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added household chemicals - #340

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household_chemicals
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added household chemicals#340
kalanakotawalagedara wants to merge 1 commit into
developmentfrom
household_chemicals

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@kalanakotawalagedara

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added bleach, detergents,disinfectants,cosmetics, surface cleaners and flame retardants SMILES

@Lyq322 Lyq322 left a comment

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A few things about your code:

  • Class names should always be pascal case (eg CorrectClassName)
  • Node names should be snake case (eg correct_node_name)
  • Dictionaries should have correct indentation and formatting. See other dictionaries in global-chem for examples.
  • Some SMILES in your code are invalid. Please use rdkit to double check all SMILES are valid before creating pull request. You can use Chem.MolFromSmiles(smiles) to see if there is an error.

Other Changes:

  • Change README.md to add your node to the list and any references you used
  • In global_chem/global_chem/global_chem.py you need to import your nodes at the top (eg from global_chem.environment.chemicals_from_biomass import ChemicalsFromBioMass)

Comment on lines +155 to +156
from global_chem.household_chemicals.organophosphate_flame_retardants import Organophosphate_flame_retardants
from global_chem.household_chemicals.Surface_cleaners import Surface_cleaners

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Class names should be all capitalized to match coding style.

Suggested change
from global_chem.household_chemicals.organophosphate_flame_retardants import Organophosphate_flame_retardants
from global_chem.household_chemicals.Surface_cleaners import Surface_cleaners
from global_chem.household_chemicals.organophosphate_flame_retardants import OrganophosphateFlameRetardants
from global_chem.household_chemicals.surface_cleaners import SurfaceCleaners

'mango_vitamins': MangoVitamins, # Damilola Bodun & Sevien Schulhofff
'mango_flavonoids': MangoFlavonoids, # Damilola Bodun & Sevien Schulhofff
'insect_sex_pheromones': InsectSexPheromones, # Yuqing Liu & Suliman Sharif
'household_chemicals' : household_chemicals, # Kalana Kotawalagedara & Anuththara Gamage

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You should add an entry to this list for every node, not just the folder household chemicals.

Suggested change
'household_chemicals' : household_chemicals, # Kalana Kotawalagedara & Anuththara Gamage
'bleach' : Bleach, # Kalana Kotawalagedara & Anuththara Gamage
cosmetics’: Cosmetics, # Kalana Kotawalagedara & Anuththara Gamage
# …etc

Comment thread global_chem/global_chem/household_chemicals/bleach.py
Comment on lines +29 to +31
smarts = {

}

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Indent to match coding style.

Suggested change
smarts = {
}
smarts = {
}

Comment on lines +16 to +21
smiles = {
'oxybenzone' : 'COC1=CC(=C(C=C1)C(=O)C2=CC=CC=C2)O',
'hydroquinone' : 'C1=CC(=CC=C1O)O',
'diethyl phthalate' : 'CCOC(=O)C1=CC=CC=C1C(=O)OCC',

}

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Indent to match coding style.

Suggested change
smiles = {
'oxybenzone' : 'COC1=CC(=C(C=C1)C(=O)C2=CC=CC=C2)O',
'hydroquinone' : 'C1=CC(=CC=C1O)O',
'diethyl phthalate' : 'CCOC(=O)C1=CC=CC=C1C(=O)OCC',
}
smiles = {
'oxybenzone' : 'COC1=CC(=C(C=C1)C(=O)C2=CC=CC=C2)O',
'hydroquinone' : 'C1=CC(=CC=C1O)O',
'diethyl phthalate' : 'CCOC(=O)C1=CC=CC=C1C(=O)OCC',
}

'hydrochloric acid' : 'Cl',
'brass' : ' [Cu].[Zn].[Pb]',
'chloroxylenol' : 'CC1=CC(=CC(=C1Cl)C)O',
'1,4- dioxane' : 'C1COCCO1',

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No space after dash in IUPAC

Suggested change
'1,4- dioxane' : 'C1COCCO1',
'1,4-dioxane' : 'C1COCCO1',

'triclosan' : 'C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl',
'benzalkonium chloride' : '[Cl-].CCCCCCCCCCCCN+(C)CC1=CC=CC=C1',
'isopropyl alcohol' : 'CC(C)O',
'chlorohexidine' : r 'C1=CC(=CC=C1N/C(=N/C(=NCCCCCCN=C(/N=C(/NC2=CC=C(C=C2)Cl)\N)N)N)/N)Cl',

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Incorrect name

Suggested change
'chlorohexidine' : r 'C1=CC(=CC=C1N/C(=N/C(=NCCCCCCN=C(/N=C(/NC2=CC=C(C=C2)Cl)\N)N)N)/N)Cl',
'chlorhexidine' : r 'C1=CC(=CC=C1N/C(=N/C(=NCCCCCCN=C(/N=C(/NC2=CC=C(C=C2)Cl)\N)N)N)/N)Cl',

'phenol' : 'C1=CC=C(C=C1)O',
'formaldehyde' : 'C=O',
'boric acid' : 'B(O)(O)O',
'triclosan' : 'C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl',

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Duplicate

Suggested change
'triclosan' : 'C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl',

'boric acid' : 'B(O)(O)O',
'triclosan' : 'C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl',
'oligo(2-(2-ethoxy)-ethoxyethyl)guanidinium chloride' : 'Cl.NC(N)=N.NCCOCCOCCN',
'polyhexamethylene guanidine' : 'Cl.NC(N)=N.NCCCCCCN',

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Wrong smiles? This picture showed up when I searched up polyhexamethylene guanidine.
image

def get_smiles():

smiles = {
'tris(1,3-dichloro-2-propyl)phosphate' : 'C(C(CCl)OP(=O)(OC(CCl)CCl)OC(CCl)CCl)Cl',

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Missing a space.

Suggested change
'tris(1,3-dichloro-2-propyl)phosphate' : 'C(C(CCl)OP(=O)(OC(CCl)CCl)OC(CCl)CCl)Cl',
'tris(1,3-dichloro-2-propyl) phosphate' : 'C(C(CCl)OP(=O)(OC(CCl)CCl)OC(CCl)CCl)Cl',

@ANUGAMAGE ANUGAMAGE Nov 8, 2024

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Thanks @Lyq322.
@kalanakotawalagedara go through above mistakes, discuss with yuquing about them correct all of them.

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3 participants