Revision history for HackaMol
0.053 2022-02-22 17:53:59-07:00 America/Denver
0.051 2019-01-06 21:09:12-07:00 America/Denver
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added centered_vector method to AtomGroupRole, see test
0.050 2018-09-13 20:10:40-06:00 America/Denver
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improve cif info parsing (TODO: convert regression test in examples to proper tests)
0.049 2018-09-11 21:13:39-06:00 America/Denver
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add pdbx/mmcif parsing, parses info like connections
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add example cif/parse_dump.pl
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added HackaMol::Roles::RcsbRole for ftping files (testing needed)
0.048 2018-08-27 20:22:45-06:00 America/Denver
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remove uc( chain ) issue #50
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add string_pdb method e.g. print $mol->string_pdb
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add string_xyz method e.g. print $mol->string_xyz
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add calc_bfps to group and bfp to atom normalized bfactors
0.047 2017-12-28 19:50:18-07:00 America/Denver
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added mol_disulfide_bonds($mol,$fudge) to HackaMol.pm
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added read_pdbfile_mol to HackaMol.pm for reading pdb header and model ids
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added attr 'info' to HM::Role::AtomGroupRole
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added attr 'model_ids' to HM::Molecule
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pdb models are again ignored if the number of atoms changes
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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
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add selection hash attribute to manage selections (todo, use it or lose it!).
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fix model read bug where number of atoms grows between models (see the unusual 2d6b)
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add x_flag to aa321 default 1, replaces unknown 3-letter code with X
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protein backbone/sidechain selection fix for the bb carbonyl oxygen
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sidechains selection -> sidechain (watch out for OXT)
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changed fudge from 0.45 to 0.15 for find_disulfide_bonds
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HackaMol.pm consumes NERFRole
0.045 2017-09-23 19:40:06-06:00 America/Denver
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move selection role from Molecule to AtomGroup for chaining selections
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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
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added support for resnames with
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added superpose_rt method to HackaMol class, grabbed from Bio::PDB::Structure
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added rmsd method to HackaMol class
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added center to AtomGroupRole, method for geometric center
0.043 2017-06-24 14:05:20-07:00 America/Vancouver
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minor fix on FileFetchRole return
0.042 2017-06-24 13:18:49-07:00 America/Vancouver
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reorganize tests
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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
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switch to HTTP::Tiny for FileFetchRole
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skip https tests unless HTTP::Tiny->can_ssl
0.040 2017-06-18 21:38:23-06:00 America/Denver
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added the group_by_atom_attrs method to HackaMol.pm
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added SelectionRole to core, consumed by HackaMol::Molecule
0.039 2017-02-02 20:05:46-07:00 America/Denver
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cleaning up tests and reducing dependencies
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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
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added a print for dirty atoms if hush_read < 0
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added qcat_print to AtomGroupRole for concatenated printing of all coordinates
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added a little padding to the PdbReadRole.
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added sasa attribute to PdbRole.
0.037 2016-03-03 15:50:27-05:00 America/Indiana/Indianapolis
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removed some array traits from API for AtomGroupRole and Groups trait in molecule (splice, shuffle)
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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
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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
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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
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storage is pulled for now
0.033 2016-02-05 11:28:45-05:00 America/Indiana/Indianapolis
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added pdb_rename to group
0.032 2015-06-17 13:51:01-04:00 America/Indiana/Indianapolis
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fixed bug in molecule->charge
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add method group_rot to HackaMol.pm
0.031 2015-06-08 13:04:53-04:00 America/Indiana/Indianapolis
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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
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another another quick fix to get tests to pass
0.029 2015-06-05 10:05:29-04:00 America/Indiana/Indianapolis
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another quick fix to get tests to pass
0.028 2015-06-03 09:59:15-04:00 America/Indiana/Indianapolis
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added is_fixed attribute to AtomGroupRole.
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test coverage has fallen to 85%
0.027 2015-06-02 16:38:50-04:00 America/Indiana/Indianapolis
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added a new simple YAML molecular format #16 on github.
0.026 2015-06-02 11:11:45-04:00 America/Indiana/Indianapolis
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allow charge method to set the current charge for molecules
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charge method now returns 0 if no charges set for atoms or molecules
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see #15 on github
0.025 2015-05-26 20:55:25-04:00 America/Indiana/Indianapolis
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minor fixes to testing filenames
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charge defaults to 0
0.024 2015-05-25 11:56:05-04:00 America/Indiana/Indianapolis
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minor fixes to testing filenames
0.023 2015-05-22 23:07:08-04:00 America/Indiana/Indianapolis
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HackaMol::Molecule atomgroups -> groups
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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
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added a bunch of array traits to the AtomGroupRole
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fixed Zmatrix Reader bug
0.021 2015-05-18 22:15:52-04:00 America/Indiana/Indianapolis
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Mixing in Moo::Roles where possible to allow speedy extensions.
