This file contains the step by step process from setting up the software to the results obtained in the end.
- Prerequisite
- Installation of concerned compiler libraries
- Reading from MolFile
- Extracting molecular formula from MolFile
- Conclusion
- Unit Testing
- Future Improvements
Before jumping into the problem itself, first, we must understand what softwares we want to work on so that it helps us in solving the problem quickly. To solve this problem I worked with the following softwares.
I worked with the community free version of VS2017. It has a very nice extension for github where you can easily make changes to your exsiting code and push the changes on Github. The Github extension comes with all the features like push, pull, commit, add files etc.. It tells you which brach you are working on and so on with other useful information.
To avail this extension you have to go to Tools -> Extension and Updates -> Online (in a new pop window) and then search for Github for Visual Studio. After downloading this extension, in a new pop window, you will be asked to enter the Github account details if you already have an account or else you can create a new account and follow up the process. Now as your account is linked so now you can easily see in the right side menu about Github. You can create a new repo or clone a preexsisting repo on Github. You can also make a project folder on your computer a repo.
The link to VS2017 is https://docs.microsoft.com/en-us/visualstudio/releasenotes/vs2017-relnotes. Here, you can download the latest version.
This is also one of the best code editors as it supports multiple programming languages. You can easily install the specific programming extension which you prefer. I in this case chose the C/C++ extension to support my code. To install the extension just click on the extension icon on the left side of VSCode window on the bar. There are very easy to understand features like debugging and compiling the code.
The download link to VSCode for latest version is https://code.visualstudio.com/.
The most important libraries needed to run the C code in VSCode are gcc, g++ and gdb. These are basically used for compiling the code. To download and install these libraries, first, we must install MinGW-w64 which is a runtime enviroment created to support the GCC compiler on windows. The download link for MinGW-w64 is https://www.mingw-w64.org/downloads/. In downloads pick the MSYS2 package and click on Installation : GitHub. This will take you to the download page where you can select the installer execution file. The step by step process is given on this page https://www.msys2.org/. Always choose the 64 bit version of MSYS2 because it only supports 64 bit machines (windows 7 or newer). While installing GCC, G++, GDB choose the 64 bit versions as they will be compatible with your machine and run smoothly.
Note: All the installations of GCC, GDB and G++ will take place in the MSYS2 MinGW x 64 app icon which can be found in windows search bar.
The next part is very important because now we want want our compilers to be added to the enviroment path. For this, look into the folder you have installed MSYS2 (it will have name "msys64") open the folder then open "mingw64" folder go to bin and copy the path from the above search tab. Now in the windows search tab write "Edit the enviroment variable", click on it. New window of "system properties" will pop up. At the bottom click on Enviroment Variables. A new window pops up, look for "path" variable in System Variables and click once on it. Then click on edit. A new "Edit Enviroment Variables" window pops up, click on add button on the top right and paste the path that you copied earlier. At the end click OK on all the open windows and now we are good to go with our C code in VSCode atlast.
While working on a problem my first approach is to look for information. The first bit of information lies in the input itself if I try to look deep enough. For this problem my input is a MolFile as described previously above. So initially, I tried to read the data from the Molfile named "Aspirin.mol". The whole process completes with the help of following functions described below. Looking into the data of input file helps to formulate the next necessary steps to be taken.
After including the required libraries and creating main(), as I am dealing with a file as an input, I created a pointer for type File.
I used a char variable array of buffer size 100, which is why I used fgets() function ahead and not gets() function as the fgets() is more secure and limits our buffer from overflowing.
After opening the file in read mode with the help of fopen(), first the program checks if the file is present afterwards it is read by the fgets() function.
Finally the file is data is printed in the output window for visualization and understanding so that next tasks can be performed correctly. The opened file is closed with the fclose() function for better memory usage in case we have multiple files.
After looking into the data from the input file the first impression in terms of solving the problem is:
Step 1: As I already have the information about the number of Carbon and Oxygen atoms so I have to come up with a way to calculate the number of C and O atoms and store them.
Solution: After trying different approaches the most suitable solution for me is that as I already actually know the number of Carbon and Oxygen atoms known from the Atom block. So, with the help of fgetc() function we would count the C and O atoms. A more detailed description is given below.
First I create the variable strings for the characters (In this case "C" & "O"), that are to be counted.
Then, I created a new function ("string_count") in the header file Program.h, that counts the specified characters.
The input to the new function is the MolFile.
The function creates a new pointer of type File for the fgetc() function.
It is important to note that fgetc() reads the input file character by character hence, fulfilling the purpose of counting the specified set of characters.
The other major use of fgetc() function is that as it returns int so again it fulfills the need because I want the function to return the integer count of the specified characters.
Infinite for loop is implemented so that when the pointer points to the end of the file, with the help of fgetc(), the loop is terminated by break.
In the end the file is closed and the character counts are returned to the main() method where they are stored in seperate variable and printed aalong with the characters.
Step 2: To calculate the number of Hydrogen atoms, I have to indicate in program that for example as Carbon atom has a valence of 4 so first of all group the integer values associated with Carbon. Which in this case are (1, 2, 3, 4, 5, 6, 7, 11, 12) after reading the input file and looking at the atom block of the mol file. Secondly, count the bond for each integer in the bond block of connection tab and store the value. Do the same for Oxygen. This way will get the Hydrogen atoms.
