func mkStructure(c *command) {
c.assertNArg(2)
brkFile := c.flags.Arg(0)
saveto := c.flags.Arg(1)
util.AssertOverwritable(saveto, flagOverwrite)
brkContents, err := ioutil.ReadAll(util.OpenFile(c.flags.Arg(0)))
util.Assert(err)
pdbFragments := bytes.Split(brkContents, []byte("TER"))
fragments := make([][]structure.Coords, 0)
for i, pdbFrag := range pdbFragments {
pdbFrag = bytes.TrimSpace(pdbFrag)
if len(pdbFrag) == 0 {
continue
}
fragments = append(fragments, coords(i, pdbFrag))
}
libName := stripExt(path.Base(brkFile))
lib, err := fragbag.NewStructureAtoms(libName, fragments)
util.Assert(err)
fragbag.Save(util.CreateFile(saveto), lib)
}
func mkPaired(c *command) {
c.assertNArg(2)
in := util.Library(c.flags.Arg(0))
outPath := c.flags.Arg(1)
util.AssertOverwritable(outPath, flagOverwrite)
if _, ok := in.(fragbag.WeightedLibrary); ok {
util.Fatalf("%s is a weighted library (not allowed)", in.Name())
}
name := fmt.Sprintf("paired-%s", in.Name())
if fragbag.IsStructure(in) {
var pairs [][]structure.Coords
lib := in.(fragbag.StructureLibrary)
nfrags := lib.Size()
for i := 0; i < nfrags; i++ {
for j := 0; j < nfrags; j++ {
if i == j {
continue
}
f1, f2 := lib.Atoms(i), lib.Atoms(j)
pairs = append(pairs, append(f1, f2...))
}
}
pairLib, err := fragbag.NewStructureAtoms(name, pairs)
util.Assert(err)
fragbag.Save(util.CreateFile(outPath), pairLib)
} else if strings.Contains(in.Tag(), "hmm") {
var pairs []*seq.HMM
lib := in.(fragbag.SequenceLibrary)
nfrags := lib.Size()
for i := 0; i < nfrags; i++ {
for j := 0; j < nfrags; j++ {
if i == j {
continue
}
f1, f2 := lib.Fragment(i).(*seq.HMM), lib.Fragment(j).(*seq.HMM)
pairs = append(pairs, seq.HMMCat(f1, f2))
}
}
pairLib, err := fragbag.NewSequenceHMM(name, pairs)
util.Assert(err)
fragbag.Save(util.CreateFile(outPath), pairLib)
} else if strings.Contains(in.Tag(), "profile") {
util.Fatalf("Sequence profiles not implemented.")
} else {
util.Fatalf("Unrecognized fragment library: %s", in.Tag())
}
}