Beispiel #1
0
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)
}
Beispiel #2
0
func getPdbChain(fp string) *pdb.Chain {
	b := path.Base(fp)
	if !strings.HasSuffix(b, ".fmap") {
		util.Fatalf("Expected file named 'something.fmap' but got '%s'.", b)
	}
	idAndChain := b[0 : len(b)-5]
	if len(idAndChain) != 5 {
		util.Fatalf("Expected 4-letter PDB id concatenated with 1-letter "+
			"chain identifier, but got '%s' instead.", idAndChain)
	}

	pdbName := idAndChain[0:4]
	chainId := idAndChain[4]
	pdbCat := idAndChain[1:3]
	pdbFile := fmt.Sprintf("pdb%s.ent.gz", pdbName)

	pdbPath := path.Join(util.FlagPdbDir, pdbCat, pdbFile)

	entry := util.PDBRead(pdbPath)
	chain := entry.Chain(chainId)
	if chain == nil {
		util.Fatalf("Could not find chain '%c' in PDB entry '%s'.",
			chainId, pdbPath)
	}
	return chain
}
Beispiel #3
0
func main() {
	flag.BoolVar(&flagAllFragments, "all-fragments", flagAllFragments,
		"When set, all fragments will be shown, even if the best fragment\n"+
			"of each ATOM set is the same.")
	util.FlagParse(
		"fraglib align.{fasta,ali,a2m,a3m} pdb-file out-csv",
		"Writes a CSV file to out-csv containing the best matching fragment\n"+
			"for each pairwise contiguous set of alpha-carbon atoms of the\n"+
			"first two proteins in the alignment and PDB file.")
	util.AssertNArg(4)
	flib := util.StructureLibrary(util.Arg(0))
	aligned := util.MSA(util.Arg(1))
	pentry := util.PDBRead(util.Arg(2))
	outcsv := util.CreateFile(util.Arg(3))

	csvWriter := csv.NewWriter(outcsv)
	csvWriter.Comma = '\t'
	defer csvWriter.Flush()

	pf := func(record ...string) {
		util.Assert(csvWriter.Write(record), "Problem writing to '%s'", outcsv)
	}
	pf("start1", "end1", "start2", "end2", "frag1", "frag2", "frag_rmsd")
	iter := newContiguous(
		flib.FragmentSize(),
		aligned.GetFasta(0), aligned.GetFasta(1),
		pentry.Chains[0], pentry.Chains[1])
	for iter.next() {
		best1 := flib.BestStructureFragment(iter.atoms1)
		best2 := flib.BestStructureFragment(iter.atoms2)
		if !flagAllFragments && best1 == best2 {
			continue
		}
		bestRmsd := structure.RMSD(flib.Atoms(best1), flib.Atoms(best2))
		pf(
			fmt.Sprintf("%d", iter.s1()),
			fmt.Sprintf("%d", iter.e1()),
			fmt.Sprintf("%d", iter.s2()),
			fmt.Sprintf("%d", iter.e2()),
			fmt.Sprintf("%d", best1),
			fmt.Sprintf("%d", best2),
			fmt.Sprintf("%f", bestRmsd),
		)
	}
}
Beispiel #4
0
func main() {
	entry := util.PDBRead(flag.Arg(0))

	if len(flagChain) > 0 {
		if len(flagChain) != 1 {
			util.Fatalf("Chain identifiers must be a single character.")
		}
		chain := entry.Chain(flagChain[0])
		if chain == nil {
			util.Fatalf("Could not find chain '%c' in PDB entry '%s'.",
				chain.Ident, entry.Path)
		}
		showMapping(chain, chain.SequenceAtoms())
	} else {
		for _, chain := range entry.Chains {
			showMapping(chain, chain.SequenceAtoms())
		}
	}
}
Beispiel #5
0
func main() {
	libPath := util.Arg(0)
	chain := util.Arg(1)
	pdbEntryPath := util.Arg(2)
	bowOut := util.Arg(3)

	lib := util.StructureLibrary(libPath)
	entry := util.PDBRead(pdbEntryPath)

	thechain := entry.Chain(chain[0])
	if thechain == nil || !thechain.IsProtein() {
		util.Fatalf("Could not find chain with identifier '%c'.", chain[0])
	}

	bow := bow.BowerFromChain(thechain).StructureBow(lib)
	if bowOut == "--" {
		fmt.Println(bow)
	} else {
		util.BowWrite(util.CreateFile(bowOut), bow)
	}
}
Beispiel #6
0
func main() {
	pdbFiles := util.RecursiveFiles(util.FlagPdbDir)
	files := make([]string, 0, flagNum)
	for i := 0; i < flagNum; i++ {
		var index int = -1
		for index == -1 || !util.IsPDB(pdbFiles[index]) {
			// not guaranteed to terminate O_O
			index = rand.Intn(len(pdbFiles))
		}
		files = append(files, pdbFiles[index])
		pdbFiles = append(pdbFiles[:index], pdbFiles[index+1:]...)
	}

