src.torsion_profile.TorsionProfileTarget Class Reference

Subclass of Target for fitting MM optimized geometries to QM optimized geometries. More...

Inheritance diagram for src.torsion_profile.TorsionProfileTarget:

Collaboration diagram for src.torsion_profile.TorsionProfileTarget:

Public Member Functions
def	__init__ (self, options, tgt_opts, forcefield)
def	read_reference_data (self)
	Read the reference ab initio data from a file such as qdata.txt. More...
def	indicate (self)
def	get (self, mvals, AGrad=False, AHess=False)

Public Attributes
	metadata
	ndim
	freeze_atoms
	mol
	Read in the coordinate files and get topology information from PDB. More...
	ns
	Number of snapshots. More...
	engine
	Option for how much data to write to disk. More...
	eqm
	Reference (QM) energies. More...
	qfnm
	The qdata.txt file that contains the QM energies and forces. More...
	smin
	wts
	PrintDict
	emm_orig
	objective

Detailed Description

Subclass of Target for fitting MM optimized geometries to QM optimized geometries.

Definition at line 24 of file torsion_profile.py.

Constructor & Destructor Documentation

__init__()

def src.torsion_profile.TorsionProfileTarget.__init__	(		self,
			options,
			tgt_opts,
			forcefield
	)

Definition at line 25 of file torsion_profile.py.

Member Function Documentation

get()

def src.torsion_profile.TorsionProfileTarget.get	(		self,
			mvals,
			AGrad = False,
			AHess = False
	)

Definition at line 118 of file torsion_profile.py.

indicate()

def src.torsion_profile.TorsionProfileTarget.indicate

(

self

)

Definition at line 112 of file torsion_profile.py.

Here is the call graph for this function:

read_reference_data()

def src.torsion_profile.TorsionProfileTarget.read_reference_data

(

self

)

Read the reference ab initio data from a file such as qdata.txt.

After reading in the information from qdata.txt, it is converted into the GROMACS energy units (kind of an arbitrary choice).

Definition at line 68 of file torsion_profile.py.

Member Data Documentation

emm_orig

src.torsion_profile.TorsionProfileTarget.emm_orig

Definition at line 162 of file torsion_profile.py.

engine

src.torsion_profile.TorsionProfileTarget.engine

Option for how much data to write to disk.

Harmonic restraint for non-torsion atoms in kcal/mol. Attenuate the weights as a function of energy Energy denominator for objective function Set upper cutoff energy Read in the reference data. Build keyword dictionaries to pass to engine. Create engine object.

Definition at line 60 of file torsion_profile.py.

eqm

src.torsion_profile.TorsionProfileTarget.eqm

Reference (QM) energies.

Definition at line 71 of file torsion_profile.py.

freeze_atoms

src.torsion_profile.TorsionProfileTarget.freeze_atoms

Definition at line 33 of file torsion_profile.py.

metadata

src.torsion_profile.TorsionProfileTarget.metadata

Definition at line 31 of file torsion_profile.py.

mol

src.torsion_profile.TorsionProfileTarget.mol

Read in the coordinate files and get topology information from PDB.

Definition at line 37 of file torsion_profile.py.

ndim

src.torsion_profile.TorsionProfileTarget.ndim

Definition at line 32 of file torsion_profile.py.

ns

src.torsion_profile.TorsionProfileTarget.ns

Number of snapshots.

Definition at line 42 of file torsion_profile.py.

objective

src.torsion_profile.TorsionProfileTarget.objective

Definition at line 196 of file torsion_profile.py.

PrintDict

src.torsion_profile.TorsionProfileTarget.PrintDict

Definition at line 120 of file torsion_profile.py.

qfnm

src.torsion_profile.TorsionProfileTarget.qfnm

The qdata.txt file that contains the QM energies and forces.

Definition at line 73 of file torsion_profile.py.

smin

src.torsion_profile.TorsionProfileTarget.smin

Definition at line 89 of file torsion_profile.py.

wts

src.torsion_profile.TorsionProfileTarget.wts

Definition at line 98 of file torsion_profile.py.

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

• torsion_profile.py