This recipe is a child of http://fold.it/portal/recipe/40004 which got unshared.

This is not a recipe that does anything, is a table of data and functions for accessing it. Using the table and functions, you can identify which atom is the first in the side chain; which atoms are donors, acceptors, or polar hydrogens; whether a residue is the first or last residue in a peptide chain; and whether a cysteine has a disulfide bond.

Changelog and API:

* Version 1.1 Brow42 May 14, 2012
*
* CountAtoms renamed to _CountAtoms
* CountAtoms is now a wrapper for structure.GetAtomCount
* GetCount renamed to GetExpectedCount and does not auto-lookup flags
* IsTerminal is now called by the various Get* functions if isFirst = nil
* A small table of nominal atom counts has been added to the top of the file, and the functions
* needed to determine if the AA is bonded also moved to the front and only require this small
* table. This is so if all you need is IsTerminal, you don't need the entire library.

* API (all in the fsl.atom namespace)

* Many functions accept option 2 or 3 boolean arguments, which indicate
* if the segment is the first and/or last segment in a polypeptide.
* The third argument boolean is true if the segment is disulfide bonded.
* These arguments can be replaced by a call to IsTerminal(). If omitted,
* IsTerminal will be called automatically, except for GetExpectedCount,
* which is used to modify the db value.
* Most functions accept either a segment number or AA code as the first argument.

* CountAtoms() and _CountAtoms() are the only useful functions for ligands
* ('M' structure). Other functions will return nil if passed a ligand segment.

* _CountAtoms(number iSeg) -- SlOW manual count all the atoms in the segment. You should use structure.GetAtomCount instead.
* GetExpectedCount(number or string iSeg, isFirst, isLast, isDisulfideBonded) -- total EXPECTED atoms in segment or AA, given flags, default false
* IsTerminal(number iSeg) -- returns bool,bool if start or end of a polypeptide
* GetBackboneHeavyAtoms(number or string iSeg, isFirst, isLast) -- range of atoms on the backbone
* GetSidechainHeavyAtoms(number or string iSeg, isFirst, isLast) -- range of atoms on the sidechain (nil for glycine)
* GetDonorAtoms(number or string iSeg, isFirst, isLast) -- list of donor atoms
* GetAcceptorAtoms(number or string iSeg, isFirst, isLast) -- list of acceptor atoms
* GetPolarHydrogens(number or string iSeg, isFirst, isLast) -- list of polar hydrogen atoms
* _IsDisulfideBonded(number iSeg) -- true if bonded to another cysteine
* _IsTerminalTest(aa,count,disulfide) -- If already called CountAtoms(), don't call IsTerminal(), call this instead.
* _NumberOrCode(number or string iSeg) -- performs a table look up given segment number or AA code.
* Test1() -- Count all atoms, compare with table, perform terminal segment check, for all segments
* Test2(mode) -- Band all atoms of a particular class. mode = sc, bb, donor, polar, acceptor
* db -- Reference table of atom numbers for each class. Should not be accessed directly since bonding changes atom counts.
* atomcount -- table of just the expected total atom counts