Defines a table of possible amino chain end points and end directions after k amino acids have been concatenated.
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Defines a table of possible amino chain end points and end directions after k amino acids have been concatenated.
constructor base from the copy of another object
- Parameters
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reference | to the original object (const LoopTable&) |
Adjusts the hash table representation, distributing its contents among all bins, according to a min -> max distribution with uniform sampling.
- Parameters
-
- Returns
- changes are made internally(void)
void cluster |
( |
double |
cutoff | ) |
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virtual |
Clusters entries below cutoff, leaving only a single representative.
- Parameters
-
- Returns
- changes are made internally(void)
unsigned short code |
( |
const double |
value, |
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const double |
min, |
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const double |
max |
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) |
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protected |
The function codes an ieee32 value as the 1 byte wide offset between min and max.
- Parameters
-
value | to consider ( const unsigned ),min and max value( const doubl,const doubl)) |
- Returns
- the corresponding value (unsigned short)
void concatenate |
( |
LoopTable & |
src1, |
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LoopTable & |
src2, |
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unsigned long |
nSrc1, |
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unsigned long |
nSrc2 |
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) |
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The function concatenates two protein tables (src1, src2) and stores the result in this. Adds the src to the vector entry.
- Parameters
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reference | to the loop tables(LoopTable& ,LoopTable& )src sizes(unsigned long,unsigned long) |
- Returns
- changes are made internally(void)
copies the original object into a new one
- Parameters
-
reference | to the original object(const LoopTable& ) |
- Returns
- changes are made internally(void)
double decode |
( |
const unsigned short |
value, |
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const double |
min, |
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const double |
max |
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) |
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protected |
The three functions below decode a ProteinTableEntry, vector or ieee32 respectively into its uncompressed form.
- Parameters
-
value | to consider ( const unsigned ),min and max value( const doubl,const doubl)) |
- Returns
- the corresponding value (double)
Find a matching entry with "minimal" deviation from destination (EP, ED, EN) and return it.
- Parameters
-
reference | to the destination loop table entry(const LoopTableEntry&), index of the current selection (unsigned int) |
- Returns
- the new loop table entry(LoopTableEntry)
unsigned int getLength |
( |
| ) |
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return the amino acids number
- Parameters
-
- Returns
- corresponding value ( unsigned int)
returns the maximum value for each coordinate
- Parameters
-
- Returns
- corresponding loop entry table( LoopTableEntry)
unsigned int getMaxBins |
( |
| ) |
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return the maximum bindings
- Parameters
-
- Returns
- corresponding value ( unsigned int)
returns the minimum value for each coordinate
- Parameters
-
- Returns
- corresponding loop entry table( LoopTableEntry)
Gets the closest N
- Parameters
-
reference | to the table( LoopTableEntry&), value of N(unsigned int ), number of amino acids (unsigned int ) |
- Returns
- vector containing the loop entry tables(vector<LoopTableEntry> )
return the Ramachandran Data
- Parameters
-
- Returns
- pointer to the data( RamachandranData* )
void initOccurrence |
( |
const unsigned long |
nSelect | ) |
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protected |
The function initializes the SuS selection mechanism.
- Parameters
-
- Returns
- changes are made internally(void)
Assigns one object into another
- Parameters
-
reference | to the original object(const LoopTable&) |
- Returns
- the reference to the the one(LoopTable&)
returns the corresponding table entry for the given index
- Parameters
-
- Returns
- reference to the loop entry table( LoopTableEntry&)
returns the corresponding table entry for the given index
- Parameters
-
- Returns
- reference to the loop entry table( LoopTableEntry&)
Adds the data into the solution queue
- Parameters
-
offset(unsigned | int),reference to the solutions queue(priority_queue<solutionQueueElem>&), reference to the loop entry table(const LoopTableEntry&) |
- Returns
- changes are made internally(void)
double pEstimateSimilarityCutoff |
( |
const LoopTableEntry & |
le, |
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unsigned int |
num |
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) |
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protected |
calculates the esptimate similarity cutoff
- Parameters
-
reference | to the loop table entry (const LoopTableEntry& ),value to consider (unsigned int) |
- Returns
- the corresponding value(double)
unsigned int pGetBin |
( |
const vgVector3< float > & |
e | ) |
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protected |
returns the corresponding binding
- Parameters
-
reference | for the coordenate values (const vgVector3<float>&) |
- Returns
- corresponding binding value( unsigned int)
Inserts a single element in table.
- Parameters
-
referecnce | to the Loop Entry table(LoopTableEntry&), reference to the loop table entry table ( vector<vector<LoopTableEntry>&) |
- Returns
- changes are made internally(void)
void printTable |
( |
unsigned int |
num | ) |
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print the table statistics (min, max):
- Parameters
-
void read |
( |
const string & |
filename | ) |
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virtual |
Reads the table contents from a file.
- Parameters
-
reference | to the file name(const string&) |
- Returns
- changes are made internally(void)
The function selects the next (random) table entry to be employed, using a SuS selection mechanism. A special case occurs if nAminoAcid = 1, see below.
- Parameters
-
- Returns
- new table entry (LoopTableEntry)
void setLength |
( |
unsigned int |
l | ) |
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Sets the length
- Parameters
-
length | value(unsigned int) |
- Returns
- changes are made internally(void)
Sets the Ramachandran Data
- Parameters
-
pointer | to the RamachandranData(RamachandranData*) |
- Returns
- changes are made internally(void)
void setToSingleAminoAcid |
( |
| ) |
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Defaults the protein table to the simple case where nAminoacid = 1.
- Parameters
-
- Returns
- changes are made internally(void)
void showDistribution |
( |
| ) |
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Prints the loop table distribution
- Parameters
-
return the entries total size
- Parameters
-
- Returns
- corresponding value ( unsigned int)
Adds the src to the vector entry. stores the results in the table
- Parameters
-
reference | to the loop table entry(const LoopTableEntry&) |
- Returns
- changes are made internally(void)
void write |
( |
const string & |
filename | ) |
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virtual |
Writes the table contents to file.
- Parameters
-
reference | to the file name(const string& ) |
- Returns
- changes are made internally(void)
void writeASCII |
( |
const string & |
filename, |
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unsigned long |
num = 0 , |
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unsigned int |
wEntry = 0 , |
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unsigned int |
wDim = 0 |
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) |
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Writes the table contents to file in ASCII format. (Useful for viewing with GNU Plot)
- Parameters
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reference | to the file name (const string& ), size(unsigned long), entry weigth( unsigned int) ,entry dimension( unsigned int) |
- Returns
- changes are made internally(void)
The documentation for this class was generated from the following files: