Feature - animated 2Ds showing transition between 2D structures from PDB files

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -11,11 +11,11 @@ repos:
     -   id: check-json
     -   id: mixed-line-ending
 -   repo: https://github.com/ambv/black
-    rev: 22.10.0
+    rev: 24.10.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/pylint
-    rev: v2.15.6
+    rev: v3.3.2
     hooks:
     -   id: pylint
         args:
@@ -26,11 +26,11 @@ repos:
                 docs/conf.py
             )$
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     -   id: isort
 - repo: https://github.com/MarcoGorelli/auto-walrus
-  rev: 'v0.2.2'
+  rev: '0.3.4'
   hooks:
     - id: auto-walrus
       name: Auto-apply the walrus operator :=

Dockerfile

@@ -1,4 +1,4 @@
-ARG BASE_IMAGE_VERSION=v2.0
+ARG BASE_IMAGE_VERSION=latest
 
 FROM rnacentral/r2dt-base:${BASE_IMAGE_VERSION}
 

base_image/Dockerfile

@@ -8,8 +8,8 @@ ENV tRNAscan_VER=2.0.11 \
     Ribovore_COMMIT=5df943c6f2866d7979bb13c948ca9d8531076898 \
     BioEasel_VER=0.11 \
     INFERNAL_VER=1.1.5 \
-    RNArtist_VER=0.4.6
-
+    RNArtist_VER=0.4.6 \
+    RNAView_COMMIT=2f74eccc47c86acdf0627004e6243454978cd4c1
 
 FROM build AS rscape
 
@@ -109,6 +109,17 @@ FROM build AS rnartist
 RUN \
     wget -q -O rnartist.jar https://github.com/fjossinet/RNArtistCore/releases/download/${RNArtist_VER}-SNAPSHOT/rnartistcore-${RNArtist_VER}-SNAPSHOT-jar-with-dependencies.jar
 
+FROM build AS rnaview
+
+# Install RNAview
+RUN \
+    git clone https://github.com/rcsb/RNAView && \
+    cd RNAView && \
+    git checkout ${RNAView_COMMIT} && \
+    make && \
+    mkdir -p /install/rnaview && \
+    cp -r ./* /install/rnaview/
+
 FROM debian:bookworm-slim AS final-build
 
 ENV \
@@ -165,11 +176,22 @@ ENV \
     PERL5LIB="$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR":"$PERL5LIB" \
     PATH="$RIBOSCRIPTSDIR":"$RRNASENSORDIR":"$PATH"
 
+
+
 ENV \
     PATH="$RIBOSCRIPTSDIR":"$RRNASENSORDIR":"$PATH" \
     PATH="$RNA/traveler/bin:$RIBODIR:$RIBOEASELDIR:$RIBOINFERNALDIR:/rna/rscape/bin:/rna/jiffy-infernal-hmmer-scripts:/rna/r2dt:/rna/RNAstructure/exe:$PATH" \
     PERL5LIB="$RIBOSCRIPTSDIR:$RIBOSEQUIPDIR:$VECPLUSDIR:$BIOEASELDIR:$RIBODIR:$EPNOPTDIR:$EPNOFILEDIR:$EPNTESTDIR:$PERL5LIB:/usr/lib/tRNAscan-SE"
 
+
+
+    ENV \
+    RNAVIEW="${RNA}/rnaview" \
+    PATH="${RNA}/rnaview/bin:${PATH}"
+
+
+COPY --from=rnaview /install/ ${RNA}/
+
 COPY --from=rscape /rna/rscape/ ${RNA}/rscape
 
 COPY --from=trnascan-se /install/ /usr

docs/usage.md

@@ -243,3 +243,39 @@ python3 utils/animate.py \
 :::{note}
 Note that the two input SVG files must have the same number of nucleotides.
 :::
+
+### Animating RNA secondary structures from PDB files
+
+R2DT can be used to generate secondary structure diagrams directly from PDB files. Additionally R2DT can generate animated SVG file of the transition between two structures between two 3D structures from PDB files.
+
+Generetion of a diagram from PDB file:
+
+```bash
+python3 utils/rnaview.py \
+    examples/PZ1_Bujnicki_1.pdb
+```
+`PZ1_Bujnicki_1.colored.svg` will be genreated.
+
+:::{note}
+Note - in cases that there are multiple interactions detected for one nucleotide, all of them will be omitted in the diagram.
+:::
+
+Animated transition between two structures from PDB:
+
+```bash
+python3 utils/animate3d.py \
+    examples/PZ1_solution_0.pdb \
+    examples/PZ1_Bujnicki_1.pdb
+```
+
+Performing animation on a reference PDB file, and a set of PDBs. User needs to specify the reference PDB file, and a directory with query PDB files:
+
+```bash
+python3 utils/animate3d.py -b \
+    examples/PZ1_solution_0.pdb \
+    examples/animate_bulk
+```
+
+:::{note}
+Note - structures in the PDB files should be of the same length [nt].
+:::

requirements.txt

@@ -14,3 +14,4 @@ scikit-image==0.21.0
 Jinja2==3.1.2
 numpy==1.26.4
 tqdm==4.66.5
+biopython==1.84