func main() {
hhmFile := util.Arg(0)
start := util.ParseInt(util.Arg(1))
end := util.ParseInt(util.Arg(2))
fhhm := util.OpenFile(hhmFile)
qhhm, err := hmm.ReadHHM(fhhm)
util.Assert(err)
util.Assert(hmm.WriteHHM(os.Stdout, qhhm.Slice(start, end)))
}
func main() {
pdbf1, chain1, s1, e1 := util.Arg(0), util.Arg(1), util.Arg(2), util.Arg(3)
pdbf2, chain2, s2, e2 := util.Arg(4), util.Arg(5), util.Arg(6), util.Arg(7)
entry1 := util.PDBRead(pdbf1)
entry2 := util.PDBRead(pdbf2)
s1n, e1n := util.ParseInt(s1), util.ParseInt(e1)
s2n, e2n := util.ParseInt(s2), util.ParseInt(e2)
r, err := pdb.RMSD(
entry1, chain1[0], s1n, e1n, entry2, chain2[0], s2n, e2n)
util.Assert(err)
fmt.Println(r)
}
func main() {
lib = util.StructureLibrary(util.Arg(0))
pdbEntry := util.PDBRead(util.Arg(1))
if util.NArg() == 2 {
for _, chain := range pdbEntry.Chains {
atoms := chain.CaAtoms()
bestFragsForRegion(chain, atoms, 0, len(atoms))
}
} else {
chainId := util.Arg(2)
chain := pdbEntry.Chain(chainId[0])
if chain == nil || !chain.IsProtein() {
util.Fatalf("Could not find protein chain with id '%c'.", chainId)
}
atoms := chain.CaAtoms()
if util.NArg() == 3 {
bestFragsForRegion(chain, atoms, 0, len(atoms))
} else {
if util.NArg() != 5 {
log.Println("Both a start and end must be provided.")
util.Usage()
}
s, e := util.Arg(3), util.Arg(4)
sn, en := util.ParseInt(s)-1, util.ParseInt(e)
if en-sn < lib.FragmentSize() {
util.Fatalf("The range [%s, %s] specifies %d alpha-carbon "+
"atoms while at least %d alpha-carbon atoms are required "+
"for the given fragment library.",
s, e, en-sn, lib.FragmentSize())
}
bestFragsForRegion(chain, atoms, sn, en)
}
}
}