Class Protein
protein structure class for rFold
Functions
| protein.new (o) | Protein class object initialiser (not a class method) |
| protein.get (id) | find the Protein with this id or new Protein if it does not exist (not a class method) |
| protein.stashId (id) | generate a new key for the data stored in protein.proteins for the passed id key. |
| protein.rename (old, new) | change the key for an entry in the protein.proteins table |
| protein.drop (id) | remove an entry from the protein.proteins table so garbage collector can free memory |
| protein.clean () | remove all entries from the protein.proteins table so garbage collector can free memory |
| protein.load (t) | add the passed table data to the protein specified (pdbid) in the table (not a class method - may create new Protein) |
| protein.copyDSSP (src, dst) | copy DSSP data from src protein object to dst protein object (not a class method) will fall over if protein objects do not otherwise match |
Fields
| Protein.id | 4 position PDB identifier for this protein |
| Protein.chains | array of chain objects indexed by chain ID |
| Protein.chainOrder | array of chain IDs indexed by integer order of chains in PDB file |
| Protein.header | pdb HEADER record if supplied |
| Protein.title | pdb TITLE record if supplied |
| Protein.title | pdb TITLE record if supplied |
| Protein.compnd | pdb COMPND record if supplied |
| Protein.filename | location of file this protein data was read from |
Methods
| Protein:internalToAtomCoords () | compute atomCoords for already loaded internal coordinates; wrapper grouping several Protein: class methods |
| Protein:stats () | return table of component counts for chains in protein similar to tostring() |
| Protein:countDihedra () | sum dihedron counts for chains |
| Protein:countDSSPs () | sum dssp counts for chains |
| Protein:tosequence () | generate sequence strings for chains in this protein |
| Protein:tostring () | generate descriptive string for Protein : id, sequence, counts of residues, DSSP entries, hedra and dihedra |
| Protein:writePDB (noRemark, range) | generate PDB format text data, adding HEADER, CAVEAT and END records to Chain:writePDB() result note Residue structures need dihedron data structures to write complete chain |
| Protein:writeInternalCoords (noTitle, range) | generate text data specifying hedra with length, angle, length ; dihedra with angle ; relevant PDB records for annotation and start coordinates |
| Protein:writeDb (rfpg, update, src) | write protein data to rfold database |
| Protein:reportDb (rfpg) | query database for info about this protein |
| Protein:dbLoad (rfpg) | populate protein object from database using supplied pdb id |
| Protein:linkResidues () | trigger linking of residues, dihedrons and hedrons within chains |
| Protein:renderDihedra () | trigger update of initial atom coordinates (dihedron coordinate space) in each dihedron according to dihedron angle |
| Protein:clearAtomCoords () | delete protein space atom coordinate data throughout protein object |
| Protein:clearInternalCoords () | delete internal coordinate data throughout protein object |
| Protein:atomsToInternalCoords () | inverse of linkResidues() and renderDihedra() : from input atom coordinates, build complete hedra and dihedra |
| Protein:assembleResidues () | trigger calculation/update of residue['backbone'] and residue['sidechain'] atom coordinates (protein coordinate space) by sequentially assembling dihedrons |
| Protein:setStartCoords () | set N, CA, C coordinates (protein coordinate space) for first residue in each chain from DSSP data for residue if available |
| Protein:report () | generate string indicating chain IDs and residues in each |
Functions
Methods- protein.new (o)
-
Protein class object initialiser (not a class method)
Parameters:
- o table with field 'id' = Brookhaven / RCSB PDB alphanumeric ID or similar
Returns:
-
minimally initialised Protein object, object added to proteins list
- protein.get (id)
-
find the Protein with this id or new Protein if it does not exist (not a class method)
Parameters:
- id Brookhaven / RCSB PDB alphanumeric ID or similar
Returns:
-
already existing or minimally initialised protein object
- protein.stashId (id)
-
generate a new key for the data stored in protein.proteins for the passed id key.
