Adicionar informações sobre smiles das moleculas #33

lipelopesoliveira · 2023-03-02T18:18:52Z

Motivação

Atualmente os blocos de construção e grupos químicos são armazenados na no formato xyz. É possível também adicionar as informações no formato smiles também:

Para o benzeno tripodal:
Organic core: C1=CC=CC=C1
Building Block: [Q]C1=C([Q])C([R1])=C([Q])C([Q])=C1[R1]

O que deve ser feito?

Alterar a forma como as informações são salvas internamente para um formato json que contenha as posições atômicas mas também outras informações sobre os blocos de construção. Considerar utilizar um formato Chemical JSON.

Os códigos para ler o BuildingBlock e criar o Retículo devem utilizar esses arquivos, além de herdar a informação do código SMILES.

Etapas para a realização desta tarefa:

O que será obtido ao final dessa tarefa?

Possui prazo limite de conclusão?

Mais alguma outra coisa?

The text was updated successfully, but these errors were encountered:

lipelopesoliveira · 2023-03-03T18:03:25Z

O código SMILES para cada bloco de construção deverá ser salvo no formato Chemaxon Extended SMILES (XSMILES, rdkit). Esse formato permite que as imagens dos blocos de construção sejam geradas com os labels Q, Rx e X:

Esse formato o bloco de construção acima possui o código:

(*)C1=C(*)C(*)=C(*)C(*)=C1(*) |$Q;;;R1;;R2;;Q;;R1;;R2$|

Será necessário desenvolver uma forma de automatizar o processo de geração desses códigos, uma vez que fazer isso manualmente será extremamente trabalhoso.

lipelopesoliveira · 2023-03-03T18:55:15Z

Tendo o código smiles da molécula com os átomos especiais, o código abaixo gera o xsmiles com os labels:

smiles_string = '[Q]C1=C([Q])C([R1])=C([Q])C([Q])=C1[R1]'

def smiles_to_xsmiles(smiles_string:str) -> str:
    '''
    Converts a SMILES string to an extended SMILES string with labels

    Parameters
    ----------
    smiles_string : str
        SMILES string to be converted
    
    Returns
    -------
    xsmiles : str
        Extended SMILES string with labels
    '''
    SPECIAL_ATOMS = ['Q', 'R', 'X']
    REGULAR_ATOMS = ['C', 'N', 'H', 'O']

    xsmiles = ''

    labels = []
    
    for i, letter in enumerate(smiles_string):

        if letter in SPECIAL_ATOMS:
            xsmiles += '*'
            labels += [letter]
        
        elif letter.isnumeric():
            if smiles_string[i-1] == 'R':
                labels[-1] = labels[-1] + letter
            else:
                xsmiles += letter
        
        elif letter in REGULAR_ATOMS:
            xsmiles += letter
            labels += ['']
        
        else:
            xsmiles += letter

    return xsmiles + ' |$' + ';'.join(labels) + '$|'

> smiles_to_xsmiles(smiles_string)
'[*]C1=C([*])C([*])=C([*])C([*])=C1[*] |$Q;;;Q;;R1;;Q;;Q;;R1$|'

lipelopesoliveira · 2023-03-03T19:03:30Z

from rdkit import Chem
from rdkit.Chem import Draw

SMILES_LIST = ['[*]C1=C([*])C([*])=C([*])C([*])=C1[*] |$Q;;;R1;;R2;;Q;;R1;;R2$|', 
               '[*]C1=C([*])C([*])=C(C2=C([*])C([*])=C([*])C([*])=C2[*])C([*])=C1[*] |$Q;;;R1;;R4;;;;R4;;R1;;Q;;R2;;R3;;R3;;R2$|', 
               'c1c(O)cccn1', 
               'c1c(F)c(C)ccn1', 
               'c1cc(Cl)c(F)cn1']

NAMES_LIST = ['Benzene', "1-1'-biphenyl", 'c1c(O)cccn1', 'c1c(F)c(C)ccn1', 'c1cc(Cl)c(F)cn1']

mols = [Chem.MolFromSmiles(smi) for smi in SMILES_LIST]

Draw.MolsToGridImage(mols, 
                     molsPerRow=3, 
                     legends=NAMES_LIST, 
                     subImgSize=(300,200),
                     useSVG=True)

Esse código gera uma imagem com todas as moléculas.

