1

COMP 3031 Assignment 2
Flex and Bison Programming
Fall 2021
Due 5pm, 5th Nov. 2021 Friday
1. Problem Description
In this assignment, you will implement a calculator for a simplified molecular-input line-entry
system (SMILES) by filling in the blanks in the provided flex and bison code skeletons.

The SMILES is a string used to describe the structure of chemical species. For example:
Structure of chemical
species
SMILES



CC(C)C(=O)C(C)C




[CH4]

The BNF grammar rules for SMILES are as follows:
::= |
::= | | |
::= |||
::= ()
::= | |
2

::= B | C | N | O | S | P | F | Cl | Br | I
::= b | c | n | o | s | p
::=
[]|[]|[]|[>]|[]
::= H | He | Li | Be | Ne | Na | Mg | Al | Si | Ar | K | Ca
::= H | H
::= 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
::= - | = | # | $ | / | \

There are 6 operators, “|”, “+”, “UNIQUE”, “MAX”, “MIN”, and the braces “{ }”.
The operators are listed in the order of decreasing precedence.

Operators Operations Associativity
{} Braces
| Count the number of a given
atom in the chemical species.
The input atom should satisfy
the grammar rules for SMILES.
Left
UNIQUE Count the total number of
unique atoms in the chemical
species.
Right
MAX, MIN The number of the most/least
atom in the chemical species.
Right
+ Number addition. Left

The following BNF grammar rules define expressions with SMILES operations:
::=
|
| UNIQUE
| MAX
| MIN
|
3

|
::= |
::= +
::= {
::= }

For example:
Input: CCC=O|C
Output: 3

Input: [CH4]|[H]
Output: 4

Input: UNIQUE N[CH](C)C(=O)O
Output: 4

Input: MAX [CH4]
Output: 4

Input: {CCC=O|C}+{CCC(CC)CO|C}
Output: 9

2. Your work
We provide a zip package containing the following files:
assignment2.pdf Assignment 2 description
helpers.h, helpers.c Helper functions
Makefile Makefile that supports “make” and “make
clean”
4

SMILEScal.lex Flex code skeleton for you to fill in
SMILEScal.y Bison code skeleton for you to fill in

You can decompose the zip file using the following command
unzip assignment2-2021fall.zip

Your tasks are:
1. Add missing flex definitions and rules in SMILEScal.lex
2. Add missing tokens and grammar rules in SMILEScal.y
We have marked the blanks that you can fill in with comment lines:
/********** Start: ... **********/
/********** End: ... *********/

Note: Do not modify the provided files Makefile, helpers.h and helpers.c..

3. Compilation and Testing
After finishing the code, you can compile your code on a CS Lab 2 machine with the command
make
After successful compilation, you can run the binary, and type in the commands to start the
SMILES calculator:
./SMILEScal
Your result SMILES calculator will work as follows:
(1) If the input expression is a single SMILES, your calculator will print the number of atoms in
the SMILES. For example,
CCC=O
4
(2) If the input expression contains operators, your calculator will compute the result of the
expression. For example,
{UNIQUE CCC=O}+{MAX CCC(CC)CO}
5

8
Your program does not need to handle input errors.

4. Helper functions
We list the helper functions in helpers.h and helpers.c in the following table:
Helper function Description
void *generateSmiles(void* smilesPtr); Generate a struct and return its pointer from
the given smiles string, the struct needs to
be passed to other helper functions.
void *count_atom(void* resultPtr1, void
*resultPtr2);
Count the number of the given atom
resultPtr2 appearing in smilesStruct
resultPtr1.
void* max_atom(void *resultPtr); Count the number of atoms that occurred
the most in the smilesStruct resultPtr
void* min_atom(void* resultPtr); Count the number of atoms that occurred
the least in the smilesStruct resultPtr
void* count_all_atoms(void* resultPtr); Count the total number of atoms in
smilesStruct resultPtr
void* unique_atom(void* resultPtr); Count the number of unique atoms in
smilesStruct resultPtr
void *addNum(void* resultPtr1, void
*resultPtr2);
Add two int numbers resultPtr1, resultPtr2
and return the result
void printElem(void *resultPtr); Print the return value resultPtr from all other
functions

5. Submission:
• Zip your two source files, SMILEScal.lex and SMILEScal.y, into a single package using
exactly the following command (case-sensitive):
zip SMILEScal.zip SMILEScal.lex SMILEScal.y
• Submit your zipped file SMILEScal.zip to Canvas.
• No late submission will be accepted.
• Your submission will be compiled and run on a CS Lab 2 machine. If it cannot be
compiled or run properly, you may get 0 marks for this assignment.
• We will use tools to detect code similarity. On confirmed cases of high code similarity,
we will follow university guidelines on academic integrity to take necessary actions.

