Tutorial:Using regular expression: Selecting sequence motifs of a Chain

This is an example on how to select sequence motifs from Chain objects. A Chain object versus a System object is used because regular expressions can not span across chains.

This tutorial is in progress, there may be missing example files, source files or bugs in the code.

Complete source of example_regular_expressions.cpp

In MSL the program grepSequence utilizes the type of code in this tutorial to search for sequences in a list of PDB files, and then structurally align them.

To compile

% make bin/example_regular_expresssions

To run the program

Go to the main directory and run the command (note, the location of the exampleFiles subdirectory needs to be provided as an argument)

% bin/example_regularExpressions exampleFiles/example0004.pdb

Program description

      System sys;
      if (!sys.readPdb(file)) {
	// reading failed, error handling code here
      }
      
       // Check to make sure chain A exits in sys
      if (!sys.exists("A")){
            // error code here.
      }

      // Get a Chain object
      Chain &ch = sys.getChain("A");

      // Regular Expression Object
      RegEx re;

      // Find 3 Prolines surrounded by two Glycines on one side and three Glycines on the other
      string regex = "GG(PPP)GGG";

      // Now do a sequence search...
      vector<pair<int,int> > matchingResidueIndices = re.getResidueRanges(ch,regex);


      // Loop over each match.
      for (uint m = 0; m < matches.size();m++){
        
                // Loop over each residue for this match
        	for (uint r = matches[m].first; r < matches[m].second;r++){
                                    
                         // Get the residue
                         Residue &res = ch.getResidue(r);

                        // .. do something cool with matched residues ...
               }
      }

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