func init() { runtime.GOMAXPROCS(runtime.NumCPU()) util.FlagUse("cpu") util.FlagParse("database-path frag-lib-dir query-pdb-file "+ "[query-pdb-file ...]", "") util.AssertLeastNArg(2) }
func init() { util.FlagUse("cpu") util.FlagParse("frag-lib-dir chain pdb-file out-bow", "Computes and outputs a BOW file for the specified chain in the\n"+ "given PDB file. If 'out-bow' is '--', then a human readable\n"+ "version of the BOW will be printed to stdout instead.") util.AssertNArg(4) }
func init() { flag.BoolVar(&flagQuiet, "quiet", flagQuiet, "When set, hhblits/hhmake output will be hidden.") util.FlagUse("seq-db") util.FlagParse("in-fasta-file out-hhm-file", "") util.AssertNArg(2) }
func init() { flag.Float64Var(&flagRmsd, "rmsd", flagRmsd, "The RMSD cut-off to use to determine true positives.") util.FlagUse("pdb-dir") util.FlagParse("fmap-file", "") util.AssertNArg(1) }
func init() { flag.IntVar(&flagNum, "n", flagNum, "The number of PDB entries to echo.") flag.BoolVar(&flagPaths, "paths", flagPaths, "When set, full file paths will be echoed instead of PDB ids.") util.FlagUse("pdb-dir") util.FlagParse("", "") rand.Seed(time.Now().UnixNano()) }
func init() { flag.IntVar(&flagRandoms, "n", flagRandoms, "The number of random permutations to use.") util.FlagUse("cpu", "cpuprof") util.FlagParse( "out-file vectors-csv 'comma-sep-cath-domains' ...", "Computes the probability that each cluster of cath domains is\n"+ "significantly different with respect to their Fragbag vectors.") util.AssertLeastNArg(3) }
func init() { flag.Float64Var(&flagThreshold, "threshold", flagThreshold, "The threshold at which to cut the tree.") flag.StringVar(&flagGobIt, "gobit", flagGobIt, "If set, alignment distances will be cached to the file given, "+ "then mattbench-cluster will quit.") util.FlagUse("cpu", "cpuprof", "verbose") util.FlagParse( "(astral-alignment-dir | alignment-distances-gob) dendrogram-tree "+ "out-clusters.csv", "Where `dendrogram-tree` is a file in Newick tree format.") if len(flagGobIt) > 0 { util.AssertNArg(1) } else { util.AssertNArg(3) } }
func init() { flag.Float64Var(&flagThreshold, "threshold", flagThreshold, "Set the distance threshold to use when computing AUC.") util.FlagUse("cpu", "cpuprof") util.FlagParse( "cath-domain-labels best-of-all-matrix"+ "(bowdb | matrix-file) out-file "+ "[ (bowdb | matrix-file) out-file ... ]", "Computes the AUC of each aligner matrix (or BOW database) given\n"+ "with respect to the 'best-of-all' matrix given. Each AUC is\n"+ "written to a separate out-file. The sizes of all matrices must\n"+ "be exactly equivalent.\n"+ "Files are interpreted as BOW databases if they have a '.bowdb'\n"+ "file extension.") util.AssertLeastNArg(4) if util.NArg()%2 != 0 { util.Fatalf("There must be an out file for each matrix or bowdb file.") } }
func init() { util.FlagUse("cpu") util.FlagParse("frag-lib-dir fmap-file out-bow", "") util.AssertNArg(3) }
func init() { util.FlagUse("cpu", "seq-db", "pdb-hhm-db", "blits", "hhfrag-min", "hhfrag-max", "hhfrag-inc") util.FlagParse("target-fasta out-fmap", "") util.AssertNArg(2) }
func init() { util.FlagUse("cpu", "seq-db", "pdb-hhm-db", "blits", "verbose", "hhfrag-min", "hhfrag-max", "hhfrag-inc") util.FlagParse("out-dir target-fasta", "") util.AssertLeastNArg(2) }