func main() {
libFile := util.Arg(0)
lib := util.FragmentLibrary(libFile)
stderrf("Loading PDB files into memory...\n")
entries := make([]*pdb.Entry, util.NArg()-1)
for i, pdbfile := range flag.Args()[1:] {
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(libFile, 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 = bow.ComputeBOW(lib, bow.PDBEntryOldStyle{entry})
} else {
newBow = bow.ComputeBOW(lib, entry)
}
// 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")
}
func main() {
dbPath := util.Arg(0)
fragLibDir := util.Arg(1)
pdbFiles := flag.Args()[2:]
util.Assert(createBowDb(dbPath, fragLibDir, pdbFiles))
db, err := bow.OpenDB(dbPath)
util.Assert(err)
bowOpts := bow.SearchDefault
bowOpts.Limit = 200
mattOpts := matt.DefaultConfig
mattOpts.Verbose = false
chains := createChains(pdbFiles)
mattArgs := createMattArgs(chains)
tabw := tabwriter.NewWriter(os.Stdout, 0, 4, 4, ' ', 0)
header := []byte(
"BOW entry\t" +
"BOW chain\t" +
"BOW dist\t" +
"Matt entry\t" +
"Matt chain\t" +
"Matt dist\n")
for i, chain := range chains {
marg := mattArgs[i]
bowOrdered := getBowOrdering(db, bowOpts, chain)
mattOrdered := getMattOrdering(mattOpts, marg, mattArgs)
fmt.Printf("Ordering for %s (chain %c)\n",
chain.Entry.IdCode, chain.Ident)
compared := comparison([2]ordering{bowOrdered, mattOrdered})
tabw.Write(header)
tabw.Write([]byte(compared.String()))
tabw.Flush()
fmt.Println("\n")
}
util.Assert(db.Close())
}
func main() {
db := util.OpenBOWDB(util.Arg(0))
// Set our search options.
bowOpts := bow.SearchDefault
bowOpts.Limit = -1
fmt.Println("QueryID\tResultID\tCosine\tEuclid")
for _, entry := range db.Entries {
results := db.SearchEntry(bowOpts, entry)
for _, result := range results {
fmt.Printf("%s\t%c\t%s\t%c\t%0.4f\t%0.4f\n",
entry.Id, result.Entry.Id, result.Cosine, result.Euclid)
}
fmt.Println("")
}
util.Assert(db.Close())
}
func main() {
fmapPath := util.Arg(0)
fmap := util.FmapRead(fmapPath)
qchain := getPdbChain(fmapPath)
stats := newSequenceStats(qchain.Sequence)
total, trueps := 0, 0
qcorrupt, tcorrupt := 0, 0
for _, frags := range fmap.Segments {
for _, frag := range frags.Frags {
hit := frag.Hit
if frag.IsCorrupt() {
tcorrupt += 1
stats.incTCorrupt(hit)
continue
}
qatoms := qchain.SequenceCaAtomSlice(hit.QueryStart-1, hit.QueryEnd)
if qatoms == nil {
qcorrupt += 1
stats.incQCorrupt(hit)
continue
}
if len(qatoms) != len(frag.CaAtoms) {
util.Fatalf("Uncomparable lengths. Query is (%d, %d) while "+
"template is (%d, %d). Length of query CaAtoms: %d, "+
"length of template CaAtoms: %d",
hit.QueryStart, hit.QueryEnd,
hit.TemplateStart, hit.TemplateEnd,
len(qatoms), len(frag.CaAtoms))
}
if rmsd.QCRMSD(qatoms, frag.CaAtoms) <= flagRmsd {
trueps += 1
stats.incTruePs(hit)
}
total += 1
stats.incTotal(hit)
}
}
coveredResidues := 0
for _, resStats := range stats {
if resStats.trueps >= 1 {
coveredResidues += 1
}
}
coverage := float64(coveredResidues) / float64(len(qchain.Sequence))
fmt.Printf("RMSDThreshold: %f\n", flagRmsd)
fmt.Printf("TotalFragments: %d\n", total)
fmt.Printf("TruePositives: %d\n", trueps)
fmt.Printf("Precision: %f\n", float64(trueps)/float64(total))
fmt.Printf("CorruptQuery: %d\n", qcorrupt)
fmt.Printf("CorruptTemplate: %d\n", tcorrupt)
fmt.Printf("TotalResidues: %d\n", len(qchain.Sequence))
fmt.Printf("CoveredResidues: %d\n", coveredResidues)
fmt.Printf("Coverage: %f\n", coverage)
}