Arg fix

[dkoes]

Fix issue with protonating charged ARG

OB was placing a third H on NH1 using a random bond vector.  The
AssignBonds, which is suppose to match known protein residue bonding
patterns, was not working because atom names were not stripped of
whitespace. Also, the original pattern in resdata.txt does not match the
convention of the double bond going to NH1 (it has NH2). Then, even if
AssignBonds sets the right bond order, the
PerceivedBonds fragment matching code undoes it, so refined the bond
typer patterns.

[ghutchis]

I'm good with this, but I think we also need to totally re-generate restate.txt from LigandExpo. If you're willing to help, I have some scripts that I used for Avogadro, e.g.
https://github.com/OpenChemistry/avogadrolibs/blob/master/scripts/getresdata.py

[ghutchis]

Can you help look at the failures in the roundtrip test you added?

1102 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/1q11_tye.sdf
[726](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:727)
pdbmol not equal: Mismatched ExplicitValence, 3 != 4
[727](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:728)
1603 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/4isk_1jy.sdf
[728](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:729)
pdbmol not equal: Could only match 0 of 80 atoms (80)
[729](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:730)
2461 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/1kmn_hso.sdf
[730](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:731)
pdbmol not equal: Could only match 0 of 22 atoms (22)
[731](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:732)
3216 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/5ot9_aoz.sdf
[732](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:733)
pdbmol not equal: Could only match 0 of 29 atoms (29)
[733](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:734)
3334 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/3hxb_bd5.sdf
[734](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:735)
pdbmol not equal: Could only match 0 of 81 atoms (81)
[735](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:736)
3516 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/1fmb_hyb.sdf
[736](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:737)
pdbmol not equal: Could only match 0 of 82 atoms (82)
[737](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:738)
3944 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/3fr3_gds.sdf
[738](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:739)
pdbmol not equal: Could only match 0 of 72 atoms (72)
[739](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:740)
4408 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/4pox_2w2.sdf
[740](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:741)
pdbmol not equal: Could only match 0 of 41 atoms (41)
[741](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:742)
6406 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/4old_2uz.sdf
[742](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:743)
pdbmol not equal: Could only match 0 of 24 atoms (24)
[743](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:744)
6497 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/1gs5_nlg.sdf
[744](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:745)
pdbmol not equal: Mismatched ExplicitValence, 3 != 4
[745](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:746)
6827 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/2y2b_mhi.sdf
[746](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:747)
pdbmol not equal: Could only match 0 of 53 atoms (53)
[747](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:748)
8336 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/2j5v_pca.sdf
[748](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:749)
pdbmol not equal: Could only match 0 of 15 atoms (15)
[749](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:750)
10070 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/5nbf_8s8.sdf
[750](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:751)
pdbmol not equal: Could only match 0 of 87 atoms (87)
[751](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:752)
10428 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/3c72_cx1.sdf
[752](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:753)
pdbmol not equal: Could only match 0 of 80 atoms (80)
[753](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:754)
11300 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/5ot8_6db.sdf
[754](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:755)
pdbmol not equal: Could only match 0 of 35 atoms (35)
[755](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:756)
13301 /home/runner/work/openbabel/openbabel/test/pdb_ligands_sdf/2x94_x94.sdf
[756](https://github.com/openbabel/openbabel/runs/7157139800?check_suite_focus=true#step:12:757)
pdbmol not equal: Could only match 0 of 52 atoms (52)