Optional Dependencies Guide

cd lobster
make install-pymol

# Add homebrew-science tap
brew install brewsci/bio/pymol

# Verify installation
pymol -c -Q
which pymol

# Install dependencies
brew install glew glm freetype libpng python@3.12

# Build from source (advanced)
git clone https://github.com/schrodinger/pymol-open-source.git
cd pymol-open-source
python setup.py build install

sudo apt-get update
sudo apt-get install pymol

# Verify
which pymol
pymol --version

# If you use conda/mamba environments
conda install -c conda-forge pymol-open-source

# Or with mamba (faster)
mamba install -c conda-forge pymol-open-source

# Install dependencies
sudo apt-get install build-essential python3-dev \
    libglew-dev libpng-dev libfreetype6-dev \
    libxml2-dev libmsgpack-dev python3-pyqt5.qtopengl

# Clone and build
git clone https://github.com/schrodinger/pymol-open-source.git
cd pymol-open-source
python setup.py build install --prefix=$HOME/.local

# Enable EPEL repository (if needed)
sudo dnf install epel-release

# Install PyMOL
sudo dnf install pymol

# Verify
pymol --version

# Install Miniconda if not already installed
# Download from: https://docs.conda.io/en/latest/miniconda.html

# Create environment with PyMOL
conda create -n pymol-env python=3.12
conda activate pymol-env
conda install -c conda-forge pymol-open-source

# Test command-line mode
pymol -c -Q -d "fetch 1AKE; quit"

# Check version
pymol --version

# Test from Lobster
lobster chat
🦞 You: /status
# Should show: "PyMOL: Available (version X.X.X)"

# Start Lobster
lobster chat

# Fetch and visualize protein structure
🦞 You: "Fetch protein structure 1AKE"
🦞 You: "Visualize 1AKE with cartoon representation"

# Link to omics data
🦞 You: "Show expression levels of ADK gene on 1AKE structure"

# Advanced styling
🦞 You: "Highlight residues 50-100 on 1AKE structure"
🦞 You: "Color 1AKE by conservation score"

# Check if installed
which pymol
dpkg -l | grep pymol  # Ubuntu/Debian
rpm -qa | grep pymol  # Fedora/RHEL

# Add to PATH (if installed but not found)
export PATH=$PATH:$HOME/.local/bin
echo 'export PATH=$PATH:$HOME/.local/bin' >> ~/.bashrc

# Reinstall
sudo apt-get install --reinstall pymol

# Test command-line mode (no GUI)
pymol -c -Q

# On remote servers, use headless mode
export DISPLAY=:0
Xvfb :0 -screen 0 1024x768x24 &

# Activate Lobster virtual environment
source .venv/bin/activate

# Install Docling
pip install docling

# With all optional features
pip install "docling[all]"

# With specific features
pip install "docling[table]"  # Table extraction
pip install "docling[ocr]"    # OCR support

# Test import
python -c "from docling.document_converter import DocumentConverter; print('✅ Docling installed')"

# Check version
python -c "import docling; print(docling.__version__)"

# Test in Lobster
lobster chat
🦞 You: /status
# Should show: "Docling: Available (version X.X.X)"

lobster chat

# Extract methods from publication
🦞 You: "Extract methods from PMID:38448586"

# With Docling: Returns detailed Methods section, parameters, tables
# Without Docling: Returns basic text extraction

# Read full publication
🦞 You: "Read full text of PMID:35042229"

# Extract from local PDF
🦞 You: "Extract methods from paper.pdf in my workspace"

# Ensure in correct environment
source .venv/bin/activate

# Reinstall
pip uninstall docling
pip install --no-cache-dir "docling[all]"

# Check dependencies
pip list | grep docling

# Via pip
pip install 'lobster-ai[vector-search]'

# As part of full install (includes all extras)
pip install 'lobster-ai[full]'

# Via lobster init (interactive prompt)
lobster init
# → Prompts: "Semantic Search (Optional)" → Choose 1 to install

# Via lobster init (non-interactive)
lobster init --install-vector-search --anthropic-key sk-...

# Via uv tool
uv tool install 'lobster-ai[vector-search,anthropic]'

# Test imports
python -c "import chromadb; import sentence_transformers; print('Semantic Search available')"

# Check in Lobster
lobster status
# Should show: "Optional Capabilities: ✓ Semantic Search"

lobster chat

# Disease matching (metadata_assistant)
You: "Match these disease terms to MONDO ontology: glioblastoma, lung adenocarcinoma, T2D"