new key of form- where n is number uch that - is available
enables re-loading file for line-by-line compare to generated daa for test (probably need prot:setStartCoords())Parameters:
- id Brookhaven / RCSB PDB alphanumeric ID or similar
Returns:
-
new key or nil if no entry exists for passed id
- protein.rename (old, new)
-
change the key for an entry in the protein.proteins table
Parameters:
- old old key
- new new key
- protein.drop (id)
-
remove an entry from the protein.proteins table so garbage collector can free memory
Parameters:
- id key to drop from table
- protein.clean ()
- remove all entries from the protein.proteins table so garbage collector can free memory
- protein.load (t)
-
add the passed table data to the protein specified (pdbid) in the table (not a class method - may create new Protein)
Parameters:
- t table with field 'pdbid' and preferably chain identifier field 'chn', passed here as callback from file parser
- protein.copyDSSP (src, dst)
-
copy DSSP data from src protein object to dst protein object (not a class method)
will fall over if protein objects do not otherwise match
Parameters:
- src Protein object with DSSP data
- dst Protein object to get DSSP data
Fields
- Protein.id
-
4 position PDB identifier for this protein
- id string
- Protein.chains
-
array of chain objects indexed by chain ID
- chains array of chain objects
- Protein.chainOrder
-
array of chain IDs indexed by integer order of chains in PDB file
- chainOrder array of char chain IDs
- Protein.header
-
pdb HEADER record if supplied
- header string
- Protein.title
-
pdb TITLE record if supplied
- title string
- Protein.title
-
pdb TITLE record if supplied
- title string
- Protein.compnd
-
pdb COMPND record if supplied
- compnd string
- Protein.filename
-
location of file this protein data was read from
- filename string
Methods
- Protein:internalToAtomCoords ()
- compute atomCoords for already loaded internal coordinates; wrapper grouping several Protein: class methods
- Protein:stats ()
-
return table of component counts for chains in protein similar to tostring()
Returns:
-
table of [chain id][residue count, dssp count, dihedron count, hedron count]
- Protein:countDihedra ()
-
sum dihedron counts for chains
Returns:
-
total number of dihedra loaded for protein
- Protein:countDSSPs ()
-
sum dssp counts for chains
Returns:
-
total number of dssp entries loaded for protein
- Protein:tosequence ()
-
generate sequence strings for chains in this protein
Returns:
-
chain sequence strings, 1n separated
- Protein:tostring ()
-
generate descriptive string for Protein : id, sequence, counts of residues, DSSP entries, hedra and dihedra
Returns:
-
descriptive string
- Protein:writePDB (noRemark, range)
-
generate PDB format text data, adding HEADER, CAVEAT and END records to Chain:writePDB() result
note Residue structures need dihedron data structures to write complete chain
Parameters:
- noRemark boolean do not write REMARK records indicating this is RFOLD output
- range start:fin filter for residues to output
Returns:
-
string containing PDB format text (complete)
- Protein:writeInternalCoords (noTitle, range)
-
generate text data specifying hedra with length, angle, length ; dihedra with angle ; relevant PDB records for annotation and start coordinates
Parameters:
- noTitle do not write TITLE line if true; DSSP does not output so compare fails
- range start:fin filter for residues to output
Returns:
-
string containing structure specification in internal coordinates (complete)
- Protein:writeDb (rfpg, update, src)
-
write protein data to rfold database
Parameters:
- rfpg open database handle
- update optional flag, if false (default at protein level only) silently skip if [pdbid,chain,filename] entry exists already in pdb_chain
- src string to put in pdb_chain:src column
- Protein:reportDb (rfpg)
-
query database for info about this protein
Parameters:
- rfpg open database handle
Returns:
-
report string for printing
- Protein:dbLoad (rfpg)
-
populate protein object from database using supplied pdb id
Parameters:
- rfpg open database handle
- Protein:linkResidues ()
- trigger linking of residues, dihedrons and hedrons within chains
- Protein:renderDihedra ()
- trigger update of initial atom coordinates (dihedron coordinate space) in each dihedron according to dihedron angle
- Protein:clearAtomCoords ()
- delete protein space atom coordinate data throughout protein object
- Protein:clearInternalCoords ()
- delete internal coordinate data throughout protein object
- Protein:atomsToInternalCoords ()
- inverse of linkResidues() and renderDihedra() : from input atom coordinates, build complete hedra and dihedra
- Protein:assembleResidues ()
- trigger calculation/update of residue['backbone'] and residue['sidechain'] atom coordinates (protein coordinate space) by sequentially assembling dihedrons
- Protein:setStartCoords ()
- set N, CA, C coordinates (protein coordinate space) for first residue in each chain from DSSP data for residue if available
- Protein:report ()
-
generate string indicating chain IDs and residues in each
Returns:
-
string