Example #1
0
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()
	}
}
Example #2
0
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)
		}
	}
}