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

Inheritance diagram for CharmmPsfFile:

Public Member Functions
def	__init__
	Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data. More...

def	writePsf
	Writes a PSF file from the stored molecule. More...

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

def	setBox
	Sets the periodic box boundary conditions. More...

def	topology
	Create an OpenMM Topology object from the stored bonded network. More...

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

def	system
	Return the cached system class – it needs to be initialized via "createSystem" first! More...

def	boxLengths
	Return tuple of 3 units. More...

def	boxLengths

def	boxVectors
	Return the box vectors. More...

def	boxVectors
	Sets the box vectors. More...

def	deleteCmap
	Deletes the CMAP terms from the CHARMM PSF. More...

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.

Example:

cs = CharmmPsfFile("testfiles/test.psf")

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.)

Example:

cs = CharmmPsfFile("testfiles/test.psf") len(cs.atom_list)

33

len(cs.bond_list)

32

Constructor & Destructor Documentation

def __init__	(	self,
		psf_name
	)

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

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

Exceptions Raised: IOError : If file "psf_name" does not exist CharmmPSFError: If any parsing errors are encountered

References simtk.openmm.app.charmmpsffile.set_molecules().

Member Function Documentation

def boxLengths ( self )

Return tuple of 3 units.

References CharmmPsfFile._boxLengths, and CharmmPsfFile.box_vectors.

Referenced by CharmmPsfFile.boxLengths(), CharmmPsfFile.createSystem(), and CharmmPsfFile.topology().

def boxLengths	(	self,
		stuff
	)

References CharmmPsfFile.boxLengths().

def boxVectors ( self )

Return the box vectors.

References CharmmPsfFile.box_vectors.

Referenced by CharmmPsfFile.boxVectors().

def boxVectors	(	self,
		stuff
	)

Sets the box vectors.

References CharmmPsfFile._boxLengths, CharmmPsfFile.box_vectors, and CharmmPsfFile.boxVectors().

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

References CharmmPsfFile._get_gb_params(), CharmmPsfFile._system, Context._system, CharmmPsfFile.ANGLE_FORCE_GROUP, CharmmPsfFile.angle_list, CharmmPsfFile.atom_list, CharmmPsfFile.BOND_FORCE_GROUP, CharmmPsfFile.bond_list, CharmmPsfFile.box_vectors, CharmmPsfFile.boxLengths(), CharmmPsfFile.CMAP_FORCE_GROUP, CharmmPsfFile.cmap_list, CharmmPsfFile.DIHEDRAL_FORCE_GROUP, CharmmPsfFile.dihedral_parameter_list, CharmmPsfFile.GB_FORCE_GROUP, CharmmPsfFile.IMPROPER_FORCE_GROUP, CharmmPsfFile.improper_list, CharmmPsfFile.loadParameters(), CharmmPsfFile.NONBONDED_FORCE_GROUP, CharmmPsfFile.UREY_BRADLEY_FORCE_GROUP, and CharmmPsfFile.urey_bradley_list.

Referenced by CharmmPsfFile.topology().

def deleteCmap ( self )

Deletes the CMAP terms from the CHARMM PSF.

References CharmmPsfFile.cmap_list.

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

Notes:

Parameters

If	any parameters that are necessary cannot be found, a MissingParameter exception is raised.
If	any dihedral or improper parameters cannot be found, I will try inserting wildcards (at either end for dihedrals and as the two central atoms in impropers) and see if that matches. Wild-cards will apply ONLY if specific parameters cannot be found.
This	method will expand the dihedral_parameter_list attribute by adding a separate Dihedral object for each term for types that have a multi-term expansion

References CharmmPsfFile.atom_list, and CharmmPsfFile.bond_list.

Referenced by CharmmPsfFile.createSystem().

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,b,c	(floats) : Lengths of the periodic cell
alpha,beta,gamma	(floats, optional) : Angles between the periodic cells.

References CharmmPsfFile._boxLengths, CharmmPsfFile._topology, and CharmmPsfFile.box_vectors.

def system ( self )

Return the cached system class – it needs to be initialized via "createSystem" first!

References CharmmPsfFile._system, and Context._system.

def topology ( self )

Create an OpenMM Topology object from the stored bonded network.

References CharmmPsfFile._topology, CharmmPsfFile.atom_list, CharmmPsfFile.bond_list, CharmmPsfFile.box_vectors, CharmmPsfFile.boxLengths(), and CharmmPsfFile.createSystem().

Referenced by DesmondDMSFile.getTopology().

def writePsf	(	self,
		dest,
		vmd = `False`
	)

Writes a PSF file from the stored molecule.

Parameters

dest	(str or file-like) : The place to write the output PSF file. If it has a "write" attribute, it will be used to print the PSF file. Otherwise, it will be treated like a string and a file will be opened, printed, then closed
vmd	(bool) : If True, it will write out a PSF in the format that VMD prints it in (i.e., no NUMLP/NUMLPH or MOLNT sections) Example: cs = CharmmPsfFile('testfiles/test.psf') cs.writePsf('testfiles/test2.psf')