func init() {
flag.StringVar(&flagChain, "chain", flagChain,
"This may be set to one or more chain identifiers. Only amino acids "+
"belonging to a chain specified will be included.")
flag.StringVar(&flagSplit, "split", flagSplit,
"When set, each FASTA entry produced will be written to a file in the "+
"specified directory with the PDB id code and chain identifier as "+
"the name.")
util.FlagParse("in-pdb-file [out-fasta-file]", "")
if util.NArg() != 1 && util.NArg() != 2 {
util.Usage()
}
}
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)
}
}
}