Recent Releases of porphystruct
porphystruct - 2.0.2
Support Platinacorrole
Full Changelog: https://github.com/JensKrumsieck/PorphyStruct/compare/v.2.0.1...v2.0.2
- C#
Published by JensKrumsieck 11 months ago
porphystruct - 2.0.1
For Downloads scroll down! Download "PorphyStruct.exe"
New Features:
- Can now apply transformations to select starting pyrrole and CW / CCW direction by Inverting the displacement diagram in Y and X Axis and shifting the starting pyrrole.
- Selecting Atoms in either 3D View or deflection diagram will now highlight which atom is selected in a pink color.
Changes:
- flipped saddling mode to match J.A. shelnutts definition of saddling (-> signs are flipped in simulations, compared with earlier versions)
- "Invert" ist now called "InvertY" to clarify. The simulation now updates on Inversion.
- Addded InvertX function
- Added Shift Button which basically rotates the ring if applicable (Cycle not Corrole or Corrphycene)
Full Changelog: https://github.com/JensKrumsieck/PorphyStruct/compare/v2.0.0...v.2.0.1
For previewing the mode references use the PorphyStruct Calculator
CLI (optional)
CLI Files (not required if you not plan to use the CLI!!!): The ZIP File contains Builds for Windows, Mac OS and Linux x64 Systems as well as Linux ARM Delete uneccessary files after unpacking.
Usage:
PorphyStruct.CLI.exe analyze "PATH/TO/YOUR_FILE.mol2" -x
Leave out .exe for non windows versions, -x is for "use extended basis"
- C#
Published by JensKrumsieck over 2 years ago
porphystruct - 2.0.0
For Downloads scroll down! Download "PorphyStruct.exe"
Version 2
Initially i wanted the next version to be an 1.1.x Release, but things went different.
The whole code for loading molecules changed to be more performant with less memory allocation - which is beneficial for larger files such as biomolecules. Also the molecule-class is now derived from undirected graphs which enables graph theory for molecules, which led to a new automated detection algorithm using subgraph isomorphism. The detection is not only faster than before but also able to detect the macrocyclic type. That also means that files with mixed macrocyclic types such as f-Block Metallocorrole-Phthalocyanine sandwiches can be analyzed more easily. Also PorphyStruct is now able to detect both corrole units in beta-fused dimers which was not possible before. PorphyStruct now also comes with a CLI (command line interface) which makes it easy to use in automated pipelines and on any system.
There are also a lot of bugfixes like the wrong corrphycene reference in Issue #85. All references are now forced to follow the same direction for the modes of both sets. so if e.g. doming1 is positive and doming2 negative they are eliminating each others strength!
The Webversion - as sharing most of the code - will also benefit from all changes (right now!) So you can already test the improvements here: https://app.porphystruct.org/
What's Changed
- CLI by @JensKrumsieck in https://github.com/JensKrumsieck/PorphyStruct/pull/72
- 2.0.x Update by @JensKrumsieck in https://github.com/JensKrumsieck/PorphyStruct/pull/78
- Bump Microsoft.NET.Test.Sdk from 17.4.0 to 17.4.1 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/90
Full Changelog: https://github.com/JensKrumsieck/PorphyStruct/compare/v1.0.3...v2.0.0
CLI
CLI Files (not required if you not plan to use the CLI!!!): The ZIP File contains Builds for Windows, Mac OS and Linux x64 Systems as well as Linux ARM and a net6.0 dependent version ("Portable") Delete uneccessary files after unpacking.
Usage:
PorphyStruct.CLI.exe analyze "PATH/TO/YOUR_FILE.mol2" -x
Leave out .exe for non windows versions, -x is for "use extended basis"
- C#
Published by JensKrumsieck almost 3 years ago
porphystruct - 2.0.0 Beta 1
For Downloads scroll down! Download "PorphyStruct.exe"
Version 2 - First Beta!
Initially i wanted the next version to be an 1.1.x Release, but things went different.
