# Changelog
All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]

## [0.2.0] - 2021-06-04
### Added
- None 

### Changed
- Use pickle5 to save data

### Removed
- None

## [0.1.2] - 2020-10-29
### Added
- add OrderedDict() function to keep input ordered independent to Python version 

### Changed
- Add check of length to order and rdf function to replace none with 0 value

### Removed
- None

## [0.1.1] - 2020-09-14
### Added
- add atom2group funtion in order to keep fixed the molecules per domain id 

### Changed
- None

### Removed
- None

## [0.1.0] - 2020-07-31
### Added
- None

### Changed
- In atomid_data function a extra check was added for residue type in order to avoid create dictionaries with empty values in keys

### Removed
- None

## [0.0.9] - 2020-07-30
### Added
- calculate rdf profile for all combination of molecules
- create ndx for order parameter calculation
- calculate order parameter properties
- debug save function

### Changed
- text that is converted to unique hashed id, is now independent of group name and filename
- combine index and gmx ndx function

### Removed
- None

## [0.0.8] - 2020-07-17
### Added
- memory optimizations
- Add check of molecule existance in .ndx file
- Merge data into unified dataset ready to be used

### Changed
- Update I/O to functions

### Removed
- Remove log message option

## [0.0.7] - 2020-07-03
### Added
- unified properties output
- Add 'if file exist' universal fuction
- debug main.py

### Changed
- None

### Removed
- None

## [0.0.6] - 2020-07-02
### Added
- Initial support for gmx commands
- Add gmx density profile function

### Changed
- more dynamic I/O of gmx_ndx

### Removed
- None

## [0.0.5] - 2020-05-21
### Added
- Add progress bar per function
- Save preprocessing arrays to pickles and read them if exist for speed up whole process
- new function to calculate surface per subdomain (different input) 
- print groups to gmx_ndx format (one ndx for each subdomain) [Future use as to create new .trr with gmx trjconv]

### Changed
- debug atomid_data function
- more dynamic I/O of whole code

### Removed
- printing .png of surface due to matplotlib unknown error

## [0.0.4] - 2020-05-19
### Added
- code for print data in json and pickle format

### Changed
- debug decomposition code

### Removed
- None

## [0.0.3] - 2020-05-14
### Added
- code for assign coordinates to subdomain
- code for creating vectors for each tail of lipid in subdomain
- code for creating surface for heads of lipids in subdomain
- code for calculating the angle between surface and vectors for every step, sudomain and resid
- clean main.py

### Changed
- change output in def atomid_data() to include resid
- adjust function that use def atomid_data() output accordigly

### Removed
- None

## [0.0.2] - 2020-05-11
### Added
- code for domain decomposition function
- code for identify desired atoms
- code for assigning desired atoms to subdomains

### Changed
- debug trr frames export

### Removed
- None

## [0.0.1] - 2020-04-27
### Added
- add gitignore
- read all or specific part of .trr files
- calculate surface from points
- calculate angle between two vectors(3D) or lines(2D)
- plot points and surface
- read .gro for determine residue type and atom type 

### Changed
- None

### Removed
- None