Python - Syntax check of molecular formulas

Question

This is going to be a long question, I hope you guys have patience.

I am writing a program that checks if the syntax for a molecular formula is correct.

I have a BNF-syntax:

<formel>::= <mol> \n
<mol>   ::= <group> | <group><mol>
<group> ::= <atom> |<atom><num> | (<mol>) <num>
<atom>  ::= <LETTER> | <LETTER><letter>
<LETTER>::= A | B | C | ... | Z
<letter>::= a | b | c | ... | z
<num>   ::= 2 | 3 | 4 | ...

and this is my code:

from linkedQFile import LinkedQ
import string
import sys

ATOMER = ["H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar"]

class FormelError(Exception):
    pass
class Gruppfel(Exception):
    pass

q = LinkedQ()
formel= "(Cl)2)3"

for symbol in formel:
    q.put(symbol)


def readNum():
    """Reads digits larger than 1. Raises exception if condition is not fulfilled."""
    try:
        if int(q.peek()) >= 2:
            print(q.peek())
            q.get()
            return
        else:
            q.get()
            print("Too small digit at the end of row: "+getRest())
            sys.exit()
    except (ValueError,TypeError):
        raise FormelError("Not a number.")

def readletter():
    """Reads lowercase letters and returns them."""
    if q.peek() in string.ascii_lowercase:
        print(q.peek())
        return q.get()
    else:
        raise FormelError("Expected lowercase letter.")

def readLetter():
    """Reads capital letters and returns them."""
    if q.peek() in string.ascii_uppercase:
        print(q.peek())
        return q.get()
    else:
        raise FormelError("Expected capital letter.")

def readAtom():
    """Reads atoms on the form X and Xx. Raises Exception if the format for an atom is not fulfilled or if the atom does not exist."""
    X = ""
    try:
        X += readLetter()
    except FormelError:
        print("Missing capital letter at end of row: "+getRest())
        sys.exit()  
        return

    try:
        x = readletter()
        atom = X+x
    except (FormelError, TypeError):
        atom = X

    if atom in ATOMER:
        return
    else:
        raise FormelError("Unknown atom.")

def readGroup():
    if q.peek() in string.ascii_uppercase or q.peek() in string.ascii_lowercase:
        try:
            readAtom()
        except:
            print("Unknown atom at end of row: "+getRest())
            sys.exit()
        try:
            while True:
                readNum()
        except FormelError:
            pass
        return
    if q.peek() == "(":
        print(q.peek())
        q.get()
        try:
            readMol()
        except FormelError:
            pass
        if q.peek() == ")":
            print(q.peek())
            q.get()
        else:
            print("Missing right parenthesis at end of row: "+ getRest())
            sys.exit()
            return
        digitfound = False
        try:
            while True:
                readNum()
                digitfound = True
        except:
            if digitfound:
                return
            print("Missing digit at end of row: "+getRest())
            sys.exit()
            return
    raise FormelError("Incorrect start of group")

def readMol():
    try:
        readGroup()
    except FormelError:
        print("Incorrect start of group at end of row: "+getRest()) 
        raise FormelError
    if q.peek() == None:
        return
    if not q.peek() == ")": 
        try:
            readMol()
        except FormelError:
            pass

def readFormel():
    try:
        readMol()
    except:
        return
    print("Correct formula")

def getRest():
    rest = ""
    while not q.isEmpty():
        rest += q.get()
    return rest

readFormel()

Now the code is supposed to accept some given formulas and provide an error code for some given incorrect formulas. Let's look at these given formulas:

Correct: Si(C3(COOH)2)4(H2O)7

Incorrect: H2O)Fe

(Cl)2)3

The program accepts the correct formula, but unfortunately also the incorrect ones. The reason for this is that the if statement in:

if not q.peek() == ")": 
    try:
        readMol()
    except FormelError:
        pass

makes it so that parentheses unbalanced to the right (with one or more parenthesis too much on the right side) slip through the code, instead of being detected as incorrect starts of a "group". How can I fix this, while still having Si(C3(COOH)2)4(H2O)7 being accepted as syntactically correct?

Thank you for your patience :)

If you thought my answer was useful, you should upvote it. – Ira Baxter Aug 27 '17 at 12:55 — Ira Baxter, Aug 27 '17 at 12:55

score 1 · Accepted Answer · edited May 23 '17 at 10:10

Your code for readMol has this erroneous test (you even told us) for ")". Your grammar doesn't show a need for such a test, if you are coding (as you are) a recursive descent parser.

In fact, you grammar has a odd rule for mol:

<mol>   ::= <group> | <group><mol>

This doesn't work well with recursive descent parsers. You have refactor such rules to share the common prefixes in each rule. In this case, it is easy:

<mol>   ::= <group> ( <mol> | empty ) ;

Then you write the code directly from the grammar rule (see link above) [You sort of did this, except for the ")" check.] It should look something like this (I'm not a python expert):

def readMol():
    try:
        readGroup()
    except FormelError:
        print("Incorrect start of group at end of row: "+getRest()) 
        raise FormelError
    try:
       readMol()
    except FormelError:
       pass

It is helpful when writing recursive descent parsers, to massage the grammar into a most-compatible form first (as I did with your mol rule). Then coding the individual recognizers is a purely mechanical task that is hard to get wrong.

Python - Syntax check of molecular formulas

1 Answers1