学霸联盟
























::= |
::= | | |
::= |||
::= ()
::= | |
2

::= B | C | N | O | S | P | F | Cl | Br | I
::= b | c | n | o | s | p
::=
[]|[]|[]|[>]|[]
::= H | He | Li | Be | Ne | Na | Mg | Al | Si | Ar | K | Ca
::= H | H
::= 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
::= - | = | # | $ | / | \

There are 6 operators, “|”, “+”, “UNIQUE”, “MAX”, “MIN”, and the braces “{ }”.
The operators are listed in the order of decreasing precedence.

Operators Operations Associativity
{} Braces
| Count the number of a given
atom in the chemical species.
The input atom should satisfy
the grammar rules for SMILES.
Left
UNIQUE Count the total number of
unique atoms in the chemical
species.
Right
MAX, MIN The number of the most/least
atom in the chemical species.
Right
+ Number addition. Left

The following BNF grammar rules define expressions with SMILES operations:
::=
|
| UNIQUE
| MAX
| MIN
|
3

|
::= |
::= +
::= {
::= }

For example:
Input: CCC=O|C
Output: 3

Input: [CH4]|[H]
Output: 4

Input: UNIQUE N[CH](C)C(=O)O
Output: 4

Input: MAX [CH4]
Output: 4

Input: {CCC=O|C}+{CCC(CC)CO|C}
Output: 9

2. Your work
We provide a zip package containing the following files:
assignment2.pdf Assignment 2 description
helpers.h, helpers.c Helper functions
Makefile Makefile that supports “make” and “make
clean”
4

SMILEScal.lex Flex code skeleton for you to fill in
SMILEScal.y Bison code skeleton for you to fill in

You can decompose the zip file using the following command
unzip assignment2-2021fall.zip

Your tasks are:
1. Add missing flex definitions and rules in SMILEScal.lex
2. Add missing tokens and grammar rules in SMILEScal.y
We have marked the blanks that you can fill in with comment lines:
/********** Start: ... **********/
/********** End: ... *********/

Note: Do not modify the provided files Makefile, helpers.h and helpers.c..

3. Compilation and Testing
After finishing the code, you can compile your code on a CS Lab 2 machine with the command
make
After successful compilation, you can run the binary, and type in the commands to start the
SMILES calculator:
./SMILEScal
Your result SMILES calculator will work as follows:
(1) If the input expression is a single SMILES, your calculator will print the number of atoms in
the SMILES. For example,
CCC=O
4
(2) If the input expression contains operators, your calculator will compute the result of the
expression. For example,
{UNIQUE CCC=O}+{MAX CCC(CC)CO}
5

8
Your program does not need to handle input errors.

4. Helper functions
We list the helper functions in helpers.h and helpers.c in the following table:
Helper function Description
void *generateSmiles(void* smilesPtr); Generate a struct and return its pointer from
the given smiles string, the struct needs to
be passed to other helper functions.
void *count_atom(void* resultPtr1, void
*resultPtr2);
Count the number of the given atom
resultPtr2 appearing in smilesStruct
resultPtr1.
void* max_atom(void *resultPtr); Count the number of atoms that occurred
the most in the smilesStruct resultPtr
void* min_atom(void* resultPtr); Count the number of atoms that occurred
the least in the smilesStruct resultPtr
void* count_all_atoms(void* resultPtr); Count the total number of atoms in
smilesStruct resultPtr
void* unique_atom(void* resultPtr); Count the number of unique atoms in
smilesStruct resultPtr
void *addNum(void* resultPtr1, void
*resultPtr2);
Add two int numbers resultPtr1, resultPtr2
and return the result
void printElem(void *resultPtr); Print the return value resultPtr from all other
functions

5. Submission:
• Zip your two source files, SMILEScal.lex and SMILEScal.y, into a single package using
exactly the following command (case-sensitive):
zip SMILEScal.zip SMILEScal.lex SMILEScal.y
• Submit your zipped file SMILEScal.zip to Canvas.
• No late submission will be accepted.
• Your submission will be compiled and run on a CS Lab 2 machine. If it cannot be
compiled or run properly, you may get 0 marks for this assignment.
• We will use tools to detect code similarity. On confirmed cases of high code similarity,
we will follow university guidelines on academic integrity to take necessary actions.

学霸联盟