lipelopesoliveira · 2023-03-03T20:39:05Z

smiles_C2 = [{'name': 'benzene',
  'smiles': '[Q]C1=C([R2])C([R1])=C([Q])C([R2])=C1[R1]',
  'code': 'BENZ',
  'xsmiles': '[*]C1=C([*])C([*])=C([*])C([*])=C1[*]',
  'xsmiles_label': '|$Q;;;R2;;R1;;Q;;R2;;R1$|'},
 {'name': 'naphthalene',
  'smiles': '[Q]C1=C([R3])C([R2])=C2C(C([R2])=C([R3])C([Q])=C2[R1])=C1[R1]',
  'code': 'NAPT',
  'xsmiles': '[*]C1=C([*])C([*])=C2C(C([*])=C([*])C([*])=C2[*])=C1[*]',
  'xsmiles_label': '|$Q;;;R3;;R2;;;;R2;;R3;;Q;;R1;;R1$|'},
 {'name': "1,1'-biphenyl",
  'smiles': '[Q]C1=C([R1])C([R3])=C(C2=C([R4])C([R2])=C([Q])C([R1])=C2[R3])C([R4])=C1[R2]',
  'code': 'BPNY',
  'xsmiles': '[*]C1=C([*])C([*])=C(C2=C([*])C([*])=C([*])C([*])=C2[*])C([*])=C1[*]',
  'xsmiles_label': '|$Q;;;R1;;R3;;;;R4;;R2;;Q;;R1;;R3;;R4;;R2$|'},
 {'name': 'anthracene',
  'smiles': '[R1]C1=C2C(C([R2])=C([R4])C([Q])=C2[R3])=C([R1])C3=C([R3])C([Q])=C([R4])C([R2])=C31',
  'code': 'ANTR',
  'xsmiles': '[*]C1=C2C(C([*])=C([*])C([*])=C2[*])=C([*])C3=C([*])C([*])=C([*])C([*])=C31',
  'xsmiles_label': '|$R1;;;;;R2;;R4;;Q;;R3;;R1;;;R3;;Q;;R4;;R2;$|'},
 {'name': '1,7-dihydro-s-indacene',
  'smiles': '[R1]C1=C2C(C([R2])=C([Q])C2[R3])=C([R1])C3=C1C([R2])C([Q])=C3[R3]',
  'code': 'DHSI',
  'xsmiles': '[*]C1=C2C(C([*])=C([*])C2[*])=C([*])C3=C1C([*])C([*])=C3[*]',
  'xsmiles_label': '|$R1;;;;;R2;;Q;;R3;;R1;;;;R2;;Q;;R3$|'},
 {'name': 'thieno[3,2-b]thiophene',
  'smiles': '[Q]C1=C([R])C2=C(S1)C([R])=C([Q])S2',
  'code': 'TTPH',
  'xsmiles': '[*]C1=C([*])C2=C(S1)C([*])=C([*])S2',
  'xsmiles_label': '|$Q;;;R;;;;;R;;Q;$|'},
 {'name': "3,3'-bipyridine",
  'smiles': '[Q]C1=C([R1])C([R3])=C(C2=C([R2])N=C([Q])C([R1])=C2[R3])C([R2])=N1',
  'code': '3BPD',
  'xsmiles': '[*]C1=C([*])C([*])=C(C2=C([*])N=C([*])C([*])=C2[*])C([*])=N1',
  'xsmiles_label': '|$Q;;;R1;;R3;;;;R2;;;Q;;R1;;R3;;R2;$|'},
 {'name': "2,2'-bithiophene",
  'smiles': '[Q]C1=C([R2])C([R1])=C(C2=C([R1])C([R2])=C([Q])S2)S1',
  'code': 'BTPH',
  'xsmiles': '[*]C1=C([*])C([*])=C(C2=C([*])C([*])=C([*])S2)S1',
  'xsmiles_label': '|$Q;;;R2;;R1;;;;R1;;R2;;Q;;$|'},
 {'name': "1,1':4',1''-terphenyl",
  'smiles': '[Q]C(C([R5])=C1[R6])=C([R4])C([R3])=C1C(C([R1])=C2[R2])=C([R2])C([R1])=C2C3=C([R3])C([R4])=C([Q])C([R5])=C3[R6]',
  'code': 'TPNY',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1C(C([*])=C2[*])=C([*])C([*])=C2C3=C([*])C([*])=C([*])C([*])=C3[*]',
  'xsmiles_label': '|$Q;;;R5;;R6;;R4;;R3;;;;R1;;R2;;R2;;R1;;;;R3;;R4;;Q;;R5;;R6$|'},
 {'name': '1,2-diphenylethyne',
  'smiles': '[Q]C(C([R4])=C1[R1])=C([R3])C([R2])=C1C#CC2=C([R1])C([R4])=C([Q])C([R3])=C2[R2]',
  'code': 'DPEY',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1C#CC2=C([*])C([*])=C([*])C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;R4;;R1;;R3;;R2;;;;;;R1;;R4;;Q;;R3;;R2$|'},
 {'name': "2,2'-bipyridine",
