FragIt v1.9.1 Release Notes

• Documentation on installation is now up to date and
  is fixed (Issue #38)
  -- thanks to Anthony Nash for pointing
  out the obsolete instructions.

  See the README file for updated installation
  instructions.

• Github actions now cover both the new installation
  approach with conda and pip as well as the old
  school approach with compilation of OpenBabel

FragIt v1.9.0 Release Notes

This is a much-needed major revision to remove bugs
and squash problems related to the old-age of FragIt

Updates since v1.8.0

• FragIt can now read fragment charges from an
  external file. This is specified in the input
  configuration files in

  [fragmentation]
  chargemodel = read test.dat

  where the MMFF94 keyword is replaced with
  read . Each line in the supplied
  file gives two values. The first value is the
  fragment index and the second value is the
  fragment charge. The following example shows
  that the charge of the first fragment is -1
  and the fifth fragment has charge +1. Fragments
  not listed are assumed to be neutral.

    1 -1
    5  1

• Includes some changes necessary for openbabel
  cooperation with especially version 3.

• Fixed a few errors in the jmol script and template.

• Switch to GitHub actions for build system testing.

• Updated the GAMESS to HMO script to python3

Developer Changes

• Made substantial changes to align FragIt with how
  python packages should be organized

• code updates and improvements all around

FragIt v1.8.0 Release Notes

This major update brings several quality of life
improvements in FragIt.

• Now full (automated) testing of multiple python
  versions (2.7, 3.5 and 3.6 as we speak) coupled
  with multiple (master and 2.4.1 release) versions
  of openbabel

• includes preliminary fixes for the upcoming openbabel
  2.5 release (no idea when it is due) specifically
  regarding OBElementsTable and implicit valence info
  which was relocated in the openbabel API.

• It is now possible to show the charges of fragments
  in PyMol. The command

  ColorFragments charge

  in the PyMol terminal will color the fragments with
  red and blue for negative and positive charges of the
  fragments, respectively.

• FragIt now dumps it's input file in standard output
  so one can actually see the options being used. This
  is mainly to be inline with other programs and to
  make sure users understand what options were set.

• FragIt now correctly warns people using explicit
  fragmentation points in combination with metal atoms
  that atoms are shifted around. This procedure has
  not been completely automated.

• A lot of internal API documentation stuff happened.

FragIt v1.6.0 Release Notes

This major update brings several changes to default keywords

and to the command line interface for FragIt

Updates since v1.5.1

  * Removed --make-config option from FragIt commandline
    tool. Instead, a fragit-conf tool is supplied which
    allows for the generation of different types of
    configuration files for many types of fragmentation jobs.

  * Added fragit-conf tool to generate configuration files
    for FragIt.
    See fragit-conf -h for details.

  * Added multiple default configurations for FragIt.
    FragIt (through fragit-conf) now supports:
    - fragment molecular orbital (FMO) specific fragmentation
      patterns.
    - polarizable embedding (PE) specific fragmentation
      patterns. This is specifically made for use through
      the polarizable embedding assistant script (PEAS).
    The default configuration settings is still FMO.
    See fragit-conf -h.

  * Default values were changed for some parameters for the
    fragmentation group. The new values are:
    - maxfragsize = 100
    - useatomnames = False  - ONLY FMO.

  * The setup script is now more self-contained.

FragIt v1.7.2 Release Notes

This is a bug-fix and minor improvements release.

Updates since v1.7.1

• Mixing metals/ions with explicit bond cutting
  can (and is still) problematic. For now, print
  a warning with possible fixes so that the user
  not only sees a "bond not found" error. (#26)
  -- Thanks to Morten S Nørby
  for reporting this issue.

FragIt v1.7.1 Release Notes

This is a bug-fix and minor improvements release.

Updates since v1.7.0

• Fixes a python3 issue with the pymol scripts and
  template system.

• PyMol scripts are now named .py instead of .pymol
  to signify that they are different from the .pml
  scripts. PyMol 1.8.6 enforces this rule.

