List of fixes for failing test cases

[zhang-ivy]

Here are the issues/fixes we discussed:

1. Wrong stereochemistry and clashes

• Fix: Add restraints
• Check atom and bond stereochemistry is biologically correct
• Also check for bad bond lengths/angles and atom clashes?

2. Truncate and cap terminal and internal loops

• Fix: Allow user to specify options OR edit fixer.missingResidues dictionary

3. Missing SEQRES

• Fix: Add warning when the PDB is missing SEQRES lines

TO DO: prepare list of test cases (PDB ids)
@jchodera @peastman @rafwiewiora

[peastman]

Fix: Add warning when the PDB is missing SEQRES lines

Should it always warn about this, or only if there are gaps in the residue numbers? If all residues in each chain have sequential numbers we know there can't be any missing loops in the middle, though of course we can't rule out missing terminal residues.

[rafwiewiora]

Should it always warn about this, or only if there are gaps in the residue numbers? If all residues in each chain have sequential numbers we know there can't be any missing loops in the middle, though of course we can't rule out missing terminal residues.

But what if you've used some tool that resets the residue numbers to sequential? I'd say always warn, better safe than sorry.