src.ffyapf Namespace Reference

Classes
class	BackedUpDict
class	FF
	Force field class. More...

Functions
def	determine_fftype (ffname, verbose=False)
	Determine the type of a force field file. More...
def	rs_override (rsfactors, termtype, Temperature=298.15)
	This function takes in a dictionary (rsfactors) and a string (termtype). More...

Variables
	logger = getLogger(__name__)
dictionary	FF_Extensions
dictionary	FF_IOModules

Function Documentation

determine_fftype()

def src.ffyapf.determine_fftype	(		ffname,
			verbose = False
	)

Determine the type of a force field file.

It is possible to specify the file type explicitly in the input file using the syntax 'force_field.ext:type'. Otherwise this function will try to determine the force field type by extension.

Definition at line 156 of file ffyapf.py.

rs_override()

def src.ffyapf.rs_override	(		rsfactors,
			termtype,
			Temperature = 298.15
	)

This function takes in a dictionary (rsfactors) and a string (termtype).

If termtype matches any of the strings below, rsfactors[termtype] is assigned to one of the numbers below.

This is LPW's attempt to simplify the rescaling factors.

Parameters

[out]	rsfactors	The computed rescaling factor.
[in]	termtype	The interaction type (corresponding to a physical unit)
[in]	Temperature	The temperature for computing the kT energy scale

Definition at line 1668 of file ffyapf.py.

Variable Documentation

FF_Extensions

dictionary src.ffyapf.FF_Extensions

Initial value:

=  {
    "itp": "gmx",
    "top": "gmx",
    "in": "qchem",
    "prm": "tinker",
    "gen": "custom",
    "xml": "openmm",
    "offxml": "smirnoff",
    "frcmod": "frcmod",
    "mol2": "mol2",
    "gbs": "gbs",
    "grid": "grid"
}

Definition at line 123 of file ffyapf.py.

FF_IOModules

dictionary src.ffyapf.FF_IOModules

Initial value:

=  {
    "gmx": gmxio.ITP_Reader,
    "qchem": qchemio.QCIn_Reader,
    "tinker": tinkerio.Tinker_Reader,
    "custom": custom_io.Gen_Reader,
    "openmm": openmmio.OpenMM_Reader,
    "smirnoff": smirnoffio.SMIRNOFF_Reader,
    "frcmod": amberio.FrcMod_Reader,
    "mol2": amberio.Mol2_Reader,
    "gbs": psi4io.GBS_Reader,
    "grid": psi4io.Grid_Reader
}

Definition at line 137 of file ffyapf.py.

logger

src.ffyapf.logger = getLogger(__name__)

Definition at line 116 of file ffyapf.py.