X2spinach.m

Reads SpinXML files and forms Spinach data structures. The file is parsed into an XML tree; a first pass collects spin elements together with their isotopes, text labels and Cartesian coordinates and sorts them into sequential spin order, and a second pass collects interaction elements. Interaction tensors may be specified as a full matrix, an isotropic scalar, eigenvalues, isotropic part with anisotropy and asymmetry, span and skew, or axiality and rhombicity; the orientation may be supplied as Euler angles, a quaternion, a direction cosine matrix, or an angle-axis pair. Hyperfine, shielding, shift, dipolar, quadrupolar, J-coupling, g-tensor, zero-field splitting, exchange and spin-rotation interactions are recognised and converted into the units that Spinach expects.

Syntax

    [sys,inter]=x2spinach(filename,shielding_refs)

Parameters

  filename       - SpinXML file name

  shielding_refs - when absolute shielding is provided, this
                   array must give absolute shielding of the
                   corresponding nuclei in the reference sub-
                   stance, e.g. {{'1H',31.5},{'13C',189.7}}.
                   This is necessary because Spinach requires
                   chemical shifts rather than shieldings.
                   If chemical shifts are provided, use an
                   empty cell array.

Outputs

  sys, inter     - Spinach spin system input structures

Notes

WARNING: this function assumes that the SpinXML file has passed the validation against the schema, which may be obtained from http://spindynamics.org/SpinXML.php

Spin and interaction identifiers must be numbered from 1; zero-base indexing is detected and rejected, and the spin id numbers must form a sequential list of integers.

See also

parsexml.m, gissmo2spinach.m, c2spinach.m, cyprinol.m, fatty_acid.m, g2spinach.m, gparse.m, karplus_fit.m, killcross.m, killdiag.m, merge_inp.m, methyl_group.m, nuclacid.m, ocparse.m, oparse.m, protein.m, read_bmrb.m, read_pdb_nuc.m, read_pdb_pro.m, v2spinach.m, weblab2nqi.m, Import,_export,_and_visualisation, Appendix_G:_SpinXML_infrastructure

Version 2.11, authors: Ilya Kuprov