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Update README.md to v1.3.0
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@molshape
molshape authored Sep 12, 2021
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Expand Up @@ -56,64 +56,66 @@ muscarine = ChemFormula("((CH3)3N)(C6H11O2)", charge = 1, name = "L-(+)-Muscarin
pyrophosphate = ChemFormula("P2O7", -4)

caffeine = ChemFormula("C8H10N4O2", name = "caffeine", cas = 58_08_2)
theine = ChemFormula("C8H10N4O2", name = "theine", cas = "58-08-2")
theine = ChemFormula("(C5N4H)O2(CH3)3", name = "theine", cas = "58-08-2")
```

The `ChemFormula` class offers the following attributes/functions

```Python
.original_formula # original chemical formula used to create the chemical formula object
.formula # original chemical formula used to create the chemical formula object

.text_formula # formula including charge as text output

.latex # formats the formula of a ChemFormula object as a string that can be used in LaTeX
.latex # formats a formula as a string that can be used in LaTeX

.html # formats the formula of a ChemFormula object as a string that can be used in HTML
.html # formats a formula as a string that can be used in HTML

.unicode # formats the formula of a ChemFormula object with unicode subscript and superscript numbers
.unicode # formats a formula with unicode subscript and superscript numbers

.format_formula( # custom formatting of the formula, .FormatFormula uses the following optional keyword arguments
formula_prefix = "", # preceeds the complete formula string
element_prefix = "", element_suffix = "", # encloses every chemical symbol (Prefix + Symbol + Suffix)
freq_prefix = "", freq_suffix = "", # encloses every element frequency (Prefix + Frequency + Suffix)
formula_suffix = "", # closes the complete formula string
bracket_prefix = "", bracket_suffix = "", # encloses all brackets: {[()]} (Prefix + Bracket + Suffix)
multiply_symbol = "", # replacement for '.' or '*'
charge_prefix = "", charge_suffix = "", # encloses every charge information (Prefix + Charge + Suffix)
charge_positive = "+", # symbol for a positive charge
charge_negative = "-" # symbol for a negative charge
.format_formula( # custom formatting of the formula, .FormatFormula uses the following optional keyword arguments
formula_prefix = "", # preceeds the complete formula string
element_prefix = "", element_suffix = "", # encloses every chemical symbol (Prefix + Symbol + Suffix)
freq_prefix = "", freq_suffix = "", # encloses every element frequency (Prefix + Frequency + Suffix)
formula_suffix = "", # closes the complete formula string
bracket_prefix = "", bracket_suffix = "", # encloses all brackets: {[()]} (Prefix + Bracket + Suffix)
multiply_symbol = "", # replacement for '.' or '*'
charge_prefix = "", charge_suffix = "", # encloses every charge information (Prefix + Charge + Suffix)
charge_positive = "+", # symbol for a positive charge
charge_negative = "-" # symbol for a negative charge
)

.sum_formula # collapsed sum formula of .OriginalFormula with all bracketed units resolved as a ChemFormula object,
# i.e. use .SumFormula.HTML to retrive an HTML representation of the sum formula
.sum_formula # collapsed sum formula of .OriginalFormula with all bracketed units resolved as a ChemFormula object,
# i.e. use .SumFormula.HTML to retrive an HTML representation of the sum formula

.hill_formula # sum formula in Hill notation as a ChemFormula object, i.e. use .HillFormula.Unicode to retrive
# a Unicode representation of the Hill formula (first Carbon, then Hydrogen (if carbon is present),
# followed by all other elements in alphabetical order of their chemical symbol)
# Source: Edwin A. Hill, J. Am. Chem. Soc., 1900 (22), 8, 478-494 (https://doi.org/10.1021/ja02046a005)
.hill_formula # sum formula in Hill notation as a ChemFormula object, i.e. use .HillFormula.Unicode to retrive
# a Unicode representation of the Hill formula (first Carbon, then Hydrogen (if carbon is present),
# followed by all other elements in alphabetical order of their chemical symbol)
# Source: Edwin A. Hill, J. Am. Chem. Soc., 1900 (22), 8, 478-494 (https://doi.org/10.1021/ja02046a005)

.formula_weight # formula weight of the chemical formula in g/mol
.formula_weight # formula weight of the chemical formula in g/mol

.mass_fractions # mass fraction of each element for the chemical formula in the form of
# key, value = chemical symbol, mass fraction
.mass_fractions # mass fraction of each element for the chemical formula in the form of
# key, value = chemical symbol, mass fraction

.name # name of the chemical formula object
.name # name of the chemical formula object

.radioactive # boolean value whether the formula is radioactive (True) or not (False)
.radioactive # boolean value whether the formula is radioactive (True) or not (False)

.charged # boolean value whether the formula is charged (True) or not (False)
.charged # boolean value whether the formula is charged (True) or not (False)

.charge # integer value carrying the charge of the chemical formula object
.charge # integer value carrying the charge of the chemical formula object

.text_dharge # formatted string of the charge of the chemical formula object (e. g. 3+, 4-, +, ...)
.text_dharge # formatted string of the charge of the chemical formula object (e. g. 3+, 4-, +, ...)

