func init() {
flag.StringVar(&flagChain, "chain", flagChain,
"When set, only this chain will be tested for a correspondence. "+
"Otherwise, all chains will be tested.")
util.FlagParse("pdb-file", "")
util.AssertNArg(1)
}
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.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.BoolVar(&flagPaths, "paths", flagPaths,
"When set, the full path of each PDB chain identifier will be\n"+
"displayed, based on the value of the PDB_PATH environment\n"+
"variable.")
util.FlagParse("pdb-select-file",
"Given a file in the PDB Select format, output a list of PDB chain "+
"identifiers (one per line).")
util.AssertNArg(1)
}
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()
}
}
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() {
util.FlagParse("fasta-file",
"Quickly count the number of sequences in a fasta file.")
util.AssertNArg(1)
}
func init() {
util.FlagParse("fmap-file", "")
util.AssertNArg(1)
}
func init() {
util.FlagParse("hhm-file start end", "")
util.AssertNArg(3)
}
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)
}
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.FlagParse("bow1 bow2", "")
util.AssertNArg(2)
}
func init() {
util.FlagParse("fasta-file out-dir",
"Split a single FASTA file into a set of files for each sequence.")
util.AssertNArg(2)
}
func init() {
u := "pdb-file chain-id start stop pdb-file chain-id start stop"
util.FlagParse(u, "")
util.AssertNArg(8)
}
func init() {
u := "fraglib pdb-file [ chain-id [ start stop ] ]"
util.FlagParse(u, "")
util.AssertLeastNArg(2)
}