ComputeBondOrders

How to compute bond orders of a ligand?

BALL offers an AssignBondOrderProcessor that computes optimal bond order assignments based on atomic penalty scores.

This work was published in

Dehof, A.K., Rurainski, A., Bui, Q.B.A., Böcker, S., Lenhof, H.-P. & Hildebrandt, A. (2011). 
Automated Bond Order Assignment as an Optimization Problem. 
Bioinformatics, 2011

The processor can be fine tuned via options, e.g.

• AssignBondOrderProcessor::Option::ALGORITHM
• AssignBondOrderProcessor::Option::INIFile
• AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS
• AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS

The processor offers three strategies to solve the optimization problem:

• A-Star
• ILP
• FPT

The FPT is best suited for larger molecules, yet currently does not support all options (e.g. partial bond order assignment, inclusion of bond length information, adding hydrogens).

An exemplary utility application can be found in BALL/source/APPLICATIONS/UTILITIES/assign_bond_orders.C.

C++

#include <BALL/STRUCTURE/assignBondOrderProcessor.h>

...
  System system;
  
  // create the processor
  AssignBondOrderProcessor abop;

  // set some options
  abop.options.setInteger(AssignBondOrderProcessor::Option::MAX_NUMBER_OF_SOLUTIONS, 0);
  abop.options.setBool(AssignBondOrderProcessor::Option::COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, false);

  // compute the current score
  cout << "Current score: " << abop.evaluatePenalty(&system) << endl;
  
  // apply the processor
  system.apply(abop);

  cout << "Number of computed solutions: " << abop.getNumberOfComputedSolutions() << endl;

  // apply the second solution to the original ligand
  abop.apply(1);
  
  cout << "Score of second solution: " << abop.getTotalPenalty(1) << endl;

Python

An exemplary python application can be found in BALL/source/EXAMPLES/PYTHON/UTILITIES/assignBondOrders.py.

import sys
from BALL import *

system = System()
...

# create an BondOrderAssignmentProcessor
abop = AssignBondOrderProcessor()
abop.options.setBool(AssignBondOrderProcessor.Option.KEKULIZE_RINGS, True) 
abop.options.set(AssignBondOrderProcessor.Option.ALGORITHM, AssignBondOrderProcessor.Algorithm.A_STAR)
abop.options.setInteger(AssignBondOrderProcessor.Option.MAX_NUMBER_OF_SOLUTIONS,10)
abop.options.setBool(AssignBondOrderProcessor.Option.COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, True)
 

print "Current penalty: " , abop.evaluatePenalty(system)

# apply the processor
system.apply(abop)

print "Computed", abop.getNumberOfComputedSolutions(), "bond order assignments:"

# print and export all assignments
for i in range(abop.getNumberOfComputedSolutions()):
  print "   solution", str(i) , ": penalty", str(abop.getTotalPenalty(i)) #, " , ", abop.getNumberOfAddedHydrogens(i) , " added hydrogens."	
  # apply the i-th solution
  if (abop.apply(i)):
    # and write the solution into an MOL2file	
    outfile_name = String(sys.argv[2]) + "_" + str(i) + ".mol2";
    print "   Writing solution", i, "as", outfile_name
    outfile = MOL2File(outfile_name, File.MODE_OUT)
    outfile.write(system)
    outfile.close()

# done
print "Done."