Gmx-mmpbsa

Fixes
`gmx_MMPBSA`
- Allow index group name for group selection (157)

`gmx_MMPBSA_ana`
- gmx_MMPBSA_ana does not open at the end of the calculation (158)

Additions
`gmx_MMPBSA`
- Support for all files generated with CHARMM-GUI for Amber force fields (ff14SB and ff19SB)
- enabled NonLinear PB solver in `sander` (63)
- enabled all `pbsa` options in `sander` (64)
- enabled all `3D-RISM` variables (68)
- Improve IE output data (91)
- New C2 Entropy method added (73)
- Option to create an [input file](input_file.mdgeneration-of-input-files-with-gmx_mmpbsa) (`--create_input`)
- New format file (h5) to store all the data result (`Experimental`)
- New method to get the `decomp` data without the API classes
- Report energy differences for every term in alanine scanning
- Automatic calculation of charge for `com` , `rec`, and `lig` groups in QM/MMGBSA
- Improve residue selection in QM/MMGBSA
- New modified PB Radii sets for GAFF (140) and CHARMM (141) force fields
- conda package (55)
- Checking structure consistency method (44)
`gmx_MMPBSA_ana`
- Chart properties selector. The following properties can be changed:
- Font size:
- Axes (Ticks, Labels)
- Title, Subtitle and legend
- Color bar
- Pallete, color or theme:
- Line plot
- Bar plot
- Heatmap plot
- PyMOL visualization
- Rotation, padding and number of ticks
- Figure size, dpi and format
- Chart type specific properties
- Highlight or split components
- Frame range and interval selection
- Chart data can be visualized in table format and copy directly to excel
- Summary table for complex, receptor, ligand, etc.
- Now the outputs files can be visualized as document in their own sub-window
- New button to launch all the graphics and functions associated to item
- Highlighted Bar and Heatmap plot
- User setting file per-system
- Frames to Time conversion
Documentation
- Code block names and annotations

Fixes
`gmx_MMPBSA`
- Protonated residues (42)
- Inconsistent energy between tleap and ParmEd topology (147)
- Error with alphanumeric residue numbers (134)
- `print_res` selection scheme
- Error when `startframe=0` (66)
- `parmchk2` always uses GAFF as force field (45)
- IE is calculated for PB and GB independently (72)
- Alanine scanning with CHARMM ff (88)
- MT approach (78)
- `get_num_terms` function run forever if TDC term not found. (98)
- Check if the groups defined for receptor and ligand are the same (86)
- Add SD and SEM calculated with [propagation formula](https://en.wikipedia.org/wiki/Propagation_of_uncertainty#Example_formulae) (105)
- Structure consistency (80, 79)
- gmx_MMPBSA launches an error when there is an `OverflowError` on IE calculation (57)
- Improve `gmx_MMPBSA.log` file (108)
- Inconsistency with multiple trajectories (120)
- Alanine Scanning ERROR on THR to ALA mutation (139)
`gmx_MMPBSA_ana`
- Tick labels in line plots (65)
- Improved PyMOL 3D visualization (85)
- Improved the system options in the init dialog
`gmx_MMPBSA_test`
- Error when `-f` option it not defined (46)

Changes
`gmx_MMPBSA`
- Recalculate the PB energy with --rewrite-output changing the value of `inp` (144)
- Removed [deprecated variables](compatibility.mdvariables)
- Input file format. Although it kept the structure of the previous version, the current one is more GROMACS alike
- `EnergyVector` changed to `ndarray` subclass
- Regen expression for `mutant_res`
- Now the COM, REC and LIG trajectories must have the same length when using MT approach
- Improve verbose logging in gmx_MMPBSA.log file (108)
- Removed `*.gro` file support in `-cs` , `-rs` and `-ls` flags
- Added `trjconv` to avoid the PBC in the tpr file (43)
`gmx_MMPBSA_ana`
- New set of chart buttons
- IE plot
`gmx_MMPBSA_test`
- Improved parallel processing
- Change command-line
Documentation
- Updated packages dependency
- Input and Output file pages

Additions
- Added two new tutorials [Protein_ligand_LPH_atoms_CHARMMff](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Protein_ligand_LPH_atoms_CHARMMff/) and [QM/MMGBSA calculations](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/QM_MMGBSA/)
- Now the program reports the `p-value` associated with the correlation coefficient when performing the correlation analysis
- Google Analytics is used as a third-party tracking service to improve documentation. Check our [Private Policy](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/private_policy/) for more details

Fixes
- Minor fixes in the documentation
- Improved parsing of `forcefields` variable
- Fixed bug when `gmx_MMPBSA_ana` runs without arguments
- Fixed compatibility with older files (`< v1.4.0`)
- Fixed error when `debug_printlevel > 1` in tleap command

Changes
- Now the command line used is added to the log file
- The `gmx_MMPBSA data` folder is exported directly rather than copied in the `$AMBERHOME` data folder.

