06_MATLAB_Conditional_Statements.md

Conditional Statements

Lesson Navigation

1. Introduction, Overview of the MATLAB GUI, and Setup
2. Variables and Arrays
3. Plotting Data
4. Scripts
5. Loops
6. Conditional Statements
7. Custom Functions

Decisions

One way to make choices in how code executes is to use the MATLAB if,elseif,else keywords. The general MATLAB syntax for these conditional statements is as follows:

if expression
   do something 1
elseif expression
   do something 2
else
   do something 3
end

Expressions generally use relational operators and logical operators to test a condition. Some examples of relational operators include == for equality and > for greater than. Logical operators allow you to test two conditions, including || for OR, and && for AND.

In a conditional if statement, the only required keywords to use are if and end. You do not need to use the elseif nor else if your code choices do not require multiple decisions. Here is an example:

>> n = 'Alabama';
if length(n) > 5
    disp('n has more than 5 characters')
end 
n has more than 5 characters

In the above code, we use the if keyword, length function, and relational operator > to determine if variable n has more than 5 characters. If it does, we display n has more than 5 characters. If we provide an n with a length fewer than 5, the expression is false, and the code will not display anything:

>> n = 'Utah';
if length(n) > 5
    disp('n has more than 5 characters')
end

We can add else to our code to execute a statement when the first expression is false:

>> n = 'Alabama';
if length(n) > 5
    disp('n has more than 5 characters')
else
    disp('n has less than 5 characters')
end
n has more than 5 characters

>> n = 'Utah';
if length(n) > 5
    disp('n has more than 5 characters')
else
    disp('n has less than 5 characters')
end
n has less than 5 characters

We can then add an elseif keyword, for example, if we wanted to test the condition that n has exactly 5 characters:

>> n = 'Alabama';
if length(n) > 5
    disp('n has more than 5 characters')
elseif length(n) == 5
    disp('n has 5 characters')
else
    disp('n has less than 5 characters')
end
n has more than 5 characters

>> n = 'Utah';
if length(n) > 5
    disp('n has more than 5 characters')
elseif length(n) == 5
    disp('n has 5 characters')
else
    disp('n has less than 5 characters')
end
n has less than 5 characters

>> n = 'Maine';
if length(n) > 5
    disp('n has more than 5 characters')
elseif length(n) == 5
    disp('n has 5 characters')
else
    disp('n has less than 5 characters')
end
n has 5 characters

We can use multiple elseif keywords to add a test for an empty string:

if length(n) > 5
    disp('n has more than 5 characters')
elseif length(n) == 5
    disp('n has 5 characters')
elseif length(n) == 0
    disp('n has no characters')
else
    disp('n has less than 5 characters')
end
n has no characters

With conditional statements, once a condition is true, the code for that condition is executed and no further conditions are tested. So, be sure to experiment often and try a variety of test cases when coding. As an example, let's say we wrote the following code expecting to test for more than 5 characters and the character a:

>> n = 'Alabama';
if length(n) > 5
    disp('n has more than 5 characters')
elseif count(n,'a') > 0
    disp('n contains the character a')
else
    disp('n has less than 5 characters and does not contain a')
end
n has more than 5 characters

Since the first statement length(n) > 5 was true, the code executed and stopped, even though the next statement count(n,'a') > 0 is also true. One way we can test for two conditions at the same time would be to rewrite the code using a logical operator:

>> n = 'Alabama';
if length(n) > 5 && count(n,'a') > 0
    disp('n has more than 5 characters and contains the character a')
else
    disp('false')
end
n has more than 5 characters and contains the character a

>> n = 'Utah';
if length(n) > 5 && count(n,'a') > 0
    disp('n has more than 5 characters and contains the character a')
else
    disp('false')
end
false

We can also combine conditional statements with loops:

>> n = {'Alabama','Georgia','Maine','Utah'};
for j = 1:length(n)
    if length(n{j}) > 5
        disp('n has more than 5 characters')
    elseif length(n{j}) == 5
        disp('n has 5 characters')
    else
        disp('n has less than 5 characters')
    end
end
n has more than 5 characters
n has more than 5 characters
n has 5 characters
n has less than 5 characters

Let's return to our myCIDdata variable and create a new variable by indexing out the first column (the SMILES):

>> smi = myCIDdata{:,1}

smi =

  574×1 cell array

    {'CCN(CC(=O)C)C(C1=CC=CC=C1)C(=O)OC(C)(C)C'                         }
    {'CCN(CC(=O)OCC)C(C1=CC=CC=C1)C(=O)OC'                              }
    {'C1=CC=C(C=C1)CN(CC2=CC=CC=C2)C(C3=CC=C(C=C3)F)C(=O)O'             }
    {'CC.CCCN1CCN(CC1)C(C2=CC=CC=C2CC)C(=O)O'                           }
...
...
    {'CCCCCCCCCC(=O)NC(C1=CC=CC=C1)C(=O)O'                              }
    {'CC1CC1N(C)C(C2=CC=CC=C2)C(=O)O.Cl'                                }
    {'CN(C)C(C1=CC=CC=C1)C(=O)[O-].[Na+]'                               }
    {'C1=CC=C(C=C1)C(C(=O)O)N(C=O)C=O'                                  }
    {'[2H]CN(C[2H])C(C1=CC=CC=C1)C(=O)O'                                }
    {'CC(C)C(C(C)C)N(C)C(C1=CC=CC=C1)C(=O)O.Cl'                         }
    {'[2H]CN(C(C1=CC=CC=C1)C(=O)O)C(=O)OC(C)(C)C'                       }
    {'C1=CC=C(C=C1)C(C(=O)O)N(CCN(CC(=O)O)CC(=O)O)C(C(=O)O)(O)O'        }
...
...

We can apply what we learned about conditional statements to find some patterns in the SMILES strings. For example, if we wanted to find out if each SMILES string contains either a '+' OR '-' character:

>> smi = myCIDdata{:,1};
result1 = cell(length(smi),1); % this preallocates our variable for speed
for j = 1:length(smi)
    if count(smi{j},'+') > 0 || count(smi{j},'-') > 0
       result1{j,1} = true; % this saves the results in row j, column 1
    else
       result1{j,1} = false;  
    end
end

>> result1

result1 =

  574×1 cell array

    {[0]}
    {[0]}
    {[0]}
    {[0]}
...
...   
    {[0]}
    {[0]}
    {[1]}
    {[0]}
    {[0]}
    {[0]}
    {[0]}
    {[0]}
    {[0]}
    {[0]}
    {[0]}    
...
...

In the above code, we use a for loop to iterate over each cell value in smi and then test the condition that the string contains at least one + symbol or - symbol. If the pattern is found a new logical value true (1) is added to the preallocated cell array, result1. If the pattern is not found (else) the value is false (0). Note that we chose to save the variables here instead of displaying 500+ results. The line `result1{j,1} tells MATLAB to save the result in the jth row (i.e., same row the SMILES being tested is on), and first column.

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Attribution

Content in this workshop have been adapted and derive from the Software Carpentry Programming with MATLAB lesson (CC BY 4.0 license for Instructional Materials and MIT License for programs and code examples). In general, we reused parts of their lesson including the basic structure, some descriptions, and logical ordering, but included our own specific variables, scripts, loops, and custom function examples. We have maintained the MIT license for program and code examples. Molecular dataset examples were retrieved from NCBI via their EDirect utility and is credited to NCBI and NLM. Please see the NCBI Website and Data Usage Policies and Disclaimers for more information regarding the data.