Opened 8 years ago

Closed 4 years ago

#1021 closed enhancement (fixed)

Compute auxiliary secondary structure info

Reported by: Eric Pettersen Owned by: Eric Pettersen
Priority: moderate Milestone: 1.4
Component: Core Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen)

on demand

Change History (5)

comment:1 by Eric Pettersen, 7 years ago

Description: modified (diff)
Priority: blocker → moderate

comment:2 by Greg Couch, 5 years ago

Milestone: → 1.3

Possible intermediate state would be for AtomicStructure::compute_secondary_structure() to optionally save the report in a Python data structure. Then the mmCIF writer could use that information to write out correct sheet information, instead of having each strand in its own sheet.

comment:3 by Eric Pettersen, 4 years ago

Milestone: 1.3 → 1.4

comment:4 by Eric Pettersen, 4 years ago

Cc: Greg Couch added
Description: modified (diff)
Summary: First class secondary structure elements → Compute auxiliary secondary structure info

Upon sober reflection, I've decided that having Helix, Sheet, etc. classes is far more trouble than it's worth. Right now its easy for a user to combine two strands separated by straight coil into one strand by reassigning ss_types and ss_ids. As classes, that would be a nightmare. And what about coordinate sets? Ouch.

Instead, have a dssp-like routine that computes the auxiliary secondary structure info on request, for the infrequent cases where it is needed.

comment:5 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: assigned → closed

This actually got implemented 9 months ago (ss_info arg to AtomicStructure::compute_secondary_structure())

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