Revision history for HackaMol

0.047     2017-12-28 19:50:18-07:00 America/Denver
  * added mol_disulfide_bonds($mol,$fudge) to HackaMol.pm
  * added read_pdbfile_mol to HackaMol.pm for reading pdb header and model ids
  * added attr 'info' to HM::Role::AtomGroupRole 
  * added attr 'model_ids' to HM::Molecule 
  * pdb models are again ignored if the number of atoms changes
  * readline_func hook added to main HackaMol class to allow modified parse of PDBs  

0.046     2017-10-10 20:36:46-06:00 America/Denver
  * add selection hash attribute to manage selections (todo, use it or lose it!).
  * fix model read bug where number of atoms grows between models (see the unusual 2d6b)
  * add x_flag to aa321 default 1, replaces unknown 3-letter code with X
  * protein backbone/sidechain selection fix for the bb carbonyl oxygen
  * sidechains selection -> sidechain (watch out for OXT)
  * changed fudge from 0.45 to 0.15 for find_disulfide_bonds   
  * HackaMol.pm consumes NERFRole
     
 
0.045     2017-09-23 19:40:06-06:00 America/Denver
  * move selection role from Molecule to AtomGroup for chaining selections
  * add pymol ranges to selections, e.g. resid 1-5+7 and chain E-I

0.044     2017-08-27 13:41:30-06:00 America/Denver
  * added support for resnames with 
  * added superpose_rt method to HackaMol class, grabbed from Bio::PDB::Structure
  * added rmsd method to HackaMol class 
  * added center to AtomGroupRole, method for geometric center

0.043     2017-06-24 14:05:20-07:00 America/Vancouver
  * minor fix on FileFetchRole return

0.042     2017-06-24 13:18:49-07:00 America/Vancouver
  * reorganize tests
  * avoid the FileFetchRole get tests for now... HTTP::Tiny->can_ssl but still fails 

0.041     2017-06-24 12:45:52-07:00 America/Vancouver
  * switch to HTTP::Tiny for FileFetchRole
  * skip https tests unless HTTP::Tiny->can_ssl

0.040     2017-06-18 21:38:23-06:00 America/Denver
  * added the group_by_atom_attrs method to HackaMol.pm
  * added SelectionRole to core, consumed by HackaMol::Molecule

0.039     2017-02-02 20:05:46-07:00 America/Denver
  * cleaning up tests and reducing dependencies 
  * todo: shrink api by moving some heafty Roles into pluggable roles, streamline tests

0.038     2016-04-06 13:38:48-04:00 America/Indiana/Indianapolis
  * added a print for dirty atoms if hush_read < 0
  * added qcat_print to AtomGroupRole for concatenated printing of all coordinates
  * added a little padding to the PdbReadRole.
  * added sasa attribute to PdbRole.

0.037     2016-03-03 15:50:27-05:00 America/Indiana/Indianapolis
  * removed some array traits from API for AtomGroupRole and Groups trait in molecule (splice, shuffle)
  * the HackaMol::Molecule push_groups() method now adds atoms that are not in the molecule already. 

0.036     2016-02-25 21:26:20-05:00 America/Indiana/Indianapolis
  * added read_string_atoms and read_string_mol... for reading molecules from in memory strings!!!

0.035     2016-02-08 14:14:20-05:00 America/Indiana/Indianapolis
  * minor fix to remove the Data::Structure::Util dependency (Thank you Slaven Rezic!!)

0.034     2016-02-08 10:43:34-05:00 America/Indiana/Indianapolis
  * storage is pulled for now 
 
0.033     2016-02-05 11:28:45-05:00 America/Indiana/Indianapolis
  * added pdb_rename to group 

0.032     2015-06-17 13:51:01-04:00 America/Indiana/Indianapolis
  * fixed bug in molecule->charge
  * add method group_rot to HackaMol.pm 

0.031     2015-06-08 13:04:53-04:00 America/Indiana/Indianapolis
  * improve the printing of pdbs for atom names of 1-3 characters

0.030     2015-06-05 13:58:12-04:00 America/Indiana/Indianapolis
  * another another quick fix to get tests to pass

0.029     2015-06-05 10:05:29-04:00 America/Indiana/Indianapolis
  * another quick fix to get tests to pass

0.028     2015-06-03 09:59:15-04:00 America/Indiana/Indianapolis
  * added is_fixed attribute to AtomGroupRole.  
  * test coverage has fallen to 85%

0.027     2015-06-02 16:38:50-04:00 America/Indiana/Indianapolis
  * added a new simple YAML molecular format #16 on github. 

0.026     2015-06-02 11:11:45-04:00 America/Indiana/Indianapolis
  * allow charge method to set the current charge for molecules
  * charge method now returns 0 if no charges set for atoms or molecules
  * see #15 on github

0.025     2015-05-26 20:55:25-04:00 America/Indiana/Indianapolis
  * minor fixes to testing filenames
  * charge defaults to 0

0.024     2015-05-25 11:56:05-04:00 America/Indiana/Indianapolis
  * minor fixes to testing filenames

0.023     2015-05-22 23:07:08-04:00 America/Indiana/Indianapolis
  * HackaMol::Molecule atomgroups -> groups
  * a molecule can now be built from a list of groups. e.g.  HackaMol::Molecule->new(groups=>[@groups])
  
0.022     2015-05-22 15:03:09-04:00 America/Indiana/Indianapolis
  * added a bunch of array traits to the AtomGroupRole
  * fixed Zmatrix Reader bug

