Recent Releases of ttclust
ttclust - TTClust 4.10.3
Include small bugs fix and code to remove/check warnings.
- Python
Published by tubiana over 3 years ago
ttclust - Small bug on the dendrogram graph fixed
The new version of matplotlib causes a bug with the dendrogram graph. It is now fixed
- Python
Published by tubiana over 4 years ago
ttclust - New RMSD Calculation
MDTraj's RMSD function realigns the protein which is incompatible with the -sa argument.
The RMSD is now calculated by a homemade implementation to combine with Numba for faster calculation (but still a little slower than MDTraj).
- Python
Published by tubiana over 5 years ago
ttclust - 4.7.4
Two new arguments added:
- axis to force "Frame" label in the barplot axis (use -axis frame)
- limitmat to decrease the trajectory size limit to generate the distance matrix. It is now 100000000 but if the distance matrix is too long to generate, you can just decrease this limit with -limitmat 10000
- Python
Published by tubiana almost 6 years ago
ttclust - TTClust 4.7.3
The version 4.7.3 contains several bugfixes.
- Python
Published by tubiana almost 6 years ago
ttclust - TTClust 4.7.0
2 new functionalities: - multiple trajectories reading (trajectories will be concatenated). To read multiple trajectories, just add them after the "-f" argument (like "-f traj1.xtc traj2.xtc" or "-f traj*.xtc) - striding (read every *th frames) with the "-s" argument ("-s 10" to read every 10th frames)
- Python
Published by tubiana about 6 years ago
ttclust - TTClust 4.6.9
bug fixe in saving the representative frame
- Python
Published by tubiana almost 7 years ago
ttclust - GUI Removed
The GUI is now removed. If you want to use the simple GUI, please install it with pip install ttclustGUI.
wxPython may cause issues on Mac & linux without X server.
- Python
Published by tubiana over 7 years ago
ttclust - TTClust 4.6.4
Two bugs fixed
- empty linear output for linear barplot
- MAC ONLY : custom "which" command to replace shutil.which (not implemented before Python 3.3).
- Python
Published by tubiana over 7 years ago
ttclust - TTClust 4.6.3
Bug fixed in logfile RMSD table.
- Python
Published by tubiana over 7 years ago
ttclust - TTClust 4.6.2
[version for zenodo DOI] - TTclust GUI is now in 1.0 - Improvments in MAC os compatibility - Adding time in barplot graph - Adding transparency in barplot & distance matrix graphs. - minor bugs fixed.
- Python
Published by tubiana almost 8 years ago
ttclust - TTclust 4.6.2
[OLD release, but same as new v4.6.2 which was published for zenodo DOI@ - TTclust GUI is now in 1.0 - Improvments in MAC os compatibility - Adding time in barplot graph - Adding transparency in barplot & distance matrix graphs. - minor bugs fixed.
- Python
Published by tubiana almost 8 years ago
ttclust - Automatic clustering (BETA) and User Interface
New TTclust udpate! Automatic clustering and Graphical User Interface.
TTclust Version 4.5 :
A new automatic clustering method was implemented based on kmeans clustering method and the Elbow method to find the optimal number of clusters. Use with Caution : to my point of view, it does not cluster enough. I will improve this automatic methode laters. To use it, just specify auto to the -ng argument.
TTclust-GUI Version 0.9 :
A GUI was implemented thanks to the GOOEY package. more information on
README.md soon (with examples case).
- Python
Published by tubiana over 8 years ago
ttclust - New graph + RNA/DNA selection
DNA and RNA selection keywords added! You can use now theses keywords : dna; rna; backbonena; base; baserna; base_dna. See README for precision.
A new graph is created (distance matrix graph, based on the RMSD matrix)
- Python
Published by tubiana almost 9 years ago
ttclust - V4.2.1
Improve DNA/RNA trajectory compatibility
Sometimes, with some trajectory (eg. traj with RNA/DNA) if you want to clusterize the DNA/RNA and align to the protein backbone, it fails because MDTRAJ didn't recognize DNA/RNA backbone.
Now the alignement is made before the extraction of the trajectory.If you don't want protein alignement, use "-sr none"
- Python
Published by tubiana about 9 years ago
ttclust - Version 4.2
README.md : - Replace USAGE examples with examples file from example folder - Replace examples graphics output.
ttclust.py:
- Now if you specify the -st argument, the subtrajectory will be saved.
- Argcomplete will be loaded only on linux (useless on MAC & Windows)
- Cleaning of ArgParse() function
- Python
Published by tubiana about 9 years ago
ttclust - v4.0.1
- New graph produced : Vertical barplot which represent the number of members of each clusters (the color correspond to the cluster color).
- Now Dendrogram node are colored with the right cluster color
- several bug fixes (one major bug in 4.0)
- changes in examples files and README
- Python
Published by tubiana about 9 years ago