Revision history for HackaMol 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