# Tissue standardization (metadata_assistant)
You: "Standardize my tissue annotations to UBERON terms"

# Cell type matching (annotation_expert)
You: "What cell types match 'CD8+ T cells' in Cell Ontology?"

# Check network connectivity
python -c "from sentence_transformers import SentenceTransformer; SentenceTransformer('cambridgeltl/SapBERT-from-PubMedBERT-fulltext')"

# If behind a proxy, set HuggingFace cache directory
export HF_HOME=/path/with/space/.cache/huggingface

# Install Xcode tools (if not already installed)
xcode-select --install

# Optional: Homebrew for easier package management
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install HDF5 (optional, for larger datasets)
brew install hdf5

sudo apt-get update
sudo apt-get install -y \
    build-essential \
    python3.12-dev \
    libhdf5-dev \
    libxml2-dev \
    libxslt1-dev \
    libffi-dev \
    libssl-dev \
    libblas-dev \
    liblapack-dev

sudo dnf install -y \
    gcc gcc-c++ make \
    python3.12-devel \
    hdf5-devel \
    libxml2-devel \
    libxslt-devel \
    openssl-devel \
    libffi-devel \
    blas-devel \
    lapack-devel

# Run pre-installation check
python check-system.py

# Check from within Lobster
lobster chat
🦞 You: /status

# Detailed system information
🦞 You: /dashboard

# Command line test
pymol -c -Q -d "fetch 1AKE; quit"

# Test in Lobster
lobster chat
🦞 You: "Test PyMOL by fetching structure 1AKE"

# Python test
python -c "from docling.document_converter import DocumentConverter; print('✅ OK')"

# Test in Lobster
lobster chat
🦞 You: "Test Docling by extracting methods from a sample publication"

# Check installed packages
dpkg -l | grep -E 'libhdf5|libblas|liblapack|libxml2'  # Ubuntu/Debian
rpm -qa | grep -E 'hdf5|blas|lapack|libxml2'          # Fedora/RHEL

# Verify pkg-config can find them
pkg-config --modversion hdf5
pkg-config --libs libxml-2.0

#!/usr/bin/env python3
"""Test optional dependencies"""

import sys

def check_pymol():
    try:
        import pymol
        print("✅ PyMOL: Available")
        return True
    except ImportError:
        print("⚠️  PyMOL: Not installed")
        return False

def check_docling():
    try:
        from docling.document_converter import DocumentConverter
        import docling
        print(f"✅ Docling: Available (version {docling.__version__})")
        return True
    except ImportError:
        print("⚠️  Docling: Not installed")
        return False

def check_vector_search():
    try:
        import chromadb
        import sentence_transformers
        print(f"✅ Semantic Search: Available (chromadb {chromadb.__version__})")
        return True
    except ImportError:
        print("⚠️  Semantic Search: Not installed")
        print("    Install: pip install 'lobster-ai[vector-search]'")
        return False

def check_system_libs():
    try:
        import h5py
        import lxml
        print("✅ System libraries: Available")
        return True
    except ImportError as e:
        print(f"⚠️  System libraries: Missing ({e.name})")
        return False

if __name__ == "__main__":
    print("Checking optional dependencies...\n")

    pymol_ok = check_pymol()
    docling_ok = check_docling()
    vector_ok = check_vector_search()
    libs_ok = check_system_libs()

    print("\n" + "="*50)
    if pymol_ok and docling_ok and vector_ok and libs_ok:
        print("✅ All optional dependencies available")
        sys.exit(0)
    else:
        print("⚠️  Some optional dependencies missing")
        print("Lobster will work with reduced functionality")
        sys.exit(0)