  'smiles': '[Q]C1=C([R1])C([R3])=C(C2=NC([R2])=C([Q])C([R1])=C2[R3])N=C1[R2]',
  'code': '2BPD',
  'xsmiles': '[*]C1=C([*])C([*])=C(C2=NC([*])=C([*])C([*])=C2[*])N=C1[*]',
  'xsmiles_label': '|$Q;;;R1;;R3;;;;;R2;;Q;;R1;;R3;;;R2$|'},
 {'name': 'pyrene',
  'smiles': '[Q]C1=C([R3])C2=C(C(C([R2])=C3[R1])=C1[R4])C(C3=C([R3])C([Q])=C4[R4])=C4C([R2])=C2[R1]',
  'code': 'PYRN',
  'xsmiles': '[*]C1=C([*])C2=C(C(C([*])=C3[*])=C1[*])C(C3=C([*])C([*])=C4[*])=C4C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;R3;;;;;R2;;R1;;R4;;;;R3;;Q;;R4;;;R2;;R1$|'},
 {'name': 'pyrene-1,3,6,8(2H,7H)-tetraone',
  'smiles': 'O=C([Q]C1=O)C2=C([R1])C([R2])=C3C4=C2C1=C([R2])C([R1])=C4C([Q]C3=O)=O',
  'code': 'PYTO',
  'xsmiles': 'O=C([*]C1=O)C2=C([*])C([*])=C3C4=C2C1=C([*])C([*])=C4C([*]C3=O)=O',
  'xsmiles_label': '|$;;Q;;;;;R1;;R2;;;;;;R2;;R1;;;Q;;;$|'},
 {'name': '1,4-bis(phenylethynyl)benzene',
  'smiles': '[Q]C(C([R4])=C1[R1])=C([R3])C([R2])=C1C#CC(C([R6])=C2[R5])=C([R5])C([R6])=C2C#CC3=C([R1])C([R4])=C([Q])C([R3])=C3[R2]',
  'code': 'BPYB',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1C#CC(C([*])=C2[*])=C([*])C([*])=C2C#CC3=C([*])C([*])=C([*])C([*])=C3[*]',
  'xsmiles_label': '|$Q;;;R4;;R1;;R3;;R2;;;;;;R6;;R5;;R5;;R6;;;;;;R1;;R4;;Q;;R3;;R2$|'},
 {'name': '(E)-1,2-diphenylethene',
  'smiles': '[Q]C(C([R4])=C1[R2])=C([R1])C([R3])=C1/C=C/C2=C([R2])C([R4])=C([Q])C([R1])=C2[R3]',
  'code': 'DPEL',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1/C=C/C2=C([*])C([*])=C([*])C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;R4;;R2;;R1;;R3;;;;;;R2;;R4;;Q;;R1;;R3$|'},
 {'name': '(E)-1,2-diphenyldiazene',
  'smiles': '[Q]C(C([R4])=C1[R2])=C([R1])C([R3])=C1/N=N/C2=C([R2])C([R4])=C([Q])C([R1])=C2[R3]',
  'code': 'DPDA',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1/N=N/C2=C([*])C([*])=C([*])C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;R4;;R2;;R1;;R3;;;;;;R2;;R4;;Q;;R1;;R3$|'},
 {'name': "benzo[1,2-b:4,5-b']dithiophene",
  'smiles': '[Q]C(S1)=C([R2])C2=C1C([R1])=C(C([R2])=C([Q])S3)C3=C2[R1]',
  'code': 'BDTP',
  'xsmiles': '[*]C(S1)=C([*])C2=C1C([*])=C(C([*])=C([*])S3)C3=C2[*]',
  'xsmiles_label': '|$Q;;;;R2;;;;R1;;;R2;;Q;;;;R1$|'},
 {'name': "benzo[1,2-d:4,5-d']bis(thiazole)",
  'smiles': '[Q]C(S1)=NC2=C1C([R1])=C(N=C([Q])S3)C3=C2[R1]',
  'code': 'BBTZ',
  'xsmiles': '[*]C(S1)=NC2=C1C([*])=C(N=C([*])S3)C3=C2[*]',
  'xsmiles_label': '|$Q;;;;;;;R1;;;;Q;;;;R1$|'},
 {'name': '1,4-diphenylbuta-1,3-diyne',
  'smiles': '[Q]C(C([R4])=C1[R1])=C([R2])C([R3])=C1C#CC#CC2=C([R1])C([R3])=C([Q])C([R2])=C2[R3]',
  'code': 'DPBY',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1C#CC#CC2=C([*])C([*])=C([*])C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;R4;;R1;;R2;;R3;;;;;;;;R1;;R3;;Q;;R2;;R3$|'},
 {'name': 's-indacene-1,3,5,7(2H,6H)-tetraone',
  'smiles': 'O=C([Q]C1=O)C2=C1C([R])=C(C([Q]C3=O)=O)C3=C2[R]',
