#134 Disconected residues in mol2 files

[kparkes]

Problem occurs using babel 2.0.0 compiled with the
fixes from Geoff Hutchison for mol2 file atom-typing.

A pdb file downloaded from www.rcsb.org (1CRN is used
in the example files) when translated to mol2 format
with babel reads as separated residues in sybyl. Each
amino acid is correctly rendered in the correct place
but the amide bonds conecting the amino acids residues
are missing. There is also a superimposed cluster of
dummy atom pairs at an approximate separation of 5.2A
bonded as if in a diatomic molecule. There are 46 of
these pairs each with coordinates (0 0 0) and (3 3 3) -
perahaps one for each missing residue link. These
artefactual atoms visually appear in the region of the
sidechain of Val-15.

In addition to the faulty converted file
(1CRN_newbabel.mol2), I've attached a sybyl generated
mol2 file of the structure for comparison
(1CRN_sybyl.mol2). I've also atttached the babel
converted file re-saved from sybyl which contains the
additional dummy atoms which appear to be a result of
sybyl's attempts to generate the @<TRIPOS>SUBSTRUCTURE
record and are not in the raw babel output
(1CRN_newbabel+sybyl.mol2).

[kparkes]

gzip tarball of the three files