Class Residue

residue structure classes for rFold

external dependencies : deque (https://github.com/catwell/cw-lua/tree/master/deque)

Functions

residue.new (o) Residue class object initialiser (not a class method)

Fields

Residue.hedra array of hedron objects indexed by hedron keys ([resPos res atom] x3)
Residue.dihedra array of dihedron objects indexed by dihedron keys ([resPos res atom] x4)
Residue.backbone array of { dihedron object, position 1..4 in dihedron specifying atom } for backbone atoms indexed by integer position of print order in PDB format file; set by linkDihedra()
Residue.sidechain array of { dihedron object, position 1..4 in dihedron specifying atom } for sidechain atoms indexed by integer position of print order in PDB format file; set by linkDihedra()
Residue.atomCoords array of 4x1 float matrices indexed by atomKey strings (resPos res atom)
Residue.ordered boolean indicating residue is ordered
Residue.res residue character GAVLIMFPSTCNQYWDEHKRX
Residue.resn residue sequence position as in PDB or DSSP file
Residue.dssp DSSP data for this residue as read by parseProteinData(), or subset (ss, ss2, psi, phi, omg, acc) if loaded from database

Methods

Residue:load (t) callback from file parser, import table data for this Residue according to contents
Residue:writeDb (rfpg, res_id, update) write residue data to rfold database
Residue:dbLoad (rfpg) populate residue object from database using supplied database res_id
Residue:tostring () generate descriptive string for Residue: 1-letter amino acid code, sequence position
Residue:countHedra () count entries in self['hedra'] table
Residue:countDihedra () count entries in self['dihedra'] table
Residue:clearAtomCoords () delete protein space atom coordinate data from this residue
Residue:clearInternalCoords () delete internal coordinate data from this chain
Residue:renderHedra () set hedron space coordinates for each point from supplied length, angle, length
Residue:renderDihedra () set dihedron space coordinates for each point from hedra and supplied dihedral angle
Residue:linkDihedra () create map of key(first 3 atom ids) to dihedron for all dihedra in Residue; create backbone and sidechain tables of (dihedron, position) for atoms in PDB order
Residue:dihedraFromAtoms () complete residue, dihedra, hedra data structures from protein space atom coordinates
Residue:writePDB (chain, ndx) generate ATOM records for this Residue
Note: OXT defined in Dihedra like other atoms, if present
Residue:dsspAtom (atomKey) create a 4x1 matrix with coordinates for specified atom token as read from DSSP
Residue:NCaCKeySplit () generate a table of atom tokens for this Residue's N, CA, C backbone atoms
Residue:assemble (atomCoordsIn) join dihedrons from N-CA-C and N-CA-CB hedrons, computing protein space coordinates for backbone and sidechain atoms


Functions

Methods
residue.new (o)
Residue class object initialiser (not a class method)

Parameters:

  • o table with fields 'res' = 1-letter amino acid code, 'resn' = sequence position of Residue in Chain

Returns:

    minimally initialised Residue object

Fields

Residue.hedra
array of hedron objects indexed by hedron keys ([resPos res atom] x3)
  • hedra array of hedron objects
Residue.dihedra
array of dihedron objects indexed by dihedron keys ([resPos res atom] x4)
  • dihedra array of dihedron objects
Residue.backbone
array of { dihedron object, position 1..4 in dihedron specifying atom } for backbone atoms indexed by integer position of print order in PDB format file; set by linkDihedra()
  • backbone {dihedron, i}
Residue.sidechain
array of { dihedron object, position 1..4 in dihedron specifying atom } for sidechain atoms indexed by integer position of print order in PDB format file; set by linkDihedra()
  • sidechain {dihedron, i}
Residue.atomCoords
array of 4x1 float matrices indexed by atomKey strings (resPos res atom)
  • atomCoords float[4][1]
Residue.ordered
boolean indicating residue is ordered
  • ordered boolean
Residue.res
residue character GAVLIMFPSTCNQYWDEHKRX
  • res char
Residue.resn
residue sequence position as in PDB or DSSP file
  • resn integer
Residue.dssp
DSSP data for this residue as read by parseProteinData(), or subset (ss, ss2, psi, phi, omg, acc) if loaded from database
  • dssp array

Methods

Residue:load (t)
callback from file parser, import table data for this Residue according to contents

Parameters:

  • t parsed file record data: DSSP record, PDB ATOM record, or hedron / dihedron specification
Residue:writeDb (rfpg, res_id, update)
write residue data to rfold database

Parameters:

  • rfpg open database handle
  • res_id residue ID in residue table
  • update optional flag, if false silently skip if [resid [atom] ] entry exists already in atomcoordinates / dssp / dihedral / angle / bond tables
Residue:dbLoad (rfpg)
populate residue object from database using supplied database res_id

Parameters:

  • rfpg open database handle
Residue:tostring ()
generate descriptive string for Residue: 1-letter amino acid code, sequence position

Returns:

    descriptive string
Residue:countHedra ()
count entries in self['hedra'] table

Returns:

    number of hedra in Residue
Residue:countDihedra ()
count entries in self['dihedra'] table

Returns:

    number of dihedra in Residue
Residue:clearAtomCoords ()
delete protein space atom coordinate data from this residue
Residue:clearInternalCoords ()
delete internal coordinate data from this chain
Residue:renderHedra ()
set hedron space coordinates for each point from supplied length, angle, length
Residue:renderDihedra ()
set dihedron space coordinates for each point from hedra and supplied dihedral angle
Residue:linkDihedra ()
create map of key(first 3 atom ids) to dihedron for all dihedra in Residue; create backbone and sidechain tables of (dihedron, position) for atoms in PDB order

See also:

Residue:dihedraFromAtoms ()
complete residue, dihedra, hedra data structures from protein space atom coordinates
Residue:writePDB (chain, ndx)
generate ATOM records for this Residue
Note: OXT defined in Dihedra like other atoms, if present

Parameters:

  • chain chain ID
  • ndx ATOM record sequence counter

Returns:

    string containing sequential ATOM records, ndx
Residue:dsspAtom (atomKey)
create a 4x1 matrix with coordinates for specified atom token as read from DSSP

Parameters:

  • atomKey atom token of form (sequence postion)(residue)(atom string)

Returns:

    4x1 matrix with protein space coordinates for atom

See also:

Residue:NCaCKeySplit ()
generate a table of atom tokens for this Residue's N, CA, C backbone atoms

Returns:

    table of atom tokens { (sequence postion)(residue)(atom string) } for N, CA, C backbone atoms

See also:

Residue:assemble (atomCoordsIn)
join dihedrons from N-CA-C and N-CA-CB hedrons, computing protein space coordinates for backbone and sidechain atoms

Parameters:

  • atomCoordsIn table of atom_token : 4x1 matrix of protein space coordinates
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