= 1.0 or logp < 4:
logp = int(100*logp)
elif logp >=4 or logp < 5:
logp = 10*int(10*logp)
return logp

if __name__ == '__main__':
if len(sys.argv) != 3:
print('Usage: python rdkit_hlogp_batch.py <smiles> <batch_size>')
exit()

BATCH_SIZE = int(sys.argv[2])
hlogp_list = list()
with open(sys.argv[1]) as smiles_file:
file_lines = smiles_file.readlines()
for line in file_lines:
if line.strip():
smiles, cid = str(line).strip().split()[:2]
mol = MolFromSmiles(smiles)
remover = SaltRemover()
res, deleted = remover.StripMolWithDeleted(mol)
if res is not None:
res.SetProp('_Name', cid)
logp = MolLogP(res)
num_heavy_atoms = res.GetNumHeavyAtoms()
if num_heavy_atoms > 99:
num_heavy_atoms = 99
scaled_logp = scale_logp_value(logp)
if logp < 0.0:
sign = 'M'
#remove the minus sign so it's not printed
scaled_logp = scaled_logp * -1
else:
sign = 'P'
key_string = 'H{:02}{}{:03}'.format(num_heavy_atoms, sign, scaled_logp)

#store in list up to batch size, then write out to new file
final_string = '{0} {1} {2}\n'.format(smiles, cid, key_string)
hlogp_list.append(final_string)

#write the key string to the file
if len(hlogp_list) >= BATCH_SIZE:
with open('{0}_hlogp'.format(sys.argv[1]), 'a+') as category_file:
for entry in hlogp_list:
category_file.write('{0}'.format(entry))
#clear list because we already wrote these
hlogp_list = list()
#write remaining molecules to file
for entry in hlogp_list:
with open('{0}_hlogp'.format(sys.argv[1]), 'a+') as category_file:
for entry in hlogp_list:
category_file.write('{0}'.format(entry))
</pre>

Rdkit hlogp batch.py - Revision history

Frodo: asdf

Jyoung at 19:15, 15 April 2020

Frodo: asdf