v2.0.0

Upgraded to groan_rs version 0.9

BREAKING CHANGES

• The short flag for specifying a structure file has been changed from -c to -s for consistency with Gromacs programs.
• The short flag for specifying a 'step' has consequently been changed from -s to -t.
• The keyword atomid is no longer supported, as per GSL v0.9.

New Features

• Added support for reading and writing trajectories in the gro format.
• Added support for reading and writing pqr structure files.

Bug Fixes

• The --whole flag now works for water molecules with SETTLE bonds.
• Regex operators can now be used inside regular expression blocks.

v1.4.0

• Upgraded to groan_rs version 0.8.1.
• TPR files can be now used without trajectories.
• Different reference groups can be now provided for each centering dimension using the options --xref, --yref, and --zref.
• If trajectory file is provided, the input file is now allowed to have undefined/unsupported/non-orthogonal simulation box as long as the individual frames of the trajectory file have a valid simulation box.

v1.3.0

• Upgraded to groan_rs version 0.7.0.
• Introduced support for TPR files as structure input. TPR files must currently be used with trajectory files.
• Reworked trajectory concatenation, enabling the use of the --step option.
• Added --whole option to keep molecules whole in centered trajectories (requires a TPR file as an input structure).

v1.2.0

• Updated to groan_rs v0.6.1 => more groan selection language keywords are supported.
• Centering can now be performed using the center of mass as a reference instead of the center of geometry.
• Centering of multiple trajectories with defined ending time is now a bit more efficient.
• When the start time is set and gcenter is jumping forward through the trajectory, the program no longer appears frozen but informs the user about what is happening.
• When autodetecting protein atoms, gcenter now prints the number of atoms detected for quick sanity check by the user.
• gcenter now returns a proper error when a pdb file with undefined simulation box is provided as a structure file.
• gcenter now internally uses ProgressPrinter from the groan_rs library to inform the user about the progress of the printing.

v1.1.0

• Updated to groan_rs v0.4.1 which allows the use of regular expressions when selecting reference atoms.
• Starting and ending time of the centering can be now specified using the -b and -e flags.
• Multiple frame stepping is now more efficient.
• Multiple input trajectories can be provided and these will be joined into one output file.

v1.0.4

• groan_rs library version 0.3.3 is now required which fixes several bugs associated with using the @water and @ions macros.

v1.0.3

• Updated to groan_rs v0.3.1
• Fixed bug which would cause gcenter to fail if a group named Reference was included in the input ndx file.
• Added more tests.
• Fixed link to GSL in readme, modified help messages, changed some errors to look like clap errors.

v1.0.2

Updated the help comments.

v1.0.1

merged