peleffy.template.impact.WritableBond¶
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class
peleffy.template.impact.WritableBond(bond)[source]¶ Writable peleffy’s Bond class
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__init__(bond)[source]¶ It initializes a WritableBond object.
- Parameters
bond (a peleffy.topology.Bond) – The Bond to create the WritableBond with
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apply_lambda(attributes_to_modify, lambda_value, reverse=False, final_state=None)¶ Given a lambda value, it modifies a set of attributes of this topological element. A lambda equal to 0 will keep the original attributes of this topological element. A lambda equal to 1 will remove completely the effects of the attributes. This behavior will be the opposite when reverse is set to True.
- Parameters
attributes_to_modify (list[str]) – The list attribute names that will be modified
lambda_value (float) – A value between 0 and 1 that defined the lambda to apply to the attributes
reverse (bool) – When set to true the effects of lambda will be the opposite
final_state (a peleffy.topology.topology._TopologyElement object) – The topology element that represents the final state when lambda equals 1.0. Default is None, which means that the final state is not defined and therefore the topological element will disappear or will start from scratch
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static
dummy_to_writable(f)¶ It converts a returned DummyAtom to a WritableAtom.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – A WritableAtom object
- Return type
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static
in_angstrom(f)¶ It expresses a simtk.unit.Quantity in angstroms.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – simtk.unit.Quantity expressed in angstroms
- Return type
float
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static
in_deg(f)¶ It expresses a simtk.unit.Quantity in degrees.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – simtk.unit.Quantity expressed in degrees
- Return type
float
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static
in_elementarycharge(f)¶ It expresses a simtk.unit.Quantity in elementary charges.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – simtk.unit.Quantity expressed in elementary charges
- Return type
float
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static
in_kcal_angstrom2mol(f)¶ It expresses a simtk.unit.Quantity in kcal/angstrom2mol.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – simtk.unit.Quantity expressed in kcal/angstrom2mol
- Return type
float
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static
in_kcal_rad2mol(f)¶ It expresses a simtk.unit.Quantity in kcal/rad2mol.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – simtk.unit.Quantity expressed in kcal/rad2mol
- Return type
float
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static
in_kcalmol(f)¶ It expresses a simtk.unit.Quantity in kcal/mol.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – simtk.unit.Quantity expressed in kcal/mol
- Return type
float
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static
none_to_dummy(f)¶ It converts a returned None to a DummyAtom.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – A DummyAtom object
- Return type
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static
none_to_zero(f)¶ It converts a returned None to zero.
- Parameters
f (function) – The function to apply the decorator to
- Returns
out – It is set to zero in case that it is None
- Return type
function’s output
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set_atom1_idx(index)¶ It sets atom1’s index.
- Parameters
index (int) – The index of the first atom involved in this Bond
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set_atom2_idx(index)¶ It sets atom2’s index.
- Parameters
index (int) – The index of the second atom involved in this Bond
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set_index(index)¶ It sets the index of the bond.
- Parameters
index (int) – The index of this Bond object
Attributes
atom1_idxBond’s atom1 index.
atom2_idxBond’s atom2 index.
eq_distBond’s equilibrium distance.
indexBond’s index.
n_writable_attrsThe number of writable attributes this topological element has.
nameThe name that this topological element has.
spring_constantBond’s spring constant.
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