A chemical structure instantiated from CHARMM files. More...

Public Member Functions
def	__init__
	Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data.
def	loadParameters
	Loads parameters from a parameter set that was loaded via CHARMM RTF, PAR, and STR files.
def	setBox
	Sets the periodic box boundary conditions.
def	topology
	Create an OpenMM Topology object from the stored bonded network.
def	createSystem
	Construct an OpenMM System representing the topology described by the prmtop file.
def	system
	Return the cached system class -- it needs to be initialized via "createSystem" first!
def	boxLengths
	Return tuple of 3 units.
def	boxLengths
def	boxVectors
	Return the box vectors.
def	boxVectors
	Sets the box vectors.
def	deleteCmap
	Deletes the CMAP terms from the CHARMM PSF.
Public Attributes
	residue_list
	atom_list
	bond_list
	angle_list
	dihedral_list
	dihedral_parameter_list
	improper_list
	cmap_list
	donor_list
	acceptor_list
	group_list
	title
	flags
	box_vectors
	urey_bradley_list
Static Public Attributes
int	BOND_FORCE_GROUP = 0
int	ANGLE_FORCE_GROUP = 1
int	DIHEDRAL_FORCE_GROUP = 2
int	UREY_BRADLEY_FORCE_GROUP = 3
int	IMPROPER_FORCE_GROUP = 4
int	CMAP_FORCE_GROUP = 5
int	NONBONDED_FORCE_GROUP = 6
int	GB_FORCE_GROUP = 6

Detailed Description

A chemical structure instantiated from CHARMM files.

This structure has numerous attributes that are lists of the elements of this structure, including atoms, bonds, torsions, etc. The attributes are

residue_list
atom_list
bond_list
angle_list
dihedral_list
dihedral_parameter_list
improper_list
cmap_list
donor_list # hbonds donors?
acceptor_list # hbond acceptors?
group_list # list of nonbonded interaction groups

Additional attribute is available if a CharmmParameterSet is loaded into this structure.

urey_bradley_list

The lengths of each of these lists gives the pointers (e.g., natom, nres, etc.)

Constructor & Destructor Documentation

def __init__	(	self,
		psf_name
	)

Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data.

Parameters:

psf_name (str) Name of the PSF file (it must exist)

Member Function Documentation

def boxLengths ( self )

Return tuple of 3 units.

def boxLengths	(	self,
		stuff
	)

def boxVectors ( self )

Return the box vectors.

def boxVectors	(	self,
		stuff
	)

Sets the box vectors.

def createSystem	(	self,
		params,
		nonbondedMethod = `ff.NoCutoff`,
		nonbondedCutoff = `1.0*u.nanometer`,
		switchDistance = `0.0*u.nanometer`,
		constraints = `None`,
		rigidWater = `True`,
		implicitSolvent = `None`,
		implicitSolventKappa = `None`,
		implicitSolventSaltConc = `0.0*u.moles/u.liter`,
		temperature = `298.15*u.kelvin`,
		soluteDielectric = `1.0`,
		solventDielectric = `78.5`,
		removeCMMotion = `True`,
		hydrogenMass = `None`,
		ewaldErrorTolerance = `0.0005`,
		flexibleConstraints = `True`,
		verbose = `False`
	)

Construct an OpenMM System representing the topology described by the prmtop file.

You MUST have loaded a parameter set into this PSF before calling createSystem. If not, AttributeError will be raised. ValueError is raised for illegal input.

Parameters:

params	(CharmmParameterSet) The parameter set to use to parametrize this molecule
nonbondedMethod	(object=NoCutoff) The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
nonbondedCutoff	(distance=1*nanometer) The cutoff distance to use for nonbonded interactions.
switchDistance	(distance=0*nanometer) The distance at which the switching function is active for nonbonded interactions. If the switchDistance evaluates to boolean False (if it is 0), no switching function will be used. Illegal values will raise a ValueError
constraints	(object=None) Specifies which bonds or angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
rigidWater	(boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
implicitSolvent	(object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, or GBn
implicitSolventKappa	(float=None) Debye screening parameter to model salt concentrations in GB solvent.
implicitSolventSaltConc	(float=0.0*u.moles/u.liter) Salt concentration for GB simulations. Converted to Debye length `kappa'
temperature	(float=298.15*u.kelvin) Temperature used in the salt concentration-to-kappa conversion for GB salt concentration term
soluteDielectric	(float=1.0) The solute dielectric constant to use in the implicit solvent model.
solventDielectric	(float=78.5) The solvent dielectric constant to use in the implicit solvent model.
removeCMMotion	(boolean=True) If true, a CMMotionRemover will be added to the System.
hydrogenMass	(mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same.
ewaldErrorTolerance	(float=0.0005) The error tolerance to use if the nonbonded method is Ewald or PME.
flexibleConstraints	(bool=True) Are our constraints flexible or not?
verbose	(bool=False) Optionally prints out a running progress report

def deleteCmap ( self )

Deletes the CMAP terms from the CHARMM PSF.

def loadParameters	(	self,
		parmset
	)

Loads parameters from a parameter set that was loaded via CHARMM RTF, PAR, and STR files.

Parameters:

parmset (CharmmParameterSet) List of all parameters

def setBox	(	self,
		a,
		b,
		c,
		alpha = `90.0*u.degrees`,
		beta = `90.0*u.degrees`,
		gamma = `90.0*u.degrees`
	)

Sets the periodic box boundary conditions.

Parameters:

a	(length) Lengths of the periodic cell
b	(length) Lengths of the periodic cell
c	(length) Lengths of the periodic cell
alpha	(floats, optional) Angles between the periodic cell vectors.
beta	(floats, optional) Angles between the periodic cell vectors.
gamma	(floats, optional) Angles between the periodic cell vectors.