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Manual Analysis 3

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Multilinear maps, tensors, alternating tensors, wedge product.

Teaching - 2017 - Analysis 3

Manifolds Basic concept of a manifold, definitions of tangent space. Fields and forms on manifolds, orientation. Integration Stokes' theorem on manifolds. Euclidean measure for submanifolds. Grad, curl, and div, the Laplacian. The classical theorems in vector analysis by Green, Gauss and Stokes. Cauchy's integral theorem and formula. Other optional topcs. Got a question about accessibility, content or structure of this website?

Skip to main content. Math Analysis III. Background and Goals:.

Module Overview

The residue ids are also returned because a typical use case is to look at CA distances before and after an alignment. Using the offset keyword one can also add a constant offset to the resids which facilitates comparison with PDB numbering. B A , — AtomGroup with the same number of atoms. Note that one can actually supply numpy arrays of the same length as the atom group so that an individual offset is added to each resid. Return sub group of group that is within distance of both A and B. A AtomGroup —.

Indicative Assessment

B AtomGroup — A and B are the groups of atoms between which atoms in group are searched for. The function works is more efficient if group is bigger than either A or B.

1. Analyze your current state

AtomGroup of atoms that fulfill the criterion. Distance analysis — MDAnalysis. See also MDAnalysis. Navigation 1.

Overview over MDAnalysis 2. The topology system 3.


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Selection commands 4. Analysis modules 4. Building blocks for Analysis 4.

Distances and contacts 4. Coordinate fitting and alignment — MDAnalysis.

PSYC | Research Methods and Data Analysis III | University of Southampton

Native contacts analysis — MDAnalysis. Calculating root mean square quantities — MDAnalysis. Calculating path similarity — MDAnalysis. Hydrogen bonding 4.

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Membranes and membrane proteins 4. Nucleic acids 4. Polymers 4. Structure 4.


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Volumetric analysis 4. Dimensionality Reduction 4.