Chris Brasnett

Reading in header information from itp file

3

I realised I buried this within #483, and might be quite ambitious, but it would be useful to read back in header information (eg. the secondary structure determined by DSSP)...

GO IDP bugfix

2

Need to add secstruc to the water bias application, otherwise can't apply across a whole protein (starting resid has to be > 1). this should fix that. And add preprint...

Lazy merge

1

Lazy merging of chains as per #587. Instead of specifying groups of chains to merge, users can just give `-merge all` and all chains get merged.

Lazy merging?

1

If I have a protein complex with many chains and just want a single merged itp out, the current input is slightly annoying in having to make list of all...

SEQRES parsing

1

First go at adding parsing of SEQRES section of PDB files to check the residues present with coordinates in the pdb vs. the SEQRES entry. The check will also do...

Raise warning if mutation not found

8

At the moment, if a -mutate flag is given, but the target residue is not found, then martinize will process the input structure as given without raising a warning. Eg,...

(protein) termini patching

1

with the -ter flag, add modifications read from the force field to the n and c termini

isomorphism propagation

3

I have a protein where I'm mutating a several identical residues to the same target. One of the major slowdowns in doing this is the graph repair - and looking...

External EN bonds itp

2

Add a flag, `-ew`, to write out bonds for elastic networks to an external en_bonds.itp file, in the style of Go or Olive bonds. This has been motivated by some...

per #666 the logic wasn't correct for writing out the contact map calculated using `-go`. This PR fixes it