Additions
- Added Covid-19 and other complex systems as examples in the documentation
- Added Q&A section to the documentation
- Implemented an adaptive `intdiel`(GB)/`indi`(PB) for Alanine scanning (Check the [input file](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/input_file/#alanine_scanning-namelist-variables) section)

Fixes
- Fixed bug when `startframe = 0` (33)
- Fixed bug when blank lines exist in [molecule] section in topology file
- Fixed pipe command-line for Gromacs execution in macOS
- Fixed compatibility issues with v1.3.x
- Improved and fixed the documentation
- Improved output file information related to ΔG binding
- Improved calculation with different entropy approximations simultaneously

Changes
- Changed `protein_forcefields` and `ligand_forcefield` by `forcefields` variable in all examples
- Now QH and IE can be calculated at the same time
- `entropy` variable was separated in `qh_entropy` and `interaction_entropy`. _The `entropy` variable is deprecated
and will be removed in the next major version (v1.5.0)._
- `entropy_seg` was replaced by `ie_segment`. _The `entropy_seg` variable is deprecated and will be removed in the
next major version (v1.5.0)._

Additions
- New class `Residue` added to handle residues selection in Gromacs format with Amber index
- Verification of the presence of water molecules in receptor and ligand groups
- Gromacs timer added

Fixes
- Gromacs topology conversion
- `qm_residues` notation
- Default path in `gmx_MMPBSA_test`
- The Entropy representation in `gmx_MMPBSA_ana`
- Bug when the structure has insertion code
- Improved ΔG Binding plot representation

Changes
- Now `forcefields` variable unifies `protein_forcefield` and `ligand_forcefield`. These variables `protein_forcefield`
and `ligand_forcefield` are deprecated and will be removed in the next major version (v1.5.0).
- Improved documentation
- Examples
- Command-line
- MPI
- Examples
- Links and references
- Updated to material 7.1.0
- Dark mode
- Material "Back to Top" button
- Grammatical corrections
- Installation section
- Figures caption
- The Ambiguous name for Entropy term in output files

This release focuses almost entirely on `gmx_MMPBSA_ana` with minor issues fixed in `gmx_MMPBSA`
Additions
- New start window to select options
- Option to make correlation (Pearson and Spearman coefficients)
- Option to hide decomposition data
- Option to not compute charts with a non-significant contribution
- Option to not include terms with a non-significant contribution in bar charts
- Selection of the components to display in addition to Delta (i.e. complex, receptor, and ligand)
- Toggle the chart toolbar for a cleaner visualization
- An informative table with selected systems data
- Option to exclude any system
- Option to change:
- The system name
- The experimental Ki for correlation
- The temperature to calculate the Experimental Energy and the Interaction Entropy
- Data reader with progress bar and multiprocessing
- Multiple systems to analyze in the same session
- Correlation dock
- Multiple models at the same time
- Graphs and correlation data for each calculated energy term (ΔH, ΔH+IE, ΔH+NMODE and ΔH+QH)
- Table with the experimental energy of the systems, and the data of the selected model
- New arguments flags for gmx_MMPBSA_ana (See the [gmx_MMPBSA_ana documentation](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/))
- replaced `-p` by `-f`
- `-f` accept a folder, single info file or a list of them
- New flag `-r`. This flag allows to load all the systems inside a selected folder
- New graphical options
- A new set of graphics (heatmap)
- Per-frame when analyzing Per-residue and pair in Per-wise
- Relation matrix for Per-wise
- Interactive visualization of PDB files with per-residue energies with `PyMOL` (up to 5 instances).
- Regression plot for correlation
- Plot features
- Added Standard deviation to bar plots
- Added rolling average to line plots
- Added indicators for the selected interval and average value in IE chart
- Added crosshair cursor for better analysis on charts
- Multiprocessing application for testing (`gmx_MMPBSA_test`)
- Embed Youtube videos for `gmx_MMPBSA_ana`

Fixes
- Now `gmx_MMPBSA_ana` shows stability results as expected
- Errors in the documentation
- MPI

Changes
- Converted analyzer.py into a sub-module for more flexibility, organization and portability
- Residues notation for mutation: CHAIN:RESNAME:RESNUMBER:ICODE instead of Amber residue index
- Improve the selection method in decomposition calculation
- Replaced variable `entropy_temp` (deprecated) by `temperature`
- IE in API
- Color Palette used in graphs
- Use seaborn and matplotlib for charts
- Use Pandas Dataframe and numpy to store data
- Changed the data structure to implement dynamic selection of frames in future versions
- Improved data export: now any item can be exported as CSV file
- Improved the documentation
- Improve examples documentation
- Added changelog button at home
- Separated changelog in a new header
- Added tags to mark the history of changes of variables and functionalities