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