  'code': 'INTO',
  'xsmiles': 'O=C([*]C1=O)C2=C1C([*])=C(C([*]C3=O)=O)C3=C2[*]',
  'xsmiles_label': '|$;;Q;;;;;;R;;;Q;;;;;;R$|'},
 {'name': "benzo[1,2-b:4,5-b']difuran",
  'smiles': '[Q]C(O1)=C([R2])C2=C1C([R1])=C(C([R2])=C([Q])O3)C3=C2[R1]',
  'code': 'BDFN',
  'xsmiles': '[*]C(O1)=C([*])C2=C1C([*])=C(C([*])=C([*])O3)C3=C2[*]',
  'xsmiles_label': '|$Q;;;;R2;;;;R1;;;R2;;Q;;;;R1$|'},
 {'name': '1,5-dihydropyrrolo[2,3-f]indole',
  'smiles': '[Q]C(N1[H])=C([R2])C2=C1C([R1])=C(C([R2])=C([Q])N3[H])C3=C2[R1]',
  'code': 'DHPI',
  'xsmiles': '[*]C(N1[H])=C([*])C2=C1C([*])=C(C([*])=C([*])N3[H])C3=C2[*]',
  'xsmiles_label': '|$Q;;;;;R2;;;;R1;;;R2;;Q;;;;;R1$|'},
 {'name': '1,7-dihydro-s-indacene',
  'smiles': '[R1]C1=C2C(C([R2])=C([Q])C2[R3])=C([R1])C3=C1C([R2])C([Q])=C3[R3]',
  'code': 'DHSI',
  'xsmiles': '[*]C1=C2C(C([*])=C([*])C2[*])=C([*])C3=C1C([*])C([*])=C3[*]',
  'xsmiles_label': '|$R1;;;;;R2;;Q;;R3;;R1;;;;R2;;Q;;R3$|'},
 {'name': 'hydrazine',
  'smiles': '[Q][Q]',
  'code': 'HDZN',
  'xsmiles': '[*][*]',
  'xsmiles_label': '|$Q;Q$|'},
 {'name': "naphtho[1,2-b:5,6-b']dithiophene",
  'smiles': '[Q]C(S1)=C([R1])C2=C1C(C([R3])=C([R2])C3=C4SC([Q])=C3[R1])=C4C([R3])=C2[R2]',
  'code': 'NDTP',
  'xsmiles': '[*]C(S1)=C([*])C2=C1C(C([*])=C([*])C3=C4SC([*])=C3[*])=C4C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;;R1;;;;;R3;;R2;;;;;Q;;R1;;;R3;;R2$|'},
 {'name': "3a,7a-dihydroanthra[2,1,9-def:6,5,10-d'e'f']diisochromene-1,3,8,10-tetraone",
  'smiles': 'O=C([Q]C1=O)C2=C(C1C([R1])=C3[R3])C4=C3C(C([R4])=C([R2])C5C([Q]C6=O)=O)=C(C5=C6C([R1])=C7[R3])C7=C4C([R4])=C2[R2]',
  'code': 'PTCD',
  'xsmiles': 'O=C([*]C1=O)C2=C(C1C([*])=C3[*])C4=C3C(C([*])=C([*])C5C([*]C6=O)=O)=C(C5=C6C([*])=C7[*])C7=C4C([*])=C2[*]',
  'xsmiles_label': '|$;;Q;;;;;;;R1;;R3;;;;;R4;;R2;;;Q;;;;;;;;R1;;R3;;;;R4;;R2$|'},
 {'name': "(E)-4,4'-dimethyl-[6,6'-bithieno[3,2-b]pyrrolylidene]-5,5'(4H,4'H)-dione",
  'smiles': 'O=C1N(C)C2=C(SC([Q])=C2[R1])/C1=C3C(SC([Q])=C4[R1])=C4N(C)C/3=O',
  'code': 'TIDA',
  'xsmiles': 'O=C1N(C)C2=C(SC([*])=C2[*])/C1=C3C(SC([*])=C4[*])=C4N(C)C/3=O',
  'xsmiles_label': '|$;;;;;;;;Q;;R1;;;;;;Q;;R1;;;;;$|'},
 {'name': "indeno[2,1-a]indene",
  'code': 'INDE',
  'smiles': '[R1]C(C([Q])=C1[R2])=C([R3])C2=C1C([R4])=C3C2=C([R4])C4=C([R2])C([Q])=C([R1])C([R3])=C43',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C2=C1C([*])=C3C2=C([*])C4=C([*])C([*])=C([*])C([*])=C43',
  'xsmiles_label': '|$R1;;;Q;;R2;;R3;;;;R4;;;;R4;;;R2;;Q;;R1;;R3;$|'},
 {'name': "indeno[1,2-b]fluorene",
  'code': 'INFL',
  'smiles': '[Q]C1=C([R2])C2=C(C([R3])=C1[R1])C3=C([R5])C4=C([R4])C5=C(C([R3])=C([R1])C([Q])=C5[R2])C4=C([R5])C3=C2[R4]',
  'xsmiles': '[*]C1=C([*])C2=C(C([*])=C1[*])C3=C([*])C4=C([*])C5=C(C([*])=C([*])C([*])=C5[*])C4=C([*])C3=C2[*]',
  'xsmiles_label': '|$Q;;;R2;;;;R3;;R1;;;R5;;;R4;;;;R3;;R1;;Q;;R2;;;R5;;;R4$|'}
]

