thank you Ed for suggesting this alternative
regards
Alfredo
Enviado desde BlueMail
En 29 de junio de 2018 05:56, en 05:56, Ed Griffen <ed.grif...@medchemica.com>
escribió:
>Using the string length to find the number of atoms in a molecule is OK
>- but you need to take account of the additional characters in SMILES
>that are not just atoms, for example:
>
>two letter elements - like silicon, chlorine etc
>brackets , ring closures, charges, explicit hydrogens
>
>It’s simple to do:
>
>Here’s a worked example:
>
>>>> SMILES = 'C[S@@+]([O-])c1ccc(cc1)[Si](C)(C)C'
>>>> print(len(SMILES))
>34
>>>> heavies = [char for char in SMILES if char not in
>'''()[]1234567890#:;,.?%-=+\/Hherlabdgfikmputvy@''']
>>>> print(len(heavies))
>13
>
>obviously you do this after splitting on the .
>
>Best regards,
>
>Ed
>
>Dr Ed Griffen,
>Technical Director,
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>> On 29 Jun 2018, at 06:37, Alfredo Quevedo <maquevedo....@gmail.com>
>wrote:
>>
>> thank you Hideyoshi for your feedback.
>> regards
>> Alfredo
>>
>> Enviado desde BlueMail <http://www.bluemail.me/r?b=13187>
>> En 28 de junio de 2018, en 21:43, "藤秀義" <hideyoshif...@gmail.com
><mailto:hideyoshif...@gmail.com>> escribió:
>> Dear Alfredo,
>>
>> Although not strictly based on the number of atoms, but on the length
>of SMILES string, the simplest way is using Python built-in functions
>as follows:
>>
>> smiles = 'CCC.CC'
>> fragment = max(smiles.split('.'), key=len)
>> print (fragment)
>>
>> Best regards,
>>
>> Hideyoshi
>>
>>
>> thank you Paolo for this help, I will study the code and try it,
>> best regards
>>
>> Alfredo
>>
>> Enviado desde BlueMail <http://www.bluemail.me/r?b=13187>
>> En 28 de junio de 2018, en 17:08, Paolo Tosco
><paolo.tosco.m...@gmail.com <mailto:paolo.tosco.m...@gmail.com>>
>escribió:
>>
>> Dear Alfredo,
>>
>> if you wish to keep only the largest disconnected fragment you may
>try
>> the following:
>>
>> mols = list(rdmolops.GetMolFrags(mol, asMols = True))
>> if (mols):
>> mols.sort(reverse = True, key = lambda m: m.GetNumAtoms())
>> mol = mols[0]
>>
>> Hope that helps, cheers
>> p.
>>
>> On 06/28/18 19:38, Alfredo Quevedo wrote:
>> Good afternoon,
>>
>> I would like to filter out small fragments from a list of molecules
>> using the below strategy:
>>
>> from rdkit import Chem
>> from rdkit.Chem import AllChem
>> from rdkit.Chem import SaltRemover fragment
>>
>> remover=SaltRemover.SaltRemover()
>> mol=Chem.MolFromSmiles('CCC.CC')
>> res=remover.StripMol(mol)
>> print(res.GetNumAtoms())
>>
>>
>> I am getting 5 atoms as output, so the ´CC´ is not being stripped
>(the
>> script workd ok for salts). Is there any way of filtering non salts
>> small fragments?
>>
>> thank you very much in advance,
>>
>> regards,
>>
>> Alfredo
>>
>>
>>
>>
>>
>>
>>
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