The whole code for loading molecules changed to be more performant with less memory allocation - which is beneficial for larger files such as biomolecules. Also the molecule-class is now derived from undirected graphs which enables graph theory for molecules, which led to a new automated detection algorithm using subgraph isomorphism. The detection is not only faster than before but also able to detect the macrocyclic type. That also means that files with mixed macrocyclic types such as f-Block Metallocorrole-Phthalocyanine sandwiches can be analyzed more easily. Also PorphyStruct is now able to detect both corrole units in beta-fused dimers which was not possible before. PorphyStruct now also comes with a CLI (command line interface) which makes it easy to use in automated pipelines and on any system.
There are also a lot of bugfixes like the wrong corrphycene reference in Issue #85. All references are now forced to follow the same direction for the modes of both sets. so if e.g. doming1 is positive and doming2 negative they are eliminating each others strength!
The Webversion - as sharing most of the code - will also benefit from all changes (right now!) So you can already test the improvements here: https://app.porphystruct.org/
As this is a Beta Version there may be some bugs - if you find any, please report them ;)
Code Changes as a full list:
What's Changed
- CLI by @JensKrumsieck in https://github.com/JensKrumsieck/PorphyStruct/pull/72
- 2.0.x Update by @JensKrumsieck in https://github.com/JensKrumsieck/PorphyStruct/pull/78
Full Changelog: https://github.com/JensKrumsieck/PorphyStruct/compare/v1.0.3...v2.0.0-beta.1
CLI
CLI Files (not required if you not plan to use the CLI!!!): The ZIP File contains Builds for Windows, Mac OS and Linux x64 Systems as well as Linux ARM and a net6.0 dependent version ("Portable") Delete uneccessary files after unpacking.
Usage:
PorphyStruct.CLI.exe analyze "PATH/TO/YOUR_FILE.mol2" -x
Leave out .exe for non windows versions, -x is for "use extended basis"
- C#
Published by JensKrumsieck about 3 years ago
porphystruct - 1.0.3
Scroll down to Download ;) or click here
CHANGELOG:
Major Changes
- Add Webversion (Beta) -> https://app.porphystruct.org/
- Documentation available at https://porphystruct.org/docs
- Fix UI lagging by removing option
- Support for .MOL Files
Minor Changes
- Remove Autodownloader for new Versions, open GitHub instead
- Minor styling improvements
- Update Targetframework to .NET6
- Update Dependencies
- Code Improvements
What's Changed
- Bump HelixToolkit.Core.Wpf from 2.17.0 to 2.20.0 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/38
- Bump Microsoft.NET.Test.Sdk from 16.10.0 to 17.0.0 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/39
- Bump MSTest.TestFramework from 2.2.5 to 2.2.7 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/35
- Bump OxyPlot.Core from 2.1.0-Preview1 to 2.1.0 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/37
- Bump MSTest.TestAdapter from 2.2.5 to 2.2.7 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/36
- Bump ChemSharp.Molecules from 1.0.10 to 1.0.15 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/46
- Bump coverlet.collector from 3.1.0 to 3.1.1 by @dependabot in https://github.com/JensKrumsieck/PorphyStruct/pull/48
- Web by @JensKrumsieck in https://github.com/JensKrumsieck/PorphyStruct/pull/49
- Create LICENSE by @JensKrumsieck in https://github.com/JensKrumsieck/PorphyStruct/pull/55
Full Changelog: https://github.com/JensKrumsieck/PorphyStruct/compare/v1.0.2...v1.0.3
- C#
Published by JensKrumsieck almost 4 years ago
porphystruct - 1.0.2
August 2021 Release
Download
Scroll down to "Assets" and select "PorphyStruct.exe" or click here
CHANGELOG
- Choose between Extended and Minimal Basis by clicking Analyze in the App Bar
- Added Automated Update Checks
- Can be disabled in preferences
- uses GitHub API to download official .exe file from here!