lipelopesoliveira · 2023-03-03T21:00:50Z

O código:

from rdkit import Chem
from rdkit.Chem import Draw


NAME = [i['name'] for i in BB_C2]
SMILES = [i['xsmiles'] + ' ' + i['xsmiles_label'] for i in BB_C2]
CODE = [i['code'] for i in BB_C2]


mols = [Chem.MolFromSmiles(smi) for smi in SMILES]

Draw.MolsToGridImage(mols, 
                     molsPerRow=4, 
                     legends=CODE, 
                     subImgSize=(500,250),
                     useSVG=True)

Gera a imagem:

lipelopesoliveira · 2023-03-03T21:45:03Z

Blocos de construção C3:

smiles_C3 = [
  {'name': 'benzene',
  'code': 'BENZ',
  'smiles': '[Q]C1=C([R1])C([Q])=C([R1])C([Q])=C1[R1]',
  'xsmiles': '[*]C1=C([*])C([*])=C([*])C([*])=C1[*]',
  'xsmiles_label': '|$Q;;;R1;;Q;;R1;;Q;;R1$|'},
 {'name': "5'-phenyl-1,1':3',1''-terphenyl",
  'code': 'TPBZ',
  'smiles': '[Q]C(C([R4])=C1[R5])=C([R3])C([R2])=C1C2=C([R1])C(C3=C([R2])C([R3])=C([Q])C([R4])=C3[R5])=C([R1])C(C4=C([R2])C([R3])=C([Q])C([R4])=C4[R5])=C2[R1]',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1C2=C([*])C(C3=C([*])C([*])=C([*])C([*])=C3[*])=C([*])C(C4=C([*])C([*])=C([*])C([*])=C4[*])=C2[*]',
  'xsmiles_label': '|$Q;;;R4;;R5;;R3;;R2;;;;R1;;;;R2;;R3;;Q;;R4;;R5;;R1;;;;R2;;R3;;Q;;R4;;R5;;R1$|'},
 {'name': 'triphenylamine',
  'code': 'TPAM',
  'smiles': '[Q]C(C([R2])=C1)=C([R1])C=C1N(C2=CC([R1])=C([Q])C([R2])=C2)C3=CC([R1])=C([Q])C([R2])=C3',
  'xsmiles': '[*]C(C([*])=C1)=C([*])C=C1N(C2=CC([*])=C([*])C([*])=C2)C3=CC([*])=C([*])C([*])=C3',
  'xsmiles_label': '|$Q;;;R2;;;R1;;;;;;;R1;;Q;;R2;;;;;R1;;Q;;R2;$|'},
 {'name': "10,15-dihydro-5H-diindolo[3,2-a:3',2'-c]carbazole",
  'code': 'DICZ',
  'smiles': '[Q]C1=C([R1])C2=C(C3=C(N2)C(C4=C([R3])C([R2])=C([Q])C([R1])=C4N5)=C5C6=C3NC7=C([R1])C([Q])=C([R2])C([R3])=C76)C([R3])=C1[R2]',
  'xsmiles': '[*]C1=C([*])C2=C(C3=C(N2)C(C4=C([*])C([*])=C([*])C([*])=C4N5)=C5C6=C3NC7=C([*])C([*])=C([*])C([*])=C76)C([*])=C1[*]',
  'xsmiles_label': '|$Q;;;R1;;;;;;;;;R3;;R2;;Q;;R1;;;;;;;;;R1;;Q;;R2;;R3;;;R3;;R2$|'},
 {'name': 'triphenylene',
  'code': 'TPNY',
  'smiles': '[Q]C1=C([R1])C2=C(C([R2])=C1)C3=C(C([R2])=CC([Q])=C3[R1])C4=C2C([R2])=CC([Q])=C4[R1]',
  'xsmiles': '[*]C1=C([*])C2=C(C([*])=C1)C3=C(C([*])=CC([*])=C3[*])C4=C2C([*])=CC([*])=C4[*]',
  'xsmiles_label': '|$Q;;;R1;;;;R2;;;;;R2;;;Q;;R1;;;;R2;;;Q;;R1$|'},
 {'name': '2,4,6-triphenoxy-1,3,5-triazine',
  'code': 'TPOB',
  'smiles': '[Q]C(C([R2])=C1)=C([R1])C=C1OC2=NC(OC3=CC([R2])=C([Q])C([R1])=C3)=NC(OC4=CC([R2])=C([Q])C([R1])=C4)=N2',
  'xsmiles': '[*]C(C([*])=C1)=C([*])C=C1OC2=NC(OC3=CC([*])=C([*])C([*])=C3)=NC(OC4=CC([*])=C([*])C([*])=C4)=N2',
  'xsmiles_label': '|$Q;;;R2;;;R1;;;;;;;;;;;R2;;Q;;R1;;;;;;;;R2;;Q;;R1;;$|'},
 {'name': '1,3,5-triphenoxybenzene',
  'code': 'TPTA',
  'smiles': '[Q]C(C([R2])=C1)=C([R1])C=C1OC2=C([R3])C(OC3=CC([R2])=C([Q])C([R1])=C3)=C([R3])C(OC4=CC([R2])=C([Q])C([R1])=C4)=C2[R3]',
  'xsmiles': '[*]C(C([*])=C1)=C([*])C=C1OC2=C([*])C(OC3=CC([*])=C([*])C([*])=C3)=C([*])C(OC4=CC([*])=C([*])C([*])=C4)=C2[*]',
  'xsmiles_label': '|$Q;;;R2;;;R1;;;;;;R3;;;;;;R2;;Q;;R1;;;R3;;;;;;R2;;Q;;R1;;;R3$|'},
 {'name': '2,4,6-triphenyl-1,3,5-triazine',
  'code': 'TPTZ',
  'smiles': '[Q]C(C([R3])=C1[R4])=C([R2])C([R1])=C1C2=NC(C3=C([R1])C([R2])=C([Q])C([R3])=C3[R4])=NC(C4=C([R1])C([R2])=C([Q])C([R3])=C4[R4])=N2',
  'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1C2=NC(C3=C([*])C([*])=C([*])C([*])=C3[*])=NC(C4=C([*])C([*])=C([*])C([*])=C4[*])=N2',
