<commit_before>package main

import (
	"fmt"

	"github.com/BurntSushi/bcbgo/cmd/util"
	"github.com/BurntSushi/bcbgo/rmsd"
)

func init() {
	u := "pdb-file chain-id start stop pdb-file chain-id start stop"
	util.FlagParse(u, "")
	util.AssertNArg(8)
}

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 := rmsd.PDB(entry1, chain1[0], s1n, e1n, entry2, chain2[0], s2n, e2n)
	util.Assert(err)
	fmt.Println(r)
}
<commit_msg>Moved the "rmsd" package to its own repository and renamed it to the "structure" package.<commit_after>package main

import (
	"fmt"

	"github.com/BurntSushi/bcbgo/cmd/util"
	"github.com/TuftsBCB/structure"
)

func init() {
	u := "pdb-file chain-id start stop pdb-file chain-id start stop"
	util.FlagParse(u, "")
	util.AssertNArg(8)
}

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 := structure.PDB(
		entry1, chain1[0], s1n, e1n, entry2, chain2[0], s2n, e2n)
	util.Assert(err)
	fmt.Println(r)
}

{'fraction_non_alphanumeric': 0.18654230512991338, 'fraction_numerical': 0.0519653564290473, 'mean_word_length': 4.402877697841727, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2708070', 'n_tokens_mistral': 721, 'n_tokens_neox': 703, 'n_words': 137}