.element # is a dictionary representation of the formula composition in the form of
# key, value = chemical symbol, frequency of this element
# e.g.: .element["C"] gives the number of carbon atoms in the corresponding formula object
.element # is a dictionary representation of the formula composition in the form of
# key, value = chemical symbol, frequency of this element
# e.g.: .element["C"] gives the number of carbon atoms in the corresponding formula object

.cas # CAS Registry Number® in a formatted way ('_____00-00-0')
# .cas is a CAS number object from the casregnum package
.cas.cas_string # CAS number as a formatted string, inherited property from casregnum.CAS
.cas.cas_integer # CAS number as an integer value, inherited property from casregnum.CAS
.cas.check_digit # CAS number check digit, inherited property from casregnum.CAS
.cas # CAS Registry Number® in a formatted way ('_____00-00-0')
# .cas is a CAS number object from the casregnum package
.cas.cas_string # CAS number as a formatted string, inherited property from casregnum.CAS
.cas.cas_integer # CAS number as an integer value, inherited property from casregnum.CAS
.cas.check_digit # CAS number check digit, inherited property from casregnum.CAS
```


Expand All @@ -133,7 +135,8 @@ caffeine = ChemFormula("C8H10N4O2", name = "caffeine", cas = 58_08_2)

print(f"\n--- Formula Depictions of {muscarine.name} ---")
print(f" Print instance: {muscarine}")
print(f" Original: {muscarine.original_formula}")
print(f" Original: {muscarine.formula}")
print(f" Text formula: {muscarine.text_formula}")
print(f" HTML: {muscarine.html}")
print(f" LaTeX: {muscarine.latex}")
print(f" Unicode: {muscarine.unicode}")
Expand All @@ -147,10 +150,10 @@ print(f" Hill formula: {muscarine.hill_formula.latex}")

print(f"\n--- Formula Weights Calculations with {ethylcinnamate.name.title()} ---")
print(f" The formula weight of {ethylcinnamate.name} ({ethylcinnamate.sum_formula.unicode}) is {ethylcinnamate.formula_weight:.2f} g/mol.")
Mole = 1.4
print(f" {Mole:.1f} mol of {ethylcinnamate.name} weight {Mole * ethylcinnamate.formula_weight:.1f} g.")
Mass = 24
print(f" {Mass:.1f} g of {ethylcinnamate.name} corresponds to {Mass/ethylcinnamate.formula_weight * 1000:.1f} mmol.")
mole = 1.4
print(f" {mole:.1f} mol of {ethylcinnamate.name} weight {mole * ethylcinnamate.formula_weight:.1f} g.")
mass = 24
print(f" {mass:.1f} g of {ethylcinnamate.name} corresponds to {mass/ethylcinnamate.formula_weight * 1000:.1f} mmol.")
print(f" The elemental composition of {ethylcinnamate.name} is as follows:")
for stringElementSymbol, floatElementFraction in ethylcinnamate.mass_fraction.items():
print(f" {stringElementSymbol:<2}: {floatElementFraction * 100:>5.2f} %")
Expand All @@ -174,6 +177,7 @@ generates the following output
--- Formula Depictions of L-(+)-Muscarine ---
Print instance: ((CH3)3N)(C6H11O2)
Original: ((CH3)3N)(C6H11O2)
Text formula: ((CH3)3N)(C6H11O2) +
HTML: <span class='ChemFormula'>((CH<sub>3</sub>)<sub>3</sub>N)(C<sub>6</sub>H<sub>11</sub>O<sub>2</sub>)<sup>+</sup></span>
LaTeX: \(\(\textnormal{C}\textnormal{H}_{3}\)_{3}\textnormal{N}\)\(\textnormal{C}_{6}\textnormal{H}_{11}\textnormal{O}_{2}\)^{+}
Unicode: ((CH₃)₃N)(C₆H₁₁O₂)⁺
Expand Down Expand Up @@ -207,6 +211,9 @@ generates the following output
Caffeine has the CAS RN 58-08-2 (or as an integer: 58082).
```

More examples can be found at [/tests/](https://github.com/molshape/ChemFormula/blob/main/tests/).


## Comparing and Sorting of Chemical Formulas

**ChemFormula** allows comparing and sorting of chemical formula objects. Chemical formula objects can be compared with the `==` operator. Two chemical formula objects are considered equal, if they have the same chemical composition (i.e. the same sum formula) and the same charge. If a CAS number is specified, the CAS number of both objects must also be identical.
Expand Down Expand Up @@ -252,7 +259,8 @@ generates the following output
6. C₆H₁₂O₆
7. C₆H₁₂S₆
```



## Atomic Weight Data

All atomic weights are taken from the IUPAC Commission on Isotopic Abundances and Atomic Weights and are based on the following reports and publications:
Expand Down

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