  'xsmiles_label': '|$Q;;;R3;;R4;;R2;;R1;;;;;;;R1;;R2;;Q;;R3;;R4;;;;;R1;;R2;;Q;;R3;;R4;$|'},
 {'name': 'None',
  'code': 'DBA1',
  'smiles': '[Q]C1=C([R3])C(C#CC2=C3C([R3])=C([Q])C([R2])=C2[R1])=C(C#CC(C([R3])=C([Q])C([R2])=C4[R1])=C4C#C3)C([R1])=C1[R2]',
  'xsmiles': '[*]C1=C([*])C(C#CC2=C3C([*])=C([*])C([*])=C2[*])=C(C#CC(C([*])=C([*])C([*])=C4[*])=C4C#C3)C([*])=C1[*]',
  'xsmiles_label': '|$Q;;;R3;;;;;;;R3;;Q;;R2;;R1;;;;;;R3;;Q;;R2;;R1;;;;;R1;;R2$|'},
 {'name': 'None',
  'code': 'DBA2',
  'smiles': '[Q]C1=C([R3])C(C#CC#CC2=C3C([R3])=C([Q])C([R2])=C2[R1])=C(C#CC#CC4=C([R3])C([Q])=C([R2])C([R1])=C4C#CC#C3)C([R1])=C1[R2]',
  'xsmiles': '[*]C1=C([*])C(C#CC#CC2=C3C([*])=C([*])C([*])=C2[*])=C(C#CC#CC4=C([*])C([*])=C([*])C([*])=C4C#CC#C3)C([*])=C1[*]',
  'xsmiles_label': '|$Q;;;R3;;;;;;;;;R3;;Q;;R2;;R1;;;;;;;;R3;;Q;;R2;;R1;;;;;;;R1;;R2$|'},
 {'name': '13,14-dihydro-1,2,3(3,6)-triphenanthrenacyclopropaphane',
  'code': 'STAR',
  'smiles': '[Q]C1=C([R1])C2=C(C3=C1C([R2])=C([R3])C(C4=C([R5])C(C(C([R6])C(C5=C([R5])C(C(C([R6])=C6C([R3])=C7[R2])=C7C([Q])=C8[R1])=C8C([R5])=C5[R4])C([R3])=C9[R2])=C9C([Q])=C%10[R1])=C%10C([R5])=C4[R4])=C3[R6])C([R5])=C6C([R4])=C2[R5]',
  'xsmiles': '[*]C1=C([*])C2=C(C3=C1C([*])=C([*])C(C4=C([*])C(C(C([*])C(C5=C([*])C(C(C([*])=C6C([*])=C7[*])=C7C([*])=C8[*])=C8C([*])=C5[*])C([*])=C9[*])=C9C([*])=C%10[*])=C%10C([*])=C4[*])=C3[*])C([*])=C6C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;R1;;;;;;R2;;R3;;;;R5;;;;R6;;;;R5;;;;R6;;;R3;;R2;;;Q;;R1;;;R5;;R4;;R3;;R2;;;Q;;R1;;;R5;;R4;;R6;;R5;;;R4;;R5$|'},
 {'name': 'None',
  'code': 'STAR1',
  'smiles': '[Q]C1=C([R1])C2=C(C3=C1C([R2])=C([R3])C(C#CC4=C([R5])C(C(C([R6])C(C#C5)C([R3])=C6[R2])=C6C([Q])=C7[R1])=C7C([R5])=C4[R4])=C3[R6])C([R5])=C(C#CC(C([R3])=C8[R2])=C([R5])C9=C8C([Q])=C([R1])C%10=C9C([R5])=C5C([R4])=C%10[R5])C([R4])=C2[R5]',
  'xsmiles': '[*]C1=C([*])C2=C(C3=C1C([*])=C([*])C(C#CC4=C([*])C(C(C([*])C(C#C5)C([*])=C6[*])=C6C([*])=C7[*])=C7C([*])=C4[*])=C3[*])C([*])=C(C#CC(C([*])=C8[*])=C([*])C9=C8C([*])=C([*])C%10=C9C([*])=C5C([*])=C%10[*])C([*])=C2[*]',
  'xsmiles_label': '|$Q;;;R1;;;;;;R2;;R3;;;;;;R5;;;;R6;;;;;R3;;R2;;;Q;;R1;;;R5;;R4;;R6;;R5;;;;;;R3;;R2;;R5;;;;Q;;R1;;;;R5;;;R4;;R5;;R4;;R5$|'},
  {'name': "benzo[1,2-b:3,4-b':5,6-b'']trithiophene",
   'code': 'BTTP',
   'smiles': '[Q]C1=C([R1])C2=C(S1)C(C([R1])=C([Q])S3)=C3C4=C2SC([Q])=C4[R1]',
   'xsmiles': '[*]C1=C([*])C2=C(S1)C(C([*])=C([*])S3)=C3C4=C2SC([*])=C4[*]',
   'xsmiles_label': '|$Q;;;R1;;;;;;R1;;Q;;;;;;;Q;;R1$|'},
  {'name': "5''-([1,1'-biphenyl]-4-yl)-1,1':4',1'':3'',1''':4''',1''''-quinquephenyl",
   'code': 'TBBZ',
   'smiles': '[Q]C(C([R2])=C1[R4])=C([R1])C([R3])=C1C(C([R6])=C2[R8])=C([R5])C([R7])=C2C3=C([R9])C(C4=C([R7])C([R5])=C(C5=C([R3])C([R1])=C([Q])C([R2])=C5[R4])C([R6])=C4[R8])=C([R9])C(C6=C([R7])C([R5])=C(C7=C([R3])C([R1])=C([Q])C([R2])=C7[R4])C([R6])=C6[R8])=C3[R9]',
   'xsmiles': '[*]C(C([*])=C1[*])=C([*])C([*])=C1C(C([*])=C2[*])=C([*])C([*])=C2C3=C([*])C(C4=C([*])C([*])=C(C5=C([*])C([*])=C([*])C([*])=C5[*])C([*])=C4[*])=C([*])C(C6=C([*])C([*])=C(C7=C([*])C([*])=C([*])C([*])=C7[*])C([*])=C6[*])=C3[*]',
   'xsmiles_label': '|$Q;;;R2;;R4;;R1;;R3;;;;R6;;R8;;R5;;R7;;;;R9;;;;R7;;R5;;;;R3;;R1;;Q;;R2;;R4;;R6;;R8;;R9;;;;R7;;R5;;;;R3;;R1;;Q;;R2;;R4;;R6;;R8;;R9$|'},
  {'name': "1,3,5-triazine",
   'code': 'TRZN',
   'smiles': '[Q]C1=NC([Q])=NC([Q])=N1',
   'xsmiles': '[*]C1=NC([*])=NC([*])=N1',
   'xsmiles_label': '|$Q;;;;Q;;;Q;$|'}
  ]

