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
}
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)
}