	for _, f := range files {
		if flagPaths {
			fmt.Println(f)
		} else {
			e := util.PDBRead(f)
			fmt.Printf("%s%c\n", strings.ToLower(e.IdCode), e.Chains[0].Ident)
		}
	}
}
Beispiel #7
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)
		}
	}
}
Beispiel #8
0
func main() {
	pdbEntry := util.PDBRead(flag.Arg(0))

	fasEntries := make([]seq.Sequence, 0, 5)
	if !flagSeparateChains {
		var fasEntry seq.Sequence
		if len(pdbEntry.Chains) == 1 {
			fasEntry.Name = chainHeader(pdbEntry.OneChain())
		} else {
			fasEntry.Name = fmt.Sprintf("%s", strings.ToLower(pdbEntry.IdCode))
		}

		seq := make([]seq.Residue, 0, 100)
		for _, chain := range pdbEntry.Chains {
			if isChainUsable(chain) {
				seq = append(seq, chain.Sequence...)
			}
		}
		fasEntry.Residues = seq

		if len(fasEntry.Residues) == 0 {
			util.Fatalf("Could not find any amino acids.")
		}
		fasEntries = append(fasEntries, fasEntry)
	} else {
		for _, chain := range pdbEntry.Chains {
			if !isChainUsable(chain) {
				continue
			}

			fasEntry := seq.Sequence{
				Name:     chainHeader(chain),
				Residues: chain.Sequence,
			}
			fasEntries = append(fasEntries, fasEntry)
		}
	}
	if len(fasEntries) == 0 {
		util.Fatalf("Could not find any chains with amino acids.")
	}

	var fasOut io.Writer
	if flag.NArg() == 1 {
		fasOut = os.Stdout
	} else {
		if len(flagSplit) > 0 {
			util.Fatalf("The '--split' option is incompatible with a single " +
				"output file.")
		}
		fasOut = util.CreateFile(util.Arg(1))
	}

	if len(flagSplit) == 0 {
		util.Assert(fasta.NewWriter(fasOut).WriteAll(fasEntries),
			"Could not write FASTA file '%s'", fasOut)
	} else {
		for _, entry := range fasEntries {
			fp := path.Join(flagSplit, fmt.Sprintf("%s.fasta", entry.Name))
			out := util.CreateFile(fp)

			w := fasta.NewWriter(out)
			util.Assert(w.Write(entry), "Could not write to '%s'", fp)
			util.Assert(w.Flush(), "Could not write to '%s'", fp)
		}
	}
}
Beispiel #9
0
func main() {
	libFile := util.Arg(0)
	brkFile := util.Arg(1)
	lib := util.StructureLibrary(libFile)

	stderrf("Loading PDB files into memory...\n")
	entries := make([]*pdb.Entry, util.NArg()-2)
	for i, pdbfile := range flag.Args()[2:] {
		entries[i] = util.PDBRead(pdbfile)
	}

	stderrf("Comparing the results of old fragbag and new fragbag on " +
		"each PDB file...\n")
	for _, entry := range entries {
		stderrf("Testing %s...\n", entry.Path)
		fmt.Printf("Testing %s\n", entry.Path)

		// Try to run old fragbag first. The output is an old-style BOW.
		oldBowStr, err := runOldFragbag(brkFile, entry.Path, lib.Size(),
			lib.FragmentSize())
		if err != nil {
			fmt.Println(err)
			fmt.Printf("The output was:\n%s\n", oldBowStr)
			divider()
			continue
		}

		oldBow, err := bow.NewOldStyleBow(lib.Size(), oldBowStr)
		if err != nil {
			fmt.Printf("Could not parse the following as an old style "+
				"BOW:\n%s\n", oldBowStr)
			fmt.Printf("%s\n", err)
			divider()
			continue
		}

		// Now use package fragbag to compute a BOW.
		var newBow bow.Bow
		if flagOldStyle {
			newBow = oldStyle{entry}.StructureBow(lib)
		} else {
			newBow = newStyle{entry}.StructureBow(lib)
		}

		// Create a diff and check if they are the same. If so, we passed.
		// Otherwise, print an error report.
		diff := bow.NewBowDiff(oldBow, newBow)
		if diff.IsSame() {
			fmt.Println("PASSED.")
			divider()
			continue
		}

		// Ruh roh...
		fmt.Println("FAILED.")
		fmt.Printf("\nOld BOW:\n%s\n\nNew BOW:\n%s\n", oldBow, newBow)
		fmt.Printf("\nDiff:\n%s\n", diff)
		divider()
	}
	stderrf("Done!\n")
}