lipelopesoliveira · 2023-03-03T22:08:01Z

Grupos R:

smiles_R = [
  {'name': 'hydrogen',
  'code': 'H',
  'smiles': '[R][H]',
  'xsmiles': '[*][H]',
  'xsmiles_label': '|$R;$|'},
 {'name': 'hydroxyl',
  'code': 'OH',
  'smiles': '[R]O',
  'xsmiles': '[*]O',
  'xsmiles_label': '|$R;$|'},
 {'name': 'methyl',
  'code': 'CH3',
  'smiles': '[R]C',
  'xsmiles': '[*]C',
  'xsmiles_label': '|$R;$|'},
 {'name': 'tert-butyl',
  'code': 'tBu',
  'smiles': '[R]C(C)(C)C',
  'xsmiles': '[*]C(C)(C)C',
  'xsmiles_label': '|$R;;;;$|'},
 {'name': 'methoxy',
  'code': 'OMe',
  'smiles': '[R]OC',
  'xsmiles': '[*]OC',
  'xsmiles_label': '|$R;;$|'},
 {'name': 'ethoxy',
  'code': 'OEt',
  'smiles': '[R]OCC',
  'xsmiles': '[*]OCC',
  'xsmiles_label': '|$R;;;$|'},
 {'name': 'amine',
  'code': 'NH2',
  'smiles': '[R]N',
  'xsmiles': '[*]N',
  'xsmiles_label': '|$R;$|'},
 {'name': 'nitro',
  'code': 'NO2',
  'smiles': '[R][N+]([O-])=O',
  'xsmiles': '[*][N+]([O-])=O',
  'xsmiles_label': '|$R;;;$|'},
 {'name': 'cyano',
  'code': 'CN',
  'smiles': '[R]C#N',
  'xsmiles': '[*]C#N',
  'xsmiles_label': '|$R;;$|'},
 {'name': 'formyl',
  'code': 'CHO',
  'smiles': '[R]C([H])=O',
  'xsmiles': '[*]C([H])=O',
  'xsmiles_label': '|$R;;;$|'},
 {'name': 'carboxy',
  'code': 'COOH',
  'smiles': '[R]C(O)=O',
  'xsmiles': '[*]C(O)=O',
  'xsmiles_label': '|$R;;;$|'},
 {'name': 'acetoxy',
  'code': 'OCOCH3',
  'smiles': '[R]OC(C)=O',
  'xsmiles': '[*]OC(C)=O',
  'xsmiles_label': '|$R;;;;$|'},
 {'name': 'thyol',
  'code': 'SH',
  'smiles': '[R]S',
  'xsmiles': '[*]S',
  'xsmiles_label': '|$R;$|'},
 {'name': 'keto',
  'code': 'O',
  'smiles': '[R]=O',
  'xsmiles': '[*]=O',
  'xsmiles_label': '|$R;$|'},
 {'name': 'nitroso',
  'code': 'NO',
  'smiles': '[R]N=O',
  'xsmiles': '[*]N=O',
  'xsmiles_label': '|$R;;$|'},
 {'name': 'fluorine',
  'code': 'F',
  'smiles': '[R]F',
  'xsmiles': '[*]F',
  'xsmiles_label': '|$R$|'},
 {'name': 'chlorine',
  'code': 'Cl',
  'smiles': '[R]Cl',
  'xsmiles': '[*]Cl',
  'xsmiles_label': '|$R;$|'},
 {'name': 'bromine',
  'code': 'Br',
  'smiles': '[R]Br',
  'xsmiles': '[*]Br',
  'xsmiles_label': '|$R$|'},
 {'name': 'iodine',
  'code': 'I',
  'smiles': '[R]I',
  'xsmiles': '[*]I',
  'xsmiles_label': '|$R$|'},
 {'name': 'sulfinic acid',
  'code': 'SO2H',
  'smiles': '[R]S(O)=O',
  'xsmiles': '[*]S(O)=O',
  'xsmiles_label': '|$R;;;$|'},
 {'name': 'sulfonic acid',
  'code': 'SO3H',
  'smiles': '[R]S(=O)(O)=O',
  'xsmiles': '[*]S(=O)(O)=O',
  'xsmiles_label': '|$R;;;;$|'},
 {'name': 'thial',
  'code': 'CHS',
  'smiles': '[R]C([H])=S',
  'xsmiles': '[*]C([H])=S',
  'xsmiles_label': '|$R;;;$|'},
 {'name': 'epoxide',
  'code': 'EPO',
  'smiles': '[R]C1CO1',
  'xsmiles': '[*]C1CO1',
  'xsmiles_label': '|$R;;;$|'},
 {'name': 'methyl epoxide',
  'code': 'MEPO',
  'smiles': '[R]CC1CO1',
  'xsmiles': '[*]CC1CO1',
  'xsmiles_label': '|$R;;;;$|'},
 {'name': 'ethyl epoxide',
  'code': 'EEPO',
  'smiles': '[R]CCC1CO1',
  'xsmiles': '[*]CCC1CO1',
  'xsmiles_label': '|$R;;;;;$|'},
 {'name': 'ethoxymethyl epoxide',
  'code': 'EMEPO',
  'smiles': '[R]COCC1CO1',
  'xsmiles': '[*]COCC1CO1',
  'xsmiles_label': '|$R;;;;;;$|'},
 {'name': 'oxiethyl epoxide',
  'code': 'OEEPO',
  'smiles': '[R]OCC1CO1',
  'xsmiles': '[*]OCC1CO1',
  'xsmiles_label': '|$R;;;;;$|'},
  {'name': 'benzene',
   'code': 'Ph',
   'smiles': '[R]C1=CC=CC=C1',
   'xsmiles': '[*]C1=CC=CC=C1',
   'xsmiles_label': '|$R;;;;;;$|'}
  ]