• the calculation of fragment labels has changed to
  a more efficient algorithm. Per default, fragment
  labels are hidden.

In addition, some behind the scene updates were made
to the template system

FragIt v1.7.0 Release Notes

This major update brings several changes to default keywords
and to the command line interface for FragIt.

Updates since v1.6.1

• FragIt is now compatible with python 3.5 after
  minor modifications to the source code mostly
  regarding imports and print statements.

• Travis-CI builds are failing for python 3.5 for
  some compilation/install of openbabel problem
  so testing is done manually for now. This is
  also why it is compatible but not entirely
  supported for now.

• Templates are now located appropriately in a
  'share' directory in the installation directory

• The PyMol template received some colorscheme
  upgrades for multilayer and FMO/FD (FDD) runs.

• The GAMESS-FMO writer now supports the hybrid
  orbital projection (HOP) scheme for fragmentation
  as well as the AFO scheme that has always been
  present. HOP orbitals are located in the
  'hmo' folder in the share directory. Limited to
  support of only SP3 C-C bonds but that should
  cover 99 % of all current use cases.

  HOP is disabled per default. You can enable it
  by specifying

  [fmo]
  dohop = True
  

  in the configuration file.

• The GAMESS-FMO writer now has improved
  support for multilayer calculations as well.
  Through a new section [qm] in the configuration
  it is possible to specify the basis set for an
  FMO calculation.

  In the case of multilayer runs FragIt
  supports the multilayer notation from FMO
  as well so one specifies basis sets on a
  per layer basis separated by colons:

  [qm]
  basis = STO-3G:3-21G
  

  In multilayer calculations the appropriate
  basis set will be added to the $DATA group
  and leave out the $BASIS group.

  For regular FMO runs just specifying basis
  sets as

  [qm]
  basis = 6-31G(d)
  

  will suffice.

• The GAMESS-FMO writer now has support to
  generate FMO/EFP input files. The feature
  is enabled by

  [fmo]
  efpwaters = 1
  

  in the configuration file. This will, if
  no multilayer options are specified, gen-
  erate an FMO input file with all water
  molecules demoted from FMO fragments to
  EFP fragments.

  This new option also supports a slightly
  more involved use case scenario where
  all water molecules some distance R from
  a central molecule, such as a ligand in
  a protein, are demoted to EFP water. The
  options are

  [fmo]
  efpwaters = 1
  
  [output]
  centralfragment = 1
  boundaries = 3.0
  

  which will convert all water molecules not
  within a distance R = 3.0 angstrom from
  fragment 1 to EFP water.

  Please note that this will disable the
  multilayer calculation as that option
  seems a little exuberant.

FragIt v1.6.1 Release Notes

This is a bug-fix and minor improvements release.

Updates since v1.6.0

• Fixes a default value in the base configuration
  for FMO input files such that atom names are
  ignored

FragIt v1.5.1 Release Notes

This is a bug-fix and minor improvements release.

Updates since v1.5.0

• Fixed issue with FMO writer which dumped errornous
  keyword in FMO input file even if no bonds were
  broken. (#15) -- Thanks to Anders S. Christensen
  for reporting this issue.

FragIt Release v1.5.0

FragIt v1.5.0 Release Notes

This major update brings changes to defaults in keywords and
a major overhaul to the information printed.

The changes to the defaults is mostly to make sure that users
of the API get something sensible back per default without having
to make too many changes before they get started.

Updates since v1.4.4

• Default values were changed for some parameters for the QM/MM
  group. The new values are:

  • includehbonddonors = False
  • includehbondacceptors = False
  • includecovalent = False

• Default values were changed for a single parameter for the OUTPUT
  group. The new value is:

  • useatomnames = True

• A new option to enable printout (especially handy when using fragit
  as an API from other programs) in the OUTPUT group:

  • verbose = False

  when set to true, FragIt will print information on its doings.

• FragIt can now correctly inform users if it fails because OpenBabel
  is missing. Previously this was not the case. Issue 13.