#include <PExtension.h>
Static Public Member Functions | |
static PProtein * | readConformation (const string &cs2File, int confNum) |
static PLightChain * | readConformationLoopOnly (const string &cs2File, int confNum) |
static PConformationSpace * | readConformationSpace (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) |
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.