Adicionar informações sobre smiles das moleculas

lipelopesoliveira commented 1 year ago

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?

lipelopesoliveira commented 1 year ago

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:

output

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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:

output

lipelopesoliveira commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

lipelopesoliveira / pyCOFBuilder