Molmodel
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This class parses PDB files, then constructs Systems and States based on them for use in Simbody. More...
#include <PDBReader.h>
Public Member Functions | |
PDBReader (std::string filename) | |
Create a PDBReader object that encapsulates the information in a PDB file. | |
~PDBReader () | |
void | createCompounds (CompoundSystem &system) |
Create one or more Compounds representing the protein or nucleic acid described in the PDB file. | |
Real | createState (const CompoundSystem &system, State &state) const |
Create a State reflecting the structure loaded from the PDB file. |
This class parses PDB files, then constructs Systems and States based on them for use in Simbody.
SimTK::PDBReader::PDBReader | ( | std::string | filename | ) | [explicit] |
Create a PDBReader object that encapsulates the information in a PDB file.
SimTK::PDBReader::~PDBReader | ( | ) |
void SimTK::PDBReader::createCompounds | ( | CompoundSystem & | system | ) |
Create one or more Compounds representing the protein or nucleic acid described in the PDB file.
You pass to this method a CompoundSystem which has all the necessary subsystems. It then creates Compounds based on the sequence in the PDB file and adds them to the CompoundSystem.
Real SimTK::PDBReader::createState | ( | const CompoundSystem & | system, |
State & | state | ||
) | const |
Create a State reflecting the structure loaded from the PDB file.
Before calling this method, you must first call createCompounds(), then call modelCompounds() on the CompoundSystem. You pass it the System that was created by createCompounds() and a State in which to store the result. It performs a nonlinear optimization to find the set of internal coordinates for the System which most closely match the structure specified in the PDB file.
Because this method actually has to solve an optimization problem, it may take a long time for large proteins.