- also works with no or slow internet connection (auto disabling)
- Improve Settings Layout
- Update Dependencies
- Fix Error with Mercury generated pdb files (ChemSharp 1.0.10)
- C#
Published by JensKrumsieck over 4 years ago
porphystruct - 1.0.1
DOWNLOAD
Scroll down to "Assets" and select "PorphyStruct.exe" or click here
CHANGELOG
- PDB Support
- Enhancements for Cofactor detection in Proteins (PDB only)
Speed Improvements
Update Dependencies
(Clip shortened by 15 seconds)
1hv4 from pdb (Hemoglobin)
July 2021 Release
Monthly Release cycle (around 10th, if there are any updates)
- C#
Published by JensKrumsieck over 4 years ago
porphystruct - 1.0.0
DOWNLOAD
Scroll down to "Assets" and select "PorphyStruct.exe" or click here
CHANGELOG
- Fix #26 (Settings file is now exposed to
%appdata%\porphystruct\settings.json - Fixed Linewidth for Ticks
- Add: Flip X Axis
- Add new Data in "Info" Popup
- Update dependencies
- C#
Published by JensKrumsieck over 4 years ago
porphystruct - 1.0.0 Release Candidate 2
DOWNLOAD
Click "Assets" below Changelog or click here!
Changelog
Major Changes
- Performance (ac1471387285a0b9ffa5df6c23d5299099cfba46), ca 10x speedup in naming method ( measured in non-optimized builds, optimized may be even faster)
- Update ChemSharp for latest Performance fixes
Minor Changes
- Update other Dependencies
- Update Readme
Outlook
- Referencematrix is built everytime "Analyze" is clicked - but reference structures may not update very often. Caching may gives further speedups
- With the new speedups a web interface may be possible
- C#
Published by JensKrumsieck almost 5 years ago
porphystruct - 1.0.0 Release Candidate 1
DOWNLOAD: Click on Assets and select "PorphyStruct.exe"! or click here https://github.com/JensKrumsieck/PorphyStruct/releases/download/v1.0.0-rc1/PorphyStruct.exe
Changelog Major: * Added extended Basis sets for alle macrocycles * Added cavity size to computed properties * Added Mode Calculator * Added Export: Analysis bar charts * Added Export: Viewport renders * :warning: [bugfix - critical] changed porphyrin simulation to not use C20 two times ;) * [bugfix] fixed UI block during detection phase * [bugfix] batch processing ignored last item in list * [bugfix] batch processing no longer reports failed items if count i 0
Minor: * Updated dependencies * Styling improvements * Refactored some asynchronous code * added depenabot alerts to repository
Note: * tried web implementation with blazor --> Slow analysis. Will be revisited after official release.
-- jk
- C#
Published by JensKrumsieck almost 5 years ago
porphystruct - 1.0.0 Beta 11
New Features: * Statistics * Batch Processing * Molecule Isolation "Wizard"
Minor Changes * Add more Properties * Improve Color Selection for Comparisons * Change CI to GitHub Actions
Roadmap: * Web Version based on Webassembly (for my Website) * Preparing Manuscript
- C#
Published by JensKrumsieck almost 5 years ago
porphystruct - 1.0.0 Beta 10
New Features: * New GUI * New Simulation-Method (Matrix-QR) * Simulation result now fits Shelnutt values! * Automatic Simulations (making a Webinterface possible in near future) * New Improved Macrocycle Detection * Uses my new Libraries: ChemSharp, TinyMVVM, ThemeCommons * Better Exports due to the new OxyPlot SkiaSharp Renderer.
Roadmap: * Web Version based on Webassembly (for my Website) * Statistics * Preparing Manuscript
- C#
Published by JensKrumsieck about 5 years ago
porphystruct - 1.0.0 Beta 9
Several Optimisations and Code Improvements
x64 only exe-file attached
- C#
Published by JensKrumsieck about 5 years ago
porphystruct - 1.0.0 Beta 8
Changelog - Updated UI - Use of MVVM - Performance Boost - Endless Comparisons are now possible instead of only 2 (Using ColorPalettes) - New PropertyHandlers - Drop XML in favor of JSON
- Added partly German Translation
- New Settings
- Adjusted Default Settings
- SVG render improved
- Minor Bugfixes
- C#
Published by JensKrumsieck almost 6 years ago
porphystruct - 1.0.0 Beta 7
Now runs on -NET Core 3.1 Added Keyboard Shortcuts
- C#
Published by JensKrumsieck about 6 years ago
porphystruct - 1.0.0 Beta 6
This PreRelease includes several Refactorings causing better performance and maintainability. Also Featured: A new Detection algorithm based on depth-first-search methods.
- C#
Published by JensKrumsieck about 6 years ago