20 November 2014 meeting, 2:00 - 3:30

Attendees
 Conrad, TomG, Sam, Eric, TomF, Greg, Elaine, Scooter

'''Agenda'''
 1. Updates on progress
 1. Next API?
 1. Final look at [http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/frameatom_spec2.html atomspec] document

'''Next Meeting'''
 1. Work through details of implementation plan

'''Action Items'''
 1. Conrad to try using Anaconda to build chimera2
 1. Greg to finish startup implementation

'''Results'''
 1. Updates
  * Conrad: 
   * !ToolShed API: working on implementing it, but sidetracked by build problems.  He finally has a useful build on Yosemite.
   * !AtomSpec implementation: waiting for !ToolShed completion.
  * Eric:
   * Revised UI to call new Graphics API routines
   * Waiting for !ToolShed to implement command line
   * Working on translating SEQRES records into Sequences
   * Had to implement C++ logging methods to prepare for !PyLogger implementation.
  * Greg:
   * Have command line working with aliases
   * Need to commit MMCIF changes
   * Looking at chimera2 startup and putting in stubs
  * Tom:
   * Working on the Graphics API implementation
   * Looked at WebGL implementation for some of Dyche Mullins data
 1. Next API?
  * Logging - Eric (next meeting)
  * Triggers
  * Preferences
  * Python versions of main data objects (Molecules, etc.)
  * IO Module (File type registration)
 1. !AtomSpec
  * [http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/frameatom_spec2.html atomspec] document
  * Remaining issues:
   * In many commands where the specification is the last argument (e.g. color), a blank specification means “all.”
     * Still true
   * Would spaces on either side of a cluster of symbols like “ &~ ” be collapsed?
     * yes
   * Asterisks (*) in input atom names will be translated to prime symbols ('), but translated back if coordinates are later saved to a file. Prime symbols in input atom names are not translated on input or output.
     * For PDB files (only), we will translate for * to ' but we will not try to translate back.
   * Any residue in PDB HETATM records (or the mmCIF equivalent) that does not already have a chain ID is assigned to chain het, unless the residue is named WAT or HOH, in which case it is assigned to chain water; residue numbers are unchanged. (See also the residue attribute isHet.) Residue specifications with chain IDs omitted will match residues in chains with single-character IDs but not residues in these special chains.
     * No.  Leave it as we read it.
   * Support selection name via ''sel=selection_name'' 
     * No, get rid of it
   * custom amino acid categories that have been defined with ResProp
     * No need: already supported through selection term
   * need to decide on a priority order of built-in classifications vs. target aliases vs. named selections in case of conflict, or disallow name conflicts at time of creation
     * Can't override built-in classifications
     * target aliases can either be symbolic or based on data
     * aliases can override previously defined aliases (as long as they aren't built-in)
   * Attribute names are case-sensitive; attribute values, if any, are case-sensitive if specified with ==, but not if specified with =. Attribute values containing spaces (some color names, for example) must be enclosed in double quote marks.
     * Keep single = only, but we may need to add "==" and "~" at a later time
   * Within an attribute specification, ~ can be used in place of = to indicate that the subsequent string should be treated as a regular expression.
     * See above
   * When placed before an attribute name, the caret ^ indicates that the atoms, residues, or models have not been assigned any value for the attribute. For example, :/^kdHydrophobicity designates residues (such as water or nucleic acids) that lack a Kyte-Doolittle hydrophobicity assignment. 
   * OK, keep it.

'''Discussion'''
 * Discussion came up about how to go about getting the first graphics up on Chimera2 screen. Specifically how much of the Hydra code to pull in.
 * Will Chimera2 have triggers or not?
 * Proposal for getting things built on Windows.  Proposal is to use Anaconda.