CreateAPeptide

How can I create a peptide from an amino acid sequence?

This is a short example on how to create a peptide. For each amino acid we define the torsion angles in an amino acid descriptor, push it into a sequence, create a builder and tell him to construct the peptide.

C++

#include <BALL/FORMAT/PDBFile.h>

#include <BALL/MATHS/angle.h>
#include <BALL/COMMON/constants.h>

#include <BALL/STRUCTURE/peptideBuilder.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <vector>

using namespace BALL;
using namespace std;

int main(int argc, char** argv)
{
   // we need to define the peptid's AA sequence as a vector of descriptors
   vector<BALL::Peptides::AminoAcidDescriptor> descriptor_seq;

   // each aminoacid is represented by a descriptor
   BALL::Peptides::AminoAcidDescriptor* aad = new BALL::Peptides::AminoAcidDescriptor;

   // define a glycin
   aad->setAminoAcidType("GLY");
   aad->setPhi(Angle(-47., false));
   aad->setPsi(Angle(-77., false));

   // add it to the sequence
   descriptor_seq.push_back(*aad);
 
   // create a builder using the sequence
   BALL::Peptides::PeptideBuilder* pb = new BALL::Peptides::PeptideBuilder(descriptor_seq);

   // "link" the fragment db for adding missing information
   FragmentDB fdb("");
   pb->setFragmentDB(&fdb);

   // now build the peptide 
   Protein* prot = pb->construct();

   // give sensible names
   pb->setChainName("new_glycin");
   pb->setProteinName("new_protein");

   // check what is done
   ResidueIterator res_it = prot->beginResidue();
   cout << "# res:" << prot->countResidues() << endl;
   for ( ; +res_it; ++res_it)
   {
      cout << res_it->getTorsionPhi() << " " << res_it->getTorsionPsi() << " " << endl; 
   }

  return 0;
}

Please note that BALL offers a special class handling angles and physical constants.

For more convenient handling try:

   BALL::Peptides::PeptideBuilder* pb2 = new BALL::Peptides::PeptideBuilder; 
   FragmentDB fdb("");
   pb->setFragmentDB(&fdb);

   pb2->addAminoAcid("SER", Angle(M_PI, true), Angle(M_PI, true));
   pb2->setChainName("my_new_chain");
   pb2->setProteinName("my_new_protein");
  
   Protein* prot2 = pb->construct();

Python

from BALL import *
import math

fdb = FragmentDB("")

PB = PeptideBuilder()
PB.addAminoAcid("A", Angle(math.pi), Angle(math.pi))
PB.addAminoAcid(Peptides.OneLetterCode(r), Angle(math.pi), Angle(math.pi))
PB.addAminoAcid("A", Angle(math.pi), Angle(math.pi))
PB.setFragmentDB(fdb)
protein = PB.construct()

print protein.countAtoms()