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#
# Anna Dehof 2011-10-20
# Compute and assign bond orders for a given
# ligand based on atomic valence penalty rules.
#
import sys
from BALL import *
# for use in BALLView
#system = getSystems()[0]
#### for command line use
# issue a usage hint if called without parameters
if (len(sys.argv) != 3 ):
print"Usage: ", sys.argv[0] , " <Ligand infile> <Ligand outfile>"
exit()
# open the file
file = MOL2File(sys.argv[1], File.MODE_IN)
if (not file):
# if file does not exist: complain and abort
print "error opening ", sys.argv[1], " for input."
exit ()
# create a system and read the contents of the PDB file
system = System()
file.read(system)
file.close()
# print the number of atoms read from the file
print "Read", system.countAtoms(), "atoms and", system.countBonds(), "bonds from file"
print " ", sys.argv[1]
# create an BondOrderAssignmentProcessor
abop = AssignBondOrderProcessor()
abop.options.setBool(AssignBondOrderProcessor.Option.KEKULIZE_RINGS, True)
abop.options.setBool(AssignBondOrderProcessor.Option.OVERWRITE_SINGLE_BOND_ORDERS, True)
abop.options.setBool(AssignBondOrderProcessor.Option.OVERWRITE_DOUBLE_BOND_ORDERS, True)
abop.options.setBool(AssignBondOrderProcessor.Option.OVERWRITE_TRIPLE_BOND_ORDERS, True)
abop.options.set(AssignBondOrderProcessor.Option.ALGORITHM, AssignBondOrderProcessor.Algorithm.A_STAR)
abop.options.setReal(AssignBondOrderProcessor.Option.BOND_LENGTH_WEIGHTING,0)
abop.options.setInteger(AssignBondOrderProcessor.Option.MAX_NUMBER_OF_SOLUTIONS,10)
abop.options.setBool(AssignBondOrderProcessor.Option.COMPUTE_ALSO_NON_OPTIMAL_SOLUTIONS, True)
abop.options.setBool(AssignBondOrderProcessor.Option.ADD_HYDROGENS, False)
print "Current penalty: " , abop.evaluatePenalty(system)
# apply the processor
system.apply(abop)
print "Computed", abop.getNumberOfComputedSolutions(), "bond order assignments:"
# print all solutions penalty
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."
# for use in BALLView
#getMainControl().update(system)
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