Engine for carrying out general purpose TINKER calculations. More...

Inheritance diagram for src.tinkerio.TINKER:

Collaboration diagram for src.tinkerio.TINKER:

Public Member Functions
def	__init__ (self, name="tinker", kwargs)

def	setopts (self, kwargs)
	Called by init ; Set TINKER-specific options. More...

def	readsrc (self, kwargs)
	Called by init ; read files from the source directory. More...

def	calltinker (self, command, stdin=None, print_to_screen=False, print_command=False, kwargs)
	Call TINKER; prepend the tinkerpath to calling the TINKER program. More...

def	prepare (self, pbc=False, kwargs)
	Called by init ; prepare the temp directory and figure out the topology. More...

def	optimize (self, shot, method="newton", align=True, crit=1e-4)
	Optimize the geometry and align the optimized geometry to the starting geometry. More...

def	evaluate_ (self, xyzin, force=False, dipole=False)
	Utility function for computing energy, and (optionally) forces and dipoles using TINKER. More...

def	get_charges (self)

def	energy_force_one (self, shot)
	Computes the energy and force using TINKER for one snapshot. More...

def	energy (self)
	Computes the energy using TINKER over a trajectory. More...

def	energy_force (self)
	Computes the energy and force using TINKER over a trajectory. More...

def	energy_dipole (self)
	Computes the energy and dipole using TINKER over a trajectory. More...

def	normal_modes (self, shot=0, optimize=True)

def	multipole_moments (self, shot=0, optimize=True, polarizability=False)
	Return the multipole moments of the 1st snapshot in Debye and Buckingham units. More...

def	energy_rmsd (self, shot=0, optimize=True)
	Calculate energy of the selected structure (optionally minimize and return the minimized energy and RMSD). More...

def	interaction_energy (self, fraga, fragb)
	Calculate the interaction energy for two fragments. More...

def	molecular_dynamics (self, nsteps, timestep, temperature=None, pressure=None, nequil=0, nsave=1000, minimize=True, anisotropic=False, threads=1, verbose=False, kwargs)
	Method for running a molecular dynamics simulation. More...

Public Attributes
	valkwd
	Keyword args that aren't in this list are filtered out. More...

	warn_vn

	tinkerpath
	The directory containing TINKER executables (e.g. More...

	key

	prm

	mol

	rigid
	Attempt to set some TINKER options. More...

	pbc

	abskey

	AtomMask
	If the coordinates do not come with TINKER suffixes then throw an error. More...

	AtomLists

	A

	B

	md_trajectory

Detailed Description

Engine for carrying out general purpose TINKER calculations.

Definition at line 313 of file tinkerio.py.

Constructor & Destructor Documentation

◆ init()

def src.tinkerio.TINKER.__init__	(	self,
		name = `"tinker"`,
		kwargs
	)

Definition at line 316 of file tinkerio.py.

Member Function Documentation

◆ calltinker()

def src.tinkerio.TINKER.calltinker	(	self,
		command,
		stdin = `None`,
		print_to_screen = `False`,
		print_command = `False`,
		kwargs
	)

Call TINKER; prepend the tinkerpath to calling the TINKER program.

Definition at line 354 of file tinkerio.py.

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◆ energy()

def src.tinkerio.TINKER.energy ( self )

Computes the energy using TINKER over a trajectory.

Definition at line 709 of file tinkerio.py.

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◆ energy_dipole()

def src.tinkerio.TINKER.energy_dipole ( self )

Computes the energy and dipole using TINKER over a trajectory.

Definition at line 734 of file tinkerio.py.

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◆ energy_force()

def src.tinkerio.TINKER.energy_force ( self )

Computes the energy and force using TINKER over a trajectory.

Definition at line 721 of file tinkerio.py.

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◆ energy_force_one()

def src.tinkerio.TINKER.energy_force_one	(	self,
		shot
	)

Computes the energy and force using TINKER for one snapshot.

Definition at line 700 of file tinkerio.py.

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◆ energy_rmsd()

def src.tinkerio.TINKER.energy_rmsd	(	self,
		shot = `0`,
		optimize = `True`
	)

Calculate energy of the selected structure (optionally minimize and return the minimized energy and RMSD).

In kcal/mol.

Definition at line 846 of file tinkerio.py.

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◆ evaluate_()

def src.tinkerio.TINKER.evaluate_	(	self,
		xyzin,
		force = `False`,
		dipole = `False`
	)

Utility function for computing energy, and (optionally) forces and dipoles using TINKER.

Inputs: xyzin: TINKER .xyz file name. force: Switch for calculating the force. dipole: Switch for calculating the dipole.

Outputs: Result: Dictionary containing energies, forces and/or dipoles.

Definition at line 647 of file tinkerio.py.

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◆ get_charges()

def src.tinkerio.TINKER.get_charges ( self )

Definition at line 694 of file tinkerio.py.

◆ interaction_energy()

def src.tinkerio.TINKER.interaction_energy	(	self,
		fraga,
		fragb
	)

Calculate the interaction energy for two fragments.

Definition at line 885 of file tinkerio.py.

