diff --git a/README.md b/README.md index 0a327584..610321db 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,15 @@ Mean of Circular Quantities (MCQ) is a dissimilarity measure useful in comparison of 3D protein and/or RNA structures. It calculates an average difference between corresponding torsion angle values (rotations around bonds). More information can be found in: > Zok, T., Popenda, M., & Szachniuk, M. (2014). MCQ4Structures to compute similarity of molecule structures. Central European Journal of Operations Research, 22(3), 457–473. https://doi.org/10.1007/s10100-013-0296-5 +## Installation + +```sh +git clone https://github.com/RNA-Puzzles/mcq-parent +cd mcq-parent +git submodule update --init +mvn install +``` + ## Contents This project consists of a few subprojets: @@ -21,4 +30,4 @@ This project consists of a few subprojets: - Use `pl.poznan.put.clustering.hierarchical.Clusterer` to construct dendrograms from a distance matrix (with `COMPLETE`, `SINGLE` or `AVERAGE` linkage option) - Use `pl.poznan.put.clustering.partitional.KMedoids` to perform partitional clustering based on distance matrix -- Use `pl.poznan.put.clustering.partitional.KScanner#parallelScan` to find optimum number of clusters with respect to silhouette score \ No newline at end of file +- Use `pl.poznan.put.clustering.partitional.KScanner#parallelScan` to find optimum number of clusters with respect to silhouette score diff --git a/bio-commons b/bio-commons index 9d92c0ad..d601b4f4 160000 --- a/bio-commons +++ b/bio-commons @@ -1 +1 @@ -Subproject commit 9d92c0adadaead3b6535a59772afa88fce085023 +Subproject commit d601b4f47f56f13db8e4931b003e9a121377dc1f diff --git a/mcq-cli b/mcq-cli index c4b701b8..1f771adf 160000 --- a/mcq-cli +++ b/mcq-cli @@ -1 +1 @@ -Subproject commit c4b701b8af90e837662209f7c894e8a5604f48d7 +Subproject commit 1f771adfeab04995ac9c8298411cf557a2f60e9d diff --git a/mcq-clustering b/mcq-clustering index 48314627..73a592de 160000 --- a/mcq-clustering +++ b/mcq-clustering @@ -1 +1 @@ -Subproject commit 483146274502a9cc6c1fe00b7b6eaccc2cd55a73 +Subproject commit 73a592de52b5961f4944aeb42e0dd19cddeb8420 diff --git a/mcq-core b/mcq-core index 1715948a..9d82d724 160000 --- a/mcq-core +++ b/mcq-core @@ -1 +1 @@ -Subproject commit 1715948ac4aae372b7ed015531483c343848bcf7 +Subproject commit 9d82d724587f87a0b69aefa894ed50dc38e41e4a diff --git a/mcq-gui b/mcq-gui index 86a844f4..e39fefe0 160000 --- a/mcq-gui +++ b/mcq-gui @@ -1 +1 @@ -Subproject commit 86a844f41923f17775e9ac8e1aaad232d074b980 +Subproject commit e39fefe05b435e179a65863edbd2c730392aa425 diff --git a/pom.xml b/pom.xml index a851d33d..48374b26 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ pl.poznan.put mcq-parent - 1.5.1 + 1.6 pom @@ -21,7 +21,6 @@ 1.10 5.2.0 - 2.9.8 UTF-8 1.7.25 @@ -34,12 +33,6 @@ 1.2.3 - - com.fasterxml.jackson.core - jackson-databind - ${jackson.version} - - commons-cli commons-cli @@ -133,6 +126,10 @@ log4j-slf4j-impl org.apache.logging.log4j + + jackson-databind + com.fasterxml.jackson.core + @@ -193,7 +190,7 @@ pl.poznan.put BioCommons - 2.2.1 + 2.3.2 @@ -205,7 +202,7 @@ pl.poznan.put TzokCommons - 1.5.1 + 1.6 diff --git a/tzok-commons b/tzok-commons index bb3ab889..e1e26918 160000 --- a/tzok-commons +++ b/tzok-commons @@ -1 +1 @@ -Subproject commit bb3ab889d34b87f66a6d131d97f0742a3276e206 +Subproject commit e1e269189772cdba984500981b336cf198a978c9