Table 1

The ten classes summarised in group "structure" with labelled difficulty level and a selection of methods available.
Class Name	Label	Methods

Structure	Basic	Returns 4-letter PDB code
		Returns HEADER, TITLE, REVDAT lines
		Extracts date from HEADER line
		Returns type of experimental method
		Returns resolution as in REMARK2 lines
		Writes out complete structure to a stream in PDB format
		Returns enumerator over all chains
		Returns chain for a given code
		Removes a chain from structure
		...

Structure Factory	Xtra	Reads structure from directory or file
		Offers parsing options from directory or file
		...

Chain	Basic	Returns code of this chain (as string/number)
		Returns chain identifier consisting of PDB and chain code
		Returns COMPND and SOURCE lines, EC code Transforms all residues/atoms in chain by transformation matrix
		Returns number of residues (amino acids and nucleic acids), standard amino acids, heterogeneous residues, solvent residues
		Provides access to residues, heterogeneous residues, solvent residues
		Adds new residue, heterogen, new solvent molecule to chain
		Removes a residue, heterogen, solvent molecule from chain
		Derives amino acid sequence from connected residues
		Derives amino acid sequence with filled gaps ("X") where missing residues occur
		Returns amino acid sequence from SEQRES entry
		Computes geometric hashing table of all residues
		Finds residues in chain which are close to given co-ordinates based on geometric hashing
		...

Chain Factory	Xtra	Creates a new chain with given code
Residue	Basic	Returns the residue name/number
		Returns the name of the standard residue as the base of this modified residue as in MODRES lines
		Returns description of residue modification as given in MODRES lines
		Translates residue name into amino acid one letter code
		Adds new atom to residue
		...

Residue Factory	Xtra	Creates new residue with number and name
		...

Atom	Basic	Returns atom name/number
		Returns temperature factor for an atom
		Returns chemical element
		Returns partial charge of atom
		Returns enumerator over all bonded atoms
		Adds bond from this atom to given atom2
		Removes all bonds
		Removes bond to atom2
		Sets atom to be of chemical type
		...

Coordinates	Basic	Calculates Euclidian distance between two co-ordinates
		Returns x, y, z from co-ordinates
		Transforms co-ordinates by transformation matrix
		...

Pairwise Structural Alignment	Basic	Provides access to first/second chain
		Computes transformation based on superimposed chains
		Re-computes transformation from selection of residue pairs
		Calculates RMSD of structural alignment
		Counts alignment positions in structural alignment
		Counts aligned pairs only
		Counts aligned pairs with distance below given cut-off
		Reads external pairwise alignment from stream in T_Coffee format and re-computes structural alignment from this
		Writes structural alignment to stream in T_Coffee library format
		...

Selection	Basic	Counts number of residues in this selection
		Returns enumerator over selected residues
		Includes/excludes a single residue to/from selection
		Adds all selected residues from selection2 to this selection
		Structurally aligns selection1 to selection2 and returns the resulting transformation matrix
		...


Diemand and Scheib BMC Bioinformatics 2004 5:39 doi:10.1186/1471-2105-5-39