Computational Representation of Biological Molecules Michel F. Sanner The Scripps Research Institute La Jolla, California The Molecular Graphics Laboratory CRBM Sept. 9-10, 2003 UCSD, San Diego, Ca TSRI Protein-Ligand Complex Assemblies Protein-Protein Molecular Surfaces AutoDock SurfDock MSMS HARMONY TSRI Tangible Models TSRI Augmented Reality TSRI The challengeVisualizationDockingMethods Folding ProteinEngineering SequenceAnalysis Modeling MM - MD Ab Initio Methods ElectrostaticsCalculations MolecularSurfaces Etc... TSRI Python to the rescue High level language as a scripting environment MolecularSurfacesMolecularSurfaces MoleculesMolecules DataBaseDataBase ElectrostaticsElectrostatics DelaunayDelaunay HomologyHomology CSGCSG 3DViewer3DViewer MM-MDMM-MD NewMethodNewMethod YourMethodYourMethod TSRI Software components MolKit: read/write/represent/manipulate and query molecules DejaVu: General purpose 3D geometry viewer ViewerFramework: Visualization application template Mslib, PyBabel, PyMead, SFF,... (Sophie I. Coon, Michel F. Sanner and Art J. Olson, Re-usable components for structural bioinformatic, (9th Python Conference 2001) TSRI from MolKit.pdbParser import PdbParser parser = PdbParser(1crn.pdb) mols = parser.parse( ) from MolKit.pdbParser import PdbParser parser = PdbParser(1crn.pdb) mols = parser.parse( ) PDB Mol2 PQR... Parser MoleculeSet PDB parserMOL2 parser Molecule Chain Residue Atom Molecule Chain Residue Atom Molecule Residue Atom Molecule Atom MolKit TSRI MolKit Numeric MolKit TreeNode.parent.children... TreeNode adopt(child) TreeNodeSet(ListSet) [TreeNode1, TreeNode2, ].__getattr__(self, name).top.elementType TreeNode [ TreeNode1.name, TreeNode2.name, ] returns.name TSRI TreeNode, TreeNodeSet TreeNodeSet: Boolean operation uniq( ) split( ) sort( ) NodesFromName( ) findChildrenOfType( ) findParentOfType( ) TreeNode: adopt( ) / remove( ) full_name( ) NodeFromName( ) split( ) / merge( ) getParentOfType( ) findType( ) compare( ) assignUniqIndex( ) isAbove( ) / isBelow( ) TSRI TreeNode and TreeNodeSet specialization TSRI Examples >>> from MolKit import Read >>> molecules = Read(./1crn.pdb) # Read returns a ProteinSet >>> mol = molecules[0] >>> print mol.chains.residues.name >>> print mol.chains.residues.atoms[20:85].full_name() >>> from MolKit.molecule import Atom >>> allAtoms = mol. findType(Atom) >>> set1 = allAtoms.get(lambda x: x.temperatureFactor >20) >>> allResidues = allAtoms.parent.uniq() >>> import Numeric >>> for r in allResidues:... coords = r.atoms.coords... r.geomCenter = Numeric.sum(coords) / len(coords) MolKit TSRI MolKit Features Pdb, PQR, mol2 parsers Support for Sets Selection mechanism using Python syntax Secondary Structure Amber parameters assignment Atomic radii assignment (regexp) TSRI MolKit Critic: BAD No well defined API Hierarchy of proteins Danger of stamping over attributes Slow for large structures Hierarchical structure not used much Requires a Python interpreter Severe Mild TSRI MolKit Critic: GOOD Clever PDB parser Lightweight and Platform independent Dynamic (on the fly creation of attributes) Introspection Support for Set and Set operations Python syntax-based selection Re-usable component (has been combined with many Python packages developed independently) TSRI DEMO