Example #1
0
func (e newStyle) StructureBow(lib fragbag.StructureLibrary) bow.Bow {
	bag := bow.NewBow(lib.Size())
	for _, chain := range e.Chains {
		for _, model := range chain.Models {
			bag = bag.Add(bow.StructureBow(lib, model.CaAtoms()))
		}
	}
	return bag
}
Example #2
0
func (fmap *FragmentMap) StructureBow(lib fragbag.StructureLibrary) bow.Bowed {
	bag := bow.NewBow(lib.Size())
	for _, fragGroup := range fmap.Segments {
		for _, frag := range fragGroup.Frags {
			bag = bag.Add(bow.StructureBow(lib, frag.CaAtoms))
		}
	}
	return bow.Bowed{Id: fmap.Name, Bow: bag}
}
Example #3
0
// StructureBow is a helper function to compute a bag-of-words given a
// structure fragment library and a list of alpha-carbon atoms.
//
// If the lib given is a weighted library, then the Bow returned will also
// be weighted.
//
// Note that this function should only be used when providing your own
// implementation of the StructureBower interface. Otherwise, BOWs should
// be computed using the StructureBow method of the interface.
func StructureBow(lib fragbag.StructureLibrary, atoms []structure.Coords) Bow {
	var best, uplimit int

	b := NewBow(lib.Size())
	libSize := lib.FragmentSize()
	uplimit = len(atoms) - libSize
	for i := 0; i <= uplimit; i++ {
		best = lib.BestStructureFragment(atoms[i : i+libSize])
		if best > -1 {
			b.Freqs[best] += 1
		}
	}
	if wlib, ok := lib.(fragbag.WeightedLibrary); ok {
		b = b.Weighted(wlib)
	}
	return b
}