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Table 1 The ten classes summarised in group "structure" with labelled difficulty level and a selection of methods available.

From: MolTalk – a programming library for protein structures and structure analysis

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
   ...
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