CS2IO Class Reference

#include <PExtension.h>

List of all members.

Detailed Description

Contains methods to read and write from CS2 (second-generation chainspace) files. See DATA_COLLECTOR_DESIGN for more information about these files.

Static Public Member Functions

static PProteinreadConformation (const string &cs2File, int confNum)
static PLightChainreadConformationLoopOnly (const string &cs2File, int confNum)
static PConformationSpacereadConformationSpace (const string &cs2File)
static pair< PLightChain *,
PLightChain * > 
getNonLoopChains (const string &cs2File)
static void appendConformation (const string &cs2File, PProtein *loop)
static void writeToFile (const string &cs2File, PProtein *loop)
static int getNumConformations (const string &cs2File)
static void createPDBDirectory (const string &cs2File, const string &directoryName)

Member Function Documentation

PProtein * CS2IO::readConformation ( const string &  cs2File,
int  confNum 
) [static]

Reads the confNum'th loop conformation from cs2File. This function creates a finalized version of the entire protein: the PProtein pointer returned to the caller points to the loop, and the entire chain may be accessed with the method getTopLevelProtein(). Conformation "1" is the original conformation from when this file was created.

PLightChain * CS2IO::readConformationLoopOnly ( const string &  cs2File,
int  confNum 
) [static]

Reads the confNum'th loop conformation from cs2File. This function returns a PLightChain containing only data for the loop, with no information about the protein's static portions.

PConformationSpace * CS2IO::readConformationSpace ( const string &  cs2File  )  [static]

Reads the entire conformation space contained in cs2File, including the protein's static portions and all loop conformations. This function allocates dynamic memory, so the resulting PConformationSpace should be deleted by the caller when no longer needed.

pair< PLightChain *, PLightChain * > CS2IO::getNonLoopChains ( const string &  cs2File  )  [static]

Reads only the static portions of the protein represented in cs2File. The first member of the pair returned is the subchain before the loop; the second member is the subchain after the loop.

void CS2IO::appendConformation ( const string &  cs2File,
PProtein loop 
) [static]

Appends a new conformation to the specified CS2 file. loop is assumed to represent only that subchain of the parent chain whose conformation has changed. Furthermore, the file cs2File must already contain at least one conformation of loop or the program will abort.

void CS2IO::writeToFile ( const string &  cs2File,
PProtein loop 
) [static]

Writes a new CS2 file to the file specified by cs2file. The output is a new file containing the PDB representation of loop's parent protein; the single "loop" line indicating the start and end residues represented by loop; and the single conformation of the atoms in loop.

int CS2IO::getNumConformations ( const string &  cs2File  )  [static]

Returns the number of conformations present within the given file.

void CS2IO::createPDBDirectory ( const string &  cs2File,
const string &  directoryName 
) [static]

Creates a directory of PDB files given input cs2File, one for each conformation.

The documentation for this class was generated from the following files:
Generated on Wed May 16 20:22:12 2007 for LoopTK: Protein Loop Kinematic Toolkit by  doxygen 1.5.1