PDBReader Class Reference

This class parses PDB files, then constructs Systems and States based on them for use in Simbody. More...

#include <PDBReader.h>

List of all members.

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.

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Detailed Description

This class parses PDB files, then constructs Systems and States based on them for use in Simbody.

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Constructor & Destructor Documentation

PDBReader

(

std::string

filename

)

Create a PDBReader object that encapsulates the information in a PDB file.

~PDBReader

(

)

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Member Function Documentation

void 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 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.

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The documentation for this class was generated from the following file:

• PDBReader.h