Interactions¶

The FuncType enum¶

Every Interaction is linked to one particular FuncType describing the types of interactions supported by OpenStructure. There are 15 possible values with Invalid defining an unknown interaction:

HarmonicBond, HarmonicAngle, UreyBradleyAngle, PeriodicDihedral, PeriodicImproper, HarmonicImproper, CMap, LJ, LJPair, GBSA, DistanceConstraint, Exclusion, HarmonicPositionRestraint, HarmonicDistanceRestraint, Invalid

The implementation guarantees that the parameter related to atom types, names, parameters are checked regarding their dimension (e.g. 3 atoms and 2 parameters for a harmonic angle)

Interaction Parametrization¶

• HarmonicBond, Interacting Particles: 2, Num Parameters: 2
  1. float bond length in nm
  2. float force constant in kJ/mol/nm^2
• HarmonicAngle, Interacting Particles: 3, Num Parameters: 2
  1. float angle in radians
  2. float force constant in kJ/mol/radian^2
• UreyBradleyAngle, Interacting Particles: 3, Num Parameters: 4
  1. float angle in radians
  2. float angle force constant in kJ/mol/radian^2
  3. float bond length in nm
  4. float bond force constant in kJ/mol/nm^2
• PeriodicDihedral, Interacting Particles: 4, Num Parameters: 3
  1. int multiplicity
  2. float phase in radians
  3. float force constant in kJ/mol/radian^2
• PeriodicImproper, Interacting Particles: 4, Num Parameters: 3
  1. int multiplicity
  2. float phase in radians
  3. float force constant in kJ/mol/radian^2
• HarmonicImproper, Interacting Particles: 4, Num Parameters: 2
  1. float angle in radians
  2. float force constant in kJ/mol/radian^2
• CMap, Interacting Particles: 5, Num Parameters: n*n+1
  1. list of float of size n*n+1, first value describes the dimension n of the cmap, the other n*n values describe the correction map in kJ/mol in the ordering (phi1,psi1),(phi1,psi2)... and torsion angles in [-pi,pi] (will be converted to the format OpenMM prefers)
• LJ, Interacting Particles: 1, Num Parameters: 2
  1. float sigma in nm
  2. float epsilon in kJ/mol
• LJPair, Interacting Particles: 2, Num Parameters: 2
  1. float sigma in nm
  2. float epsilon in kJ/mol
• GBSA, Interacting Particles: 1, Num Parameters: 2
  1. float GBSA radius in nm
  2. float OBC scaling factor
• DistanceConstraint, Interacting Particles: 2, Num Parameters: 1
  1. float constraint distance
• Exclusion, Interacting Particles: 2, Num Parameters: 0
• HarmonicPositionRestraint, Interacting Particles: 1, Num Parameters: 7
  1. float ref pos x
  2. float ref pos y
  3. float ref pos z
  4. float force constant
  5. float x_scale
  6. float y_scale
  7. float z_scale
• HarmonicDistanceRestraint, Interacting Particles: 2, Num Parameters: 2
  1. float restraint length
  2. float force constant

The Interaction Class¶

class Interaction(func_type)¶

Parameters:	func_type – FuncType defining a particular interaction

SetTypes(types)¶

Sets the forcefield specific atom types.

Parameters:	types (list) – Strings describing the force field specific atom types.
Raises:	RuntimeError when size of input is not consistent with the interactions functype

SetNames(names)¶

Sets atom names

Parameters:	names (list) – Strings describing the atom names
Raises:	RuntimeError when size of input is not consistent with the interactions functype

SetParam(param)¶

Sets interaction specific parameters.

Parameters:	param (list) – Float values .
Raises:	RuntimeError when size of input is not consistent with the interactions functype

GetTypes()¶

Get previously set types

Returns:	list

GetNames()¶

Get previously set names

Returns:	list

GetParam()¶

Get previously set parameters

Returns:	list

GetAtoms(residue)¶

Returns an AtomHandleList containing the atoms in residue matching the atom names of the interaction

Parameters:	residue (ResidueHandle) – Residue from which atoms are extracted
Returns:	AtomHandleList
Raises:	RuntimeError when an atom cannot be found in residue

GetFuncType()¶

Returns the functype enum of the interaction

Returns:	FuncType

ReplaceAtom(name, new_name, new_type)¶

Searches for given atom name. If found, this particular atom name gets changed to new_name. If the atom types are set as well, the associated atom type gets also reset to new_type.

Parameters:	name (str) – Name of atom to be replaces new_name (str) – Its new name new_type (str) – Its new type
Returns:	bool whether replacement was successful or not

MatchTypes(atom_types)¶

Checks, whether the given types match the internal types. The match can be “as is” or in reversed order

Parameters:	atom_types (list) – Atom types to be matched
Returns:	bool

MatchNames(atom_names)¶

Checks, whether the given names match the internal names. The match can be “as is” or in reversed order

Parameters:	atom_names (list) – Atom names to be matched
Returns:	bool

HasName(name)¶

Checks, whether the given name is present in the internal names

Parameters:	name (str) – Name to be checked
Returns:	bool

HasType(type)¶

Checks, whether the given type is present in the internal types

Parameters:	type (str) – Type to be checked
Returns:	bool

IsParametrized()¶

Checks, whether the parameters have been set

Returns:	bool

HasTypeWildcard()¶

Checks, whether one of the types is a wildcard (‘X’)

Returns:	bool

HasNameWildcard()¶

Checks, whether one of the names is a wildcard (‘X’)

Returns:	bool