◆ molecular_dynamics()

def src.tinkerio.TINKER.molecular_dynamics	(	self,
		nsteps,
		timestep,
		temperature = `None`,
		pressure = `None`,
		nequil = `0`,
		nsave = `1000`,
		minimize = `True`,
		anisotropic = `False`,
		threads = `1`,
		verbose = `False`,
		kwargs
	)

Method for running a molecular dynamics simulation.

Required arguments: nsteps = (int) Number of total time steps timestep = (float) Time step in FEMTOSECONDS temperature = (float) Temperature control (Kelvin) pressure = (float) Pressure control (atmospheres) nequil = (int) Number of additional time steps at the beginning for equilibration nsave = (int) Step interval for saving and printing data minimize = (bool) Perform an energy minimization prior to dynamics threads = (int) Specify how many OpenMP threads to use

Returns simulation data: Rhos = (array) Density in kilogram m^-3 Potentials = (array) Potential energies Kinetics = (array) Kinetic energies Volumes = (array) Box volumes Dips = (3xN array) Dipole moments EComps = (dict) Energy components

Definition at line 916 of file tinkerio.py.

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◆ multipole_moments()

def src.tinkerio.TINKER.multipole_moments	(	self,
		shot = `0`,
		optimize = `True`,
		polarizability = `False`
	)

Return the multipole moments of the 1st snapshot in Debye and Buckingham units.

Definition at line 783 of file tinkerio.py.

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◆ normal_modes()

def src.tinkerio.TINKER.normal_modes	(	self,
		shot = `0`,
		optimize = `True`
	)

Definition at line 745 of file tinkerio.py.

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◆ optimize()

def src.tinkerio.TINKER.optimize	(	self,
		shot,
		method = `"newton"`,
		align = `True`,
		crit = `1e-4`
	)

Optimize the geometry and align the optimized geometry to the starting geometry.

Definition at line 567 of file tinkerio.py.

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◆ prepare()

def src.tinkerio.TINKER.prepare	(	self,
		pbc = `False`,
		kwargs
	)

Called by init ; prepare the temp directory and figure out the topology.

Definition at line 398 of file tinkerio.py.

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◆ readsrc()

def src.tinkerio.TINKER.readsrc	(	self,
		kwargs
	)

Called by init ; read files from the source directory.

Definition at line 341 of file tinkerio.py.

◆ setopts()

def src.tinkerio.TINKER.setopts	(	self,
		kwargs
	)

Called by init ; Set TINKER-specific options.

Definition at line 324 of file tinkerio.py.

Member Data Documentation

◆ A

src.tinkerio.TINKER.A

Definition at line 888 of file tinkerio.py.

◆ abskey

src.tinkerio.TINKER.abskey

Definition at line 502 of file tinkerio.py.

◆ AtomLists

src.tinkerio.TINKER.AtomLists

Definition at line 515 of file tinkerio.py.

◆ AtomMask

src.tinkerio.TINKER.AtomMask

If the coordinates do not come with TINKER suffixes then throw an error.

Call analyze to read information needed to build the atom lists. Parse the output of analyze.

Definition at line 514 of file tinkerio.py.

◆ B

src.tinkerio.TINKER.B

Definition at line 889 of file tinkerio.py.

◆ key

src.tinkerio.TINKER.key

Definition at line 344 of file tinkerio.py.

◆ md_trajectory

src.tinkerio.TINKER.md_trajectory

Definition at line 985 of file tinkerio.py.

◆ mol

src.tinkerio.TINKER.mol

Definition at line 347 of file tinkerio.py.

◆ pbc

src.tinkerio.TINKER.pbc

Definition at line 466 of file tinkerio.py.

◆ prm

src.tinkerio.TINKER.prm

Definition at line 345 of file tinkerio.py.

◆ rigid

src.tinkerio.TINKER.rigid

Attempt to set some TINKER options.

Definition at line 404 of file tinkerio.py.

◆ tinkerpath

src.tinkerio.TINKER.tinkerpath

The directory containing TINKER executables (e.g.

dynamic)

Definition at line 329 of file tinkerio.py.

◆ valkwd

src.tinkerio.TINKER.valkwd

Keyword args that aren't in this list are filtered out.

Definition at line 318 of file tinkerio.py.

◆ warn_vn

src.tinkerio.TINKER.warn_vn

Definition at line 319 of file tinkerio.py.

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

tinkerio.py

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ calltinker()

◆ energy()

◆ energy_dipole()

◆ energy_force()

◆ energy_force_one()

◆ energy_rmsd()

◆ evaluate_()

◆ get_charges()

◆ interaction_energy()

◆ molecular_dynamics()

◆ multipole_moments()

◆ normal_modes()

◆ optimize()

◆ prepare()

◆ readsrc()

◆ setopts()

Member Data Documentation

◆ A

◆ abskey

◆ AtomLists

◆ AtomMask

◆ B

◆ key

◆ md_trajectory

◆ mol

◆ pbc

◆ prm

◆ rigid

◆ tinkerpath

◆ valkwd

◆ warn_vn

◆ init()