Add file links.cif

[wojdyr]

First step in splitting link descriptions out of list/mon_lib_list.cif. For now, the link description is just duplicated:

sed -n '/^data_link_list/,$p' list/mon_lib_list.cif > links.cif

When we have major programs reading links.cif, this part can be deleted from mon_lib_list.cif.

The goal is to make reading of links faster (in particular, that's important when reading from a web server). The size of links.cif is only 8% of mon_lib_list.cif (312406 vs 3990585 bytes).

[keitaroyam]

There was a plan to add modifications for different protonations (for example). Would they go in this file?

[wojdyr]

If they were to go into mon_lib_list.cif, then yes.

[keitaroyam]

Then should it be something like links_and_modifications.cif or links_mods.cif?

[wojdyr]

The name can be changed. Of these two, I'd prefer the shorter one.

[wojdyr]

changed to links_and_mods.cif, as was discussed with Garib

[keitaroyam]

When can we remove links and modifications from mon_lib_list.cif? What is a plan? Until then we will need to maintain two files.

[wojdyr]

when major programs can read links_and_mods.cif

[GaribMurshudov]

I can try to change refmac not to read mon_lib_list.cif. To do this we must make sure that refmacat fully replaces refmac5. I think it can be done after ccp4 9 release.

[keitaroyam]

But if refmacat fully replaces refmac5, no change would be needed in refmac5?

[GaribMurshudov]

İt is true. However, I do not know what happens if I remove this particular file reading. In any case, we want servalcat to replace refmac5, we might need to speed up this.

[keitaroyam]

Added a test for this file