Extra exercises on functions

This chapter contains some extra exercises on functions. In the end, practice makes perfect…

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hands_on Exercise 10.2.1

Download this matrix file (Matrix.txt) and save it in your directory. Then write a function to read a matrix file in this format, reorder the rows by the values in the given column, and printing out the result. The function should take as argument a file name and a column number.

solution Solution

def sortMatrixByColumn(fileName,columnNumber):
    #
    # Read the tab-delimited file and store the values
    #
 
    fin = open(fileName)
    lines = fin.readlines()
    fin.close()
 
    #
    # Convert the data from the file into a Python list
    #
 
    matrix = []

    for matrixRow in lines:
        # Tab-delimited, so split line by \t - this will give a list of strings
        matrixColumns = matrixRow.rstrip().split("\t") 
 
        # Add a row to the matrix
        matrix.append([])
 
        # Add the columns, but convert the strings from the file into a float
        for matrixValue in matrixColumns:
            matrix[-1].append(float(matrixValue))
 
    #
    # Now sort by column - but have to track the row number as well!
    #
 
    selectedColumnValues = []
 
    for rowNumber in range(len(matrix)):
 
        selectedColumnValues.append((matrix[rowNumber][columnNumber],rowNumber))
 
        selectedColumnValues.sort()
 
    #
    # Now print out the new matrix - the column value is now not interesting
    # we want the row number!!
    #
 
    for (columnValue,rowNumber) in selectedColumnValues:  
        columnValueStrings = []
        for value in matrix[rowNumber]:
            columnValueStrings.append("{:.3f}".format(value))
        print("\t".join(columnValueStrings))
 
 
sortMatrixByColumn("data/matrix.txt",3)

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hands_on Exercise 10.2.2

Modify the program to read in the TestFile.pdb file by using separate functions to

1. get the title,
2. dissect the information from the ATOM line and

3. to calculate the distance to the reference distance

   solution Solution

   def getTitle(line,cols):
    
       # Gets the title
    
       title = line.replace(cols[0],'')
       title = title.strip()
    
       return ("The title is '%s'" % title)
    
   def getAtomInfo(cols):
    
       # Get relevant information from an ATOM line and convert to the right type
    
       atomSerial = int(cols[1])
       atomName = cols[2]
       residueNumber = int(cols[5])
       x = float(cols[6])
       y = float(cols[7])
       z = float(cols[8])
    
       return (atomSerial,atomName,residueNumber,x,y,z)
    
   def calculateDistance(coordinate1,coordinate2):
    
       # Calculate the distance between two 3 dimensional coordinates
    
       return ((coordinate1[0] - coordinate2[0]) ** 2 + (coordinate1[1] - coordinate2[1]) ** 2 + (coordinate1[2] - coordinate2[2]) ** 2 ) ** 0.5
    
   
   # Open the file
   fileHandle = open("data/TestFile.pdb")
    
   # Read all the lines in the file (as separated by a newline character), and store them in the lines list
   # Each element in this list corresponds to one line of the file!
   lines = fileHandle.readlines()
    
   # Close the file
   fileHandle.close()
    
   # Initialise some information
   searchCoordinate = (-8.7,-7.7,4.7)
   modelNumber = None
    
   # Loop over the lines, and do some basic string manipulations
   for line in lines:
    
       line = line.strip()  # Remove starting and trailing spaces/tabs/newlines
    
       # Only do something if it's not an empty line
       if line:
           cols = line.split()   # Split the line by white spaces; depending on the format this could be commas, ...
    
           # Print off the title
           if cols[0] == 'TITLE':
               print(getTitle(line,cols))
    
           # Track the model number
           elif cols[0] == 'MODEL':
               modelNumber = int(cols[1])
    
           # For atom lines, calculate the distance
           elif cols[0] == 'ATOM':
               (atomSerial,atomName,residueNumber,x,y,z) = getAtomInfo(cols)
    
               # Calculate the distance
               distance = calculateDistance((x,y,z),searchCoordinate)
    
               if distance < 2.0:
                   print("Model {}, residue {}, atom {} (serial {}) is {:.2f} away from reference.".format(modelNumber,residueNumber,atomName,atomSerial,distance))
   

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Useful literature

Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.