harirakul/chemlib

🧪 A comprehensive chemistry library for Python.

chemlib's Issues

A few features to request

Nice lib! A good starting point for what I'm looking for. Currently I'm looking forward to below functionalities, ranked by extent of expectations from highest to suggestive:

• Create compound from accessions of online databases, say, PubChem CIDs and Reactome identifiers.
• Reaction integration with biochemical reactions from Reactome, whose API, as shown in Content Service, can be utilized.
• Reaction search with available compounds to see what we can do with chemicals at hand and what compounds are yet to obtain to accomplish a certain reaction.
• Perform virtual experiments and warn about safety concerns of the given procedures.

Ds, Rg and Cn are not objects in Element

Ds, Rg and Cn cannot be accessed through chemlib.Element("Symbol")

smarter parsing

Formula parsing should be able to handle different 'ways' of writing compounds

For example:
-> Checking for consecutive elements in CH3COO (currently need to input as C2H3O2)

empirical-formula-method

Empirical formula from percent composition returning incorrect results sometimes.

P = 43.64
O = 56.36

Should get: P2O5, instead getting P1O3

Accuracy

chemlib==2.2.3

In [15]: r = Reaction.by_formula('KOH + H3PO4 --> K2HPO4 + H2O')

In [16]: r.balance()

In [17]: r.formula
Out[17]: '2K₁O₁H₁ + 1H₃P₁O₄ --> 1K₂H₁P₁O₄ + 2H₂O₁'

In [18]: dict(zip(r.constituents, [c["grams"] for c in r.get_amounts(3, grams=1)]))
Out[18]: {'K₁O₁H₁': 0.673, 'H₃P₁O₄': 0.588, 'K₂H₁P₁O₄': 1, 'H₂O₁': 0.216}

In [19]: dict(zip(r.constituents, [c["grams"] for c in r.get_amounts(3, grams=1000)]))
Out[19]: {'K₁O₁H₁': 644.255, 'H₃P₁O₄': 562.561, 'K₂H₁P₁O₄': 1000, 'H₂O₁': 206.906}

I'd expect KOH to be something like 673.xxx

Balancer only takes 2 reacts/products

Using this code for a project that requires equations with up to 4 products to be balanced. Noticed that the balancer only processes a maximum of 2 reactants and 2 products.
`from chemlib import Compound, Reaction
from chemlib import Compound, Reaction

H2 = Compound('H2')
C7H8O2 = Compound("C7H8O2")
C6H6O1 = Compound("C6H6O1")
C1H4 = Compound('C1H4')
H2O1 = Compound('H2O1')
r=Reaction(reactants = [H2,C7H8O2],products = [C6H6O1,C1H4,H2O1])

r.formula
'1H₂ + 1O₂ --> 1H₂O₁'

r.is_balanced
False

r.balance()

print(r.formula)
'2H₂ + 1O₂ --> 2H₂O₁'

r.is_balanced
True`

`---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
in
16 False
17
---> 18 r.balance()
19
20 print(r.formula)

~\Anaconda3\lib\site-packages\chemlib\chemistry.py in balance(self)
256
257 if compounds[sol].formula in self.product_formulas:
--> 258 final_products.append([compounds[sol]]*solutions[sol])
259
260 final_reactants = sum(final_reactants, [])

IndexError: list index out of range`

Error

On a Mac, with PIL installed, I am getting a font error trying to run:

from chemlib import Galvanic_Cell
g = Galvanic_Cell("Pb", "Zn")

Is there a way to default to a font that is available, or hold off on the image generation, rather than erroring on the initial call of Galvanic_Cell()?

/usr/local/lib/python3.9/site-packages/chemlib/electrochemistry.py in font(size)
     62     def draw(self):
     63         def font(size):
---> 64             return ImageFont.truetype("arial.ttf", size, encoding="unic")
     65 
     66         img = Image.open(DIAGRAM_PATH)

/usr/local/lib/python3.9/site-packages/PIL/ImageFont.py in truetype(font, size, index, encoding, layout_engine)
    850 
    851     try:
--> 852         return freetype(font)
    853     except OSError:
    854         if not isPath(font):

/usr/local/lib/python3.9/site-packages/PIL/ImageFont.py in freetype(font)
    847 
    848     def freetype(font):
--> 849         return FreeTypeFont(font, size, index, encoding, layout_engine)
    850 
    851     try:

/usr/local/lib/python3.9/site-packages/PIL/ImageFont.py in __init__(self, font, size, index, encoding, layout_engine)
    207                         load_from_bytes(f)
    208                     return
--> 209             self.font = core.getfont(
    210                 font, size, index, encoding, layout_engine=layout_engine
    211             )

OSError: cannot open resource

oxidation number

chemlib==2.2.3

----> 1 Compound('CuSO4').oxidation_numbers()

File /opt/homebrew/lib/python3.10/site-packages/chemlib/chemistry.py:129, in Compound.oxidation_numbers(self)
    126         left.remove(sym)
    128 if len(left) > 1:
--> 129     raise NotImplementedError
    131 ox_nums[left[0]] = int(-current()/self.occurences[left[0]])
    132 return ox_nums

Compounds in SMILES format

Is there a simple way to provide lists of compounds, eg in a reaction, in SMILES format?

Also, is it possible to suppress the 1 digit in the compound display (or is the digit used to help parse the separate elements out in a compound string?)

Key Error while using limiting reagent function.

While using the limiting reagent function,
terminal cites line 337 : data = [a[-1][mode.capitalize()] for a in eq_amounts]
and shows : KeyError: 'Grams'

This is code where it is used:
if eventlr == 'Apply':
x=int(float(valueslr['R1']))
y=int(float(valueslr['R2']))
lr = rxn.limiting_reagent(x, y, mode = type)
winlr('lr').Update(value=lr.formula)

It is a program made using pysimplegui and chemlib
type is a string variable (grams,moles or molecules)
and x and y are integers

Please Help

Insoluble salts in galvanic elements

I think it would be better if the standard salts in the galvanic elements were nitrates instead of sulphates to avoid ending up with insoluble salts when drawing the elements.

Also, the method "diagram" does not longer work (although "draw" works), but it is still used in the documentation.

Galvanic cell diagram drawing fails if the font "arial.ttf" does not exist

The galvanic cell drawer assumes there exists a font called "arial.ttf". This is the case on Windows, but not on Linux or Mac, leading to an OSError when attempting to draw such a diagram.

There could perhaps be different fonts based on platform, or might be possible to use the load_default() method.

Combustion of benzene

Balancing the combustion (both incomplete and complete) of benzene seems to miss one oxygen on the left side:

from chemlib import Compound, Reaction

A = Compound("H6C6")
B = Compound("O2")


C = Compound("CO")
D = Compound("H2O")

r = Reaction([A,B], [C,D])
r.balance()
print(r)

This gives: 1H₆C₆ + 4O₂ --> 6C₁O₁ + 3H₂O₁, lacking one O-atom on the left side. The same happens when switching CO with CO₂.