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Topology

The Topology object is an abstract representation of a protein structure or any combination of particles that interact with each other in some way. Being initialized with a list of masses representing the particles, the topology allows to define arbitrary forces between these particles. The Topology gets internally translated to a molecular mechanics system as soon as a Simulation is set up. To make setting up a Topology more convenient, the TopologyCreator class allows to create a Topology based on an mm Settings object, that should suffice for most needs.

Automatically create topologies

class TopologyCreator
Create(entity, settings)

Creates a topology given an EntityHandle and a Settings object. Note, that the EntityHandle is passed by reference and gets altered by rebuilding bonds, adding hydrogens and modification of terminal residues based on the information given by the Settings/Forcefield. The Topology Creation process consists of:

  1. Rename to the Gromacs standard
  2. Kill all bonds
  3. Build difulfide bonds if flag is set in settings
  4. Rename residues/atoms to the standard defined in the forcefield
  5. Extract the building blocks from the forcefield for every residue
  6. Apply BlockModifiers on termini and reconstruct hydrogens with HydrogenConstructors
  7. Reconnect based on the connectivity definitions in the building blocks
  8. Check, whether the residues match with the building blocks
  9. Extract bonds/angles etc. based on the flags in the settings
  10. Impropers and CMaps get only extracted when they are defined in the BuildingBlock
  11. Add Parametrization from Forcefield to the Topology. Note, that you can override the Forcefield parametrization if you add this particular Interaction in a parameterized form in the BuildingBlock
  12. Rename entity back to PDB naming if flag is set accordingly in settings
Parameters:
Raises:

RuntimeError if settings has no Forcefield assigned

Raises:

RuntimeError if there is a residue with no appropriate BuildingBlock in the Forcefield

Raises:

RuntimeError if there is a ResidueHandle not matching the BuildingBlock definition in the Forcefield

Raises:

RuntimeError if there is an interaction that has no parameters in the forcefield. This RuntimeError can be supressed by setting the appropriate flag in the Settings object.

The Topology Class

class Topology(masses)
Parameters:masseslist of the particles’masses
Save(filename)

Dump Toplogy into binary file

Parameters:filename (str) – Name of file
Load(filename)

Load binary topology from disk

Parameters:filename (str) – Name of file
Returns:loaded Topology
Raises:RuntimeError when file can’t be found
Merge(other)

Merges in another Topology and adds all their particles and interactions. Assuming the actual Topology containing n particles, the indexing of the other Topology gets altered by adding n everywhere.

Parameters:other (Topology) – Topology to merge in
Raises:RuntimeError if fudge parameters are not consistent
Raises:RuntimeError if current Topology contains charges but the other not
Raises:RuntimeError if current Topology contains sigmas but the other not
Raises:RuntimeError if current Topology contains epsilons but the other not
Raises:RuntimeError if current Topology contains GBSA Radii but the other not
Raises:RuntimeError if current Topology contains OBC scalings but the other not
Merge(ent, other, other_ent)

Merges in another Topology and adds all their particles and interactions. Assuming the actual Topology contains n particles, the indexing of the other Topology gets altered by adding n everywhere. This version of the Merge function assumes the current topology describes the EntityHandle ent and the other