Updated Step 2
To solve the problem of counting the total number of Hydrogen atoms I created a stack that stores the integers associated with Carbon and Oxygen respectively.
Stack follows the LIFO (Last In First Out) policy where the integer (item) stored in the last is popped out the first.
So, in my case here the last element for Carbon is 12 hence the program will look into the 1st and 2nd columns of the bond block and calculate the total number of bonds no. 12 atom has.
As, I have already set that the carbon atom can only have maximum bonds of 4.
Hence, I have added the bond type Single or Double in terms of integers from the 3rd column and subtract it from the maximum bonds that an atom can hold. (max. for "C" is 4 and "O" is 2)
In this scenario, I have got the total number of Hydrogen atoms left (if any) from all of the connections of Carbon and Oxygen atoms, checking the integers in stack one by one.
After calculating each Hydrogen atom I have stored it in an array which I have summed up in the end to get the total number of Hydrogen atomns, printed along with Carbon and Oxygen as Output.
New Update for Step 2:
The approach in finding the Hydrogen atoms involves multiple concepts in terms of reaching to the desired output.
First of all I have introduced the cnt integer that skips the rows containing not useful information at the start.
As, the actual information about the number of atoms and bonds lies at the 4th row where we have, in case of Aspirin.mol, 13 13 that means 13 atoms and 13 bonds. So, I started my cnt variable to have the bond information from the 4th row.
Then, storing the total number of bonds in a variable declared as bond_size.
bond_size is used in the program ahead for counting the bonds in the bond block of Mol File.
The counting process depends upon the array declared, in this case, arr[20][3] as well as the stack capacity of Carbon And Oxygen which is also set at 20.
The program first looks into the integers associated with Carbon (stored in the form of string in str_c) row wise, following Last In First Out (LIFO) approach.
So, for example, if our last in is 11 in case of Aspirin.mol file and this number is associated with Carbon, then, the program looks into all the rows of bond block for the first 2 columns for the number 11.
Then, the program takes the bond value (single or double) in the 3rd column for every connection involving 11 and adds them to the c_joined integer.
The above process is repeated for every integer associated with carbon and the result is added to the c_joined integer.
The same steps are repeated for the integers associated with Oxygen (stored in the form of string in str_o) and later added to the integer o_joined.
In the end, by applying the Formula that is ((Total number of atoms (carbon or Oxygen)) * (maximum bond connections (carbon or oxygen))) - calculated bond connections (c_joined or o_joined) we get the number of Hydrogen atoms.
The above formula is to be applied on both carbon and oxygen seperately and then add the results into an integer denoting total number of Hydrogen atoms.
With printf command, the output window shows us the Chemical Formula.
Step 3:
After completing the procedure for Carbon and Oxygen it is also very important to include Nitrogen to this program so that it can pass all the tests.
The steps defined in the Update for step 2 are followed similiarly for the case of Nitrogen.
The program looks for integers associated with Nitrogen (stored in the form of string in str_n) and adds the result of each integer into a new integer value n_joined.
After that, the above mentioned formula is applied on the max bond connections of Nitrogen minus n_joined.
The results of Carbon, Oxygen and Nitrogen are added to a new integer Hydrogen, showing total number of Hydrogen atoms.
After thinking about the steps above I come to a early conclusion that this program must be modulated with respect to the input file molecular formula.
If we have a Nitrogen atom, with a valence of 3, we have to indicate in our program about Nytrogen first with its respective atom integers in the file and then proceed with the above steps.
After getting all the results right for formulas that not only involve Carbon and Oxygen but also Nitrogen I came across an interesting situation.
The input files Aspirin.mol and Test01.mol only involve the bond connections from Carbon and Oxygen with Hydrogen simultaneously. But, in the input file Test02.mol we have Nitrogen also.
So, if I want to printf the result formula normally without any if else statements then, input files Aspirin.mol and Test01.mol will also give a zero Nitrogen in the formula which I don't need.
To solve this issue I had to implement if else statements around the printf commands for Carbon, Oxygen and Nitrogen so that if the program has not found any of the chemical element it should omit it's symbol also.
I was able to read the input files in the Mol format which helped me to visualiize the bond structure mathematically in the output window.
The program operates perfectly well on the Mol files holding chemical elements like Carbon, Nitrogen and Oxygen.
The program rightly finds the Hydrogen atoms from the chemical structure present in the Aspirin.mol file.
The program also gives accurate results on the test files, giving chemical formulas from Test01.mol as well as Test02.mol input files.
I created a small test function in C for unit testing my C program.
The unit test is a seperate file with c code saved in the file named Unit_Test.c.
The test basically checks on the string_count function. (for detail code check Program.h)
With the help of access function I can verify if the program has the ability to access the File.
In this unit test I made use of the R_OK flag, which is used to check for read permission bit.
The test is passed as the R_OK flag verify the access for read permission for the input file.
This program is flexible and holds the possibilty of adding different other chemical elements.