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The NonbondXFFA module provides a method to construct an exclusion list for one of two Energy terms: SoftSphereX or VanderWaalsX.
The exclusions are based on the initial structure of the model; use
this class only if you need this functionality. This module is located
in Yup/Models/Null/. The import statement is some variant of: from
Yup.Models.Null.NonbondXFFA import NonbondXFFA.
The NonbondXFFA Class
The NonbondXFFA module defines a class NonbondXFFA and the constructor function is:
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Name
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Arguments
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Return |
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NonbondXFFA
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required: label, optional: SSX, settings
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- |
| Argument |
Type |
Preset |
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label
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A string to be used to identify this term.
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- |
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SSX
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Whether to use the SoftSphereX term (if not zero) or the VanderWaalsX term (if zero)
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1 |
| settings |
If
not the value None, this must be a dictionary containing argument-value
pairs for the constructor functions of the term selected in the
previous argument. |
None |
This class must be mixed-in with the FFA class from the Yup.Models.Null.FFA module.
If a dictionary is supplied for settings, it must have an entry for all
the optional arguments of the appropriate constructor functions: SoftSphereX() or VanderWaalsX().
Method
The Exclude() method creates the exclusion list of atom pairs that are within a multiple of the contact distance.
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Name
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Arguments
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Return |
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Exclude
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required: atoms, coords; optional: cutratio
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- |
| Argument |
Type |
Preset |
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atoms
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Tuple of atom AtomMaps
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- |
| coords |
Corresponding tuple of tuples of coordinates |
- |
| cutratio |
A multiplier for the actual contact distance |
1.01 |
The atoms tuple is assumed to contain all the atoms of the nascent model and coords is assumed to contain the corresponding coordinates.
The
contact distance for the SoftSphereX term is uncontroversial. The
contact distance for the VanderWaalsX term is taken as twice the
distance of minimum energy. In either case, these values are multipled
by the factor cutratio to yield the cutoff distance.
Each atom pair is then examined. If two atoms are within the cutoff distance the pair is added to the exclusion list.
Exclusions
are normally based on bonding proximity, i.e., the number of bonds that
separate a pair. Use this class only if you need to eliminate nonbond
contacts using the procedure of Exclude().
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