0.021     2015-05-18 22:15:52-04:00 America/Indiana/Indianapolis
  * Mixing in Moo::Roles where possible to allow speedy extensions.
    see how it works with mixed Moose/Moo
  * Better warnings from the Zmatrix reader--- still no tests and bad POD
  * Fix links in POD


0.020     2015-05-15 14:37:36-04:00 America/Indiana/Indianapolis
  * Fix bug in Zmatrix reader

0.019     2015-05-14 23:22:44-04:00 America/Indiana/Indianapolis
  * Minor fix and added the method pdbid_mol 

0.018     2015-05-14 14:23:22-04:00 America/Indiana/Indianapolis
  * simplify atoms_bin in AtomGroupRole
  * Rework POD for HackaMol.pm
  * support for Z-matrix reading

0.017     2015-02-27 09:15:16-05:00 America/Indiana/Indianapolis

0.016     2015-02-26 21:41:39-05:00 America/Indiana/Indianapolis
  * dist.ini dependencies again

0.015     2015-02-26 15:25:55-05:00 America/Indiana/Indianapolis
  * Fix dist.ini dependencies for testing lib versions
  * minor test improvements
  
0.014     2015-02-17 22:33:21-05:00 America/Indiana/Indianapolis
  * added FileFetchRole that uses LWP to get and getstore files from pdb.org
  * notebooks

0.013     2015-02-01 20:13:47-05:00 America/New_York
  * fixed t/HackaMol-DirRole.t for windows installs

0.012     2015-01-19 15:47:59-05:00 America/Indiana/Indianapolis
    * fixed the github link for metacpan.

0.011     2015-01-19 15:26:19-05:00 America/Indiana/Indianapolis
    * fixed version issue using dzil.

0.01      2015-01-12 16:31:52-05:00 America/Indiana/Indianapolis
    * first release: 0.01

0.00_22   2015-01-02 11:04:34-05:00 America/Indiana/Indianapolis
    * reorganize examples.  Still need more
    * reformat TODO list to follow P5 conventions

0.00_21   2014-07-25 13:29:06-04:00 America/Indiana/Indianapolis
    * adjusted defaults on PdbRole attributes 
    * energy_func no longer return 0 without calculation for default force constant params 
    * energy_func -> efunc rename

0.00_20   2014-05-27 20:41:40EDT-0400 America/New_York
    * added fix_serial method to AtomGroupRole 
    * find_disulfide_bonds generalized to work with nonprotein sulfurs 
    * GSSG examples added

0.00_19   2014-05-04 20:48:54EDT-0400 America/New_York
    * examples are reorganized, still not organized enough #TODO
    * PathRole files are now 'rw'.  The 'rw' is hard to resist 

0.00_18   2014-04-23 14:15:49EDT-0400 America/New_York
    * merged FileRole and ScratchRole into PathRole

0.00_17   2014-04-23 10:46:53EDT-0400 America/New_York
    * switched FileRole and ScratchRole over to MooseX::Types::Path::Tiny

0.00_16   2014-04-22 14:27:46EDT-0400 America/New_York
    * added FileRole for managing files. Loaded into HackaMol.pm builder
    * added ExeRole  for managing executables.  Loaded into HackaMol.pm builder. Limited functionality
      can/should be tested with scripts that run exe, capture output, etc.  use Capture::Tiny 
  
0.00_15   2014-04-20 20:54:36EDT-0400 America/New_York
    * minor update test for scratchrole

0.00_14   2014-04-17 21:07:40EDT-0400 America/New_York
    * added ScratchRole for managing directories. Available in HackaMol builder

0.00_13   2014-04-15 22:09:31EDT-0400 America/New_York
    * added hush_read to MolReadRole    
    * added MooseX::StrictConstructor to classes
  
0.00_12   2014-04-07 10:48:37EDT-0400 America/New_York
    * added aa321 to PdbRole; gens 1-letter aa code from resname

0.00_11   2014-04-02 16:46:03EDT-0400 America/New_York
    * minor fix for pdbqt reading: A -> C
  
0.00_10   2014-04-02 15:27:08EDT-0400 America/New_York
    * AtomGroupRole adjustments:
      - added print_pdb_ts and print_xyz_ts for printing many configs
      - improved tmax method 

0.00_09   2014-04-01 17:46:14EDT-0400 America/New_York
    * PDB reading will atom->is_dirty if the element(s) unknown. Carp warning
    * added minimal pdbqt reading (i.e. no branch info pulled)

0.00_08   2014-02-20 14:53:19 America/New_York
    * improve PDB reading and writing 
    * for PDB guess element from atom name 
 
0.00_07   2013-11-19 22:57:36 America/New_York
    * Reduced size of test directory
    * Improved reading of PDBs with multiple (sometimes erroneous) models

0.00_06   2013-11-18 21:28:05 America/New_York
    * Added find_disulfides to HackaMol.pm
    * Added read_file_mol to HackaMol.pm
    * Added read_file_append_mol to HackaMol.pm
    * Adjusted reading and writing of PDB files 

0.00_05   2013-10-02 16:19:31 America/New_York
    * Adjusted builders in HackaMol.pm added pdb_print for groups
  
0.00_04   2013-09-20 06:56:56 America/New_York
    * Fixing one test that needs recent MVR to work    

0.00_03   2013-09-19 21:51:03 America/New_York
    * Fixing POD and tests further 

0.00_02   2013-09-19 16:53:36 America/New_York
    * Fixing POD and tests based on how things look and cpantesters

0.00_01   2013-09-18 23:46:53 America/New_York
    * First Devel release