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 | ||
... |