Compares proteins by there isosufaces and clusters them.
Call:
./CompareIsosurfaces.R _parameterfile_The parameterfile contains following parameters:
| Name | Parameter | Description |
|---|---|---|
| PathToData | .../ProteinComp/Input/ | Path to the protein data, every protein in it own folder that contain the .dx file |
| PathToOutput | .../ProteinComp/Output/ | Path to the Outputfolder |
| n | 100 | How many points will be selected in every round |
| m | 500 | How often the calculation will be done |
| PathToCPProgram | .../ComparingProteins/LowerBounds/FirstLowerBound/main | Path of to the Cpp program on your machine |
| PathToRProgram | .../ComparingProteins/EMDandClustering/AllLowerB_EMD_Clust.R | Path of to the R program on your machine |
Comments can be added by a '#' in the parameterfile. The parametername and parameter have to be seperated by a '='
└─── ProteinComp
│ └─── Input
│ │ └─── Prot01
│ │ │ Prot01.dx
│ │ │ ...
│ │ └─── Prot02
│ │ │ Prot02.dx
│ │ │ ...
│ │ ....
│ │ └─── Protk
│ └─── Output
│ │ └─── Prot01_negative_n
│ │ │ Prot01_Prot01_negative_n
│ │ │ Prot01_Prot02_negative_n
│ │ │ ...
│ │ │ Prot01_Protk_negative_n
│ │ └─── Prot01_positive_n
│ │ │ Prot01_Prot01_positive_n
│ │ │ Prot01_Prot02_positive_n
│ │ │ ...
│ │ │ Prot01_Protk_positive_n
│ │ └─── Prot02_negative_n
│ │ │ Prot02_Prot02_negative_n
│ │ │ Prot02_Prot03_negative_n
│ │ │ ...
│ │ │ Prot02_Protk_negative_n
│ │ ....
│ │ └─── Protk_positive_n
│ │ │ Protk_Protk_positive_n
| | ListofEMD_negative_n
| | ListofEMD_positive_n
| | Dendrogram_UPGMA_Max
| | Dendrogram_UPGMA_Mean
| | Dendrogram_UPGMA_Neg
| | Dendrogram_UPGMA_Pos
There are three lower bounds of the Gromov-Wasserstein distance in this repositories. The first lower bound has a time complexity of O(n^2) the second O(n^4) and the third O(n^5). It is recommended to use the first lower bound, since it is much fuster than the other two. For more details see "Quantitative comparison of protein isosurfaces with approximated Gromov-Wasserstein-distance" from Felix Berens or "Gromov-Wasserstein Distances and the Metric Approach to Object Matching" from Facundo Mémoli.
For the third lower bound a linear program has to be solved. This is done with the library lpsolve_5.5, which can be downloaded here https://sourceforge.net/projects/lpsolve/files/lpsolve/5.5.2.0/lp_solve_5.5.2.0_source.tar.gz/download
Just add the forgoten protein structure or delete the unneeded structure and rerun the program. The program autmatical recognises, which structures were already compared.
I am only interested in the lower bound values of two specific protein structures (for example: Prot01 and Prot02), what can I do?
For this you already need the files containing the coordinates on the isosurfaces (here those four: Prot01_pot_neg.pts , Prot02_pot_neg.pts , Prot01_pot_pos.pts , Prot_02_pot_pos.pts). Then you can start the lower bounds with the following call from the terminal: ./main inputfile1 inputfile2 n m So for example if you are in the folder ProeinComp and want to compare Prot01 and Prot02 with 100 points each 500 times, you have to call those two lines:
./[pathToComparingProteins]/ComparingProteins/LowerBounds/FirstLowerBound/main Input/Prot01/Prot01_pot_neg.pts Input/Prot02/Prot02_pot_neg.pts./[pathToComparingProteins]/ComparingProteins/LowerBounds/FirstLowerBound/main Input/Prot01/Prot01_pot_pos.pts Input/Prot02/Prot02_pot_pos.pts