Add gemmi for Meeko; fix numpy conflict with PyMOL

Dockerfile

@@ -31,26 +31,24 @@ RUN conda config --add channels bioconda && \
 # Install mamba for faster package installation
 RUN conda install -n base -c conda-forge mamba -y
 
-# Install AMBER tools, PyMOL, AutoDock Vina, Open Babel, and RDKit
+# Install AMBER tools, PyMOL, AutoDock Vina, Open Babel, RDKit, and gemmi (for Meeko)
 RUN mamba install -y python=3.11 \
     conda-forge::ambertools conda-forge::pymol-open-source \
-    conda-forge::vina conda-forge::openbabel conda-forge::rdkit
+    conda-forge::vina conda-forge::openbabel conda-forge::rdkit conda-forge::gemmi
 
 # Clean up conda/mamba cache to reduce image size
 RUN conda clean -afy
 
-# Install Python packages via pip (meeko has no conda package; others for version pinning)
+# Install Python packages via pip (only packages not provided by conda or that need pip)
+# Note: numpy, pandas, matplotlib are already installed by conda; don't override to avoid conflicts
 RUN pip install --no-cache-dir \
     flask==2.3.3 \
     flask-cors==4.0.0 \
-    biopython==1.81 \
-    numpy==1.24.3 \
-    pandas==2.0.3 \
-    matplotlib==3.7.2 \
-    seaborn==0.12.2 \
-    mdanalysis==2.5.0 \
+    biopython \
+    seaborn \
+    mdanalysis \
     gunicorn==21.2.0 \
-    requests==2.31.0 \
+    requests \
     meeko>=0.7.0
 
 # Set working directory