lipelopesoliveira · 2023-03-03T22:22:45Z

Grupos Q:

smiles_Q = [
 {'name': 'amine',
  'code': 'NH2',
  'smiles': '[Q]N',
  'xsmiles': '[*]N',
  'xsmiles_label': '|$Q;$|'},
 {'name': 'aldehyde',
  'code': 'CHO',
  'smiles': '[Q]C([H])=O',
  'xsmiles': '[*]C([H])=O',
  'xsmiles_label': '|$Q;;;$|'},
 {'name': 'boronic acid',
  'code': 'BOH2',
  'smiles': '[Q]B(O)O',
  'xsmiles': '[*]B(O)O',
  'xsmiles_label': '|$Q;;$|'},
 {'name': 'acetohydrazide',
  'code': 'CONHNH2',
  'smiles': '[Q]C(NN)=O',
  'xsmiles': '[*]C(NN)=O',
  'xsmiles_label': '|$Q;;;;$|'},
 {'name': 'methylhydrazine',
  'code': 'NHNH2',
  'smiles': '[Q]NN',
  'xsmiles': '[*]NN',
  'xsmiles_label': '|$Q;;$|'},
 {'name': 'nitrile',
  'code': 'CN',
  'smiles': '[Q]C#N',
  'xsmiles': '[*]C#N',
  'xsmiles_label': '|$Q;;$|'},
 {'name': 'bromine',
  'code': 'Br',
  'smiles': '[Q]Br',
  'xsmiles': '[*]Br',
  'xsmiles_label': '|$Q;$|'},
 {'name': 'chlorine',
  'code': 'Cl',
  'smiles': '[Q]Cl',
  'xsmiles': '[*]Cl',
  'xsmiles_label': '|$Q;$|'},
 {'name': 'oxigem',
  'code': 'O',
  'smiles': '[Q]O',
  'xsmiles': '[*]O',
  'xsmiles_label': '|$Q;$|'},
 {'name': 'dihydroxy',
   'code': 'OH2',
   'smiles': '[Q]O[B]O1',
   'xsmiles': '[*]O[B]O1',
   'xsmiles_label': '|$Q;;B;$|'},
]

lipelopesoliveira · 2023-03-03T22:34:49Z

lipelopesoliveira added the 📶 enhancement New feature or request label Mar 2, 2023

lipelopesoliveira self-assigned this Mar 2, 2023

This was referenced Mar 4, 2023

Update codes for v0.0.3 #30

Merged

Adicionar suporte a SMILES e SELFIES #4

Closed

Converter blocos de construção para formato xyz #1

Closed

lipelopesoliveira closed this as completed in #30 Apr 25, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Adicionar informações sobre smiles das moleculas #33

Adicionar informações sobre smiles das moleculas #33

lipelopesoliveira commented Mar 2, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023

Adicionar informações sobre smiles das moleculas #33

Adicionar informações sobre smiles das moleculas #33

Comments

lipelopesoliveira commented Mar 2, 2023 • edited Loading

Motivação

O que deve ser feito?

Etapas para a realização desta tarefa:

O que será obtido ao final dessa tarefa?

Possui prazo limite de conclusão?

Mais alguma outra coisa?

lipelopesoliveira commented Mar 3, 2023 • edited Loading

lipelopesoliveira commented Mar 3, 2023 • edited Loading

lipelopesoliveira commented Mar 3, 2023

lipelopesoliveira commented Mar 3, 2023 • edited Loading

lipelopesoliveira commented Mar 3, 2023

lipelopesoliveira commented Mar 3, 2023 • edited Loading

lipelopesoliveira commented Mar 3, 2023 • edited Loading

lipelopesoliveira commented Mar 3, 2023 • edited Loading

lipelopesoliveira commented Mar 3, 2023

lipelopesoliveira commented Mar 2, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading

lipelopesoliveira commented Mar 3, 2023 •

edited

Loading