see how it works with mixed Moose/Moo
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Better warnings from the Zmatrix reader--- still no tests and bad POD
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Fix links in POD
0.020 2015-05-15 14:37:36-04:00 America/Indiana/Indianapolis
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Fix bug in Zmatrix reader
0.019 2015-05-14 23:22:44-04:00 America/Indiana/Indianapolis
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Minor fix and added the method pdbid_mol
0.018 2015-05-14 14:23:22-04:00 America/Indiana/Indianapolis
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simplify atoms_bin in AtomGroupRole
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Rework POD for HackaMol.pm
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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
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dist.ini dependencies again
0.015 2015-02-26 15:25:55-05:00 America/Indiana/Indianapolis
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Fix dist.ini dependencies for testing lib versions
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minor test improvements
0.014 2015-02-17 22:33:21-05:00 America/Indiana/Indianapolis
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added FileFetchRole that uses LWP to get and getstore files from pdb.org
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notebooks
0.013 2015-02-01 20:13:47-05:00 America/New_York
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fixed t/HackaMol-DirRole.t for windows installs
0.012 2015-01-19 15:47:59-05:00 America/Indiana/Indianapolis
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fixed the github link for metacpan.
0.011 2015-01-19 15:26:19-05:00 America/Indiana/Indianapolis
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fixed version issue using dzil.
0.01 2015-01-12 16:31:52-05:00 America/Indiana/Indianapolis
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first release: 0.01
0.00_22 2015-01-02 11:04:34-05:00 America/Indiana/Indianapolis
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reorganize examples. Still need more
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reformat TODO list to follow P5 conventions
0.00_21 2014-07-25 13:29:06-04:00 America/Indiana/Indianapolis
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adjusted defaults on PdbRole attributes
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energy_func no longer return 0 without calculation for default force constant params
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energy_func -> efunc rename
0.00_20 2014-05-27 20:41:40EDT-0400 America/New_York
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added fix_serial method to AtomGroupRole
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find_disulfide_bonds generalized to work with nonprotein sulfurs
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GSSG examples added
0.00_19 2014-05-04 20:48:54EDT-0400 America/New_York
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examples are reorganized, still not organized enough #TODO
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PathRole files are now 'rw'. The 'rw' is hard to resist
0.00_18 2014-04-23 14:15:49EDT-0400 America/New_York
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merged FileRole and ScratchRole into PathRole
0.00_17 2014-04-23 10:46:53EDT-0400 America/New_York
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switched FileRole and ScratchRole over to MooseX::Types::Path::Tiny
0.00_16 2014-04-22 14:27:46EDT-0400 America/New_York
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added FileRole for managing files. Loaded into HackaMol.pm builder
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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
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minor update test for scratchrole
0.00_14 2014-04-17 21:07:40EDT-0400 America/New_York
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added ScratchRole for managing directories. Available in HackaMol builder
0.00_13 2014-04-15 22:09:31EDT-0400 America/New_York
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added hush_read to MolReadRole
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added MooseX::StrictConstructor to classes
0.00_12 2014-04-07 10:48:37EDT-0400 America/New_York
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added aa321 to PdbRole; gens 1-letter aa code from resname
0.00_11 2014-04-02 16:46:03EDT-0400 America/New_York
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minor fix for pdbqt reading: A -> C
0.00_10 2014-04-02 15:27:08EDT-0400 America/New_York
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AtomGroupRole adjustments:
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added print_pdb_ts and print_xyz_ts for printing many configs
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improved tmax method
0.00_09 2014-04-01 17:46:14EDT-0400 America/New_York
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PDB reading will atom->is_dirty if the element(s) unknown. Carp warning
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added minimal pdbqt reading (i.e. no branch info pulled)
0.00_08 2014-02-20 14:53:19 America/New_York
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improve PDB reading and writing
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for PDB guess element from atom name
0.00_07 2013-11-19 22:57:36 America/New_York
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Reduced size of test directory
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Improved reading of PDBs with multiple (sometimes erroneous) models
0.00_06 2013-11-18 21:28:05 America/New_York
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Added find_disulfides to HackaMol.pm
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Added read_file_mol to HackaMol.pm
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Added read_file_append_mol to HackaMol.pm
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Adjusted reading and writing of PDB files
0.00_05 2013-10-02 16:19:31 America/New_York
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Adjusted builders in HackaMol.pm added pdb_print for groups
0.00_04 2013-09-20 06:56:56 America/New_York
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Fixing one test that needs recent MVR to work
0.00_03 2013-09-19 21:51:03 America/New_York
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Fixing POD and tests further
0.00_02 2013-09-19 16:53:36 America/New_York
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Fixing POD and tests based on how things look and cpantesters
0.00_01 2013-09-18 23:46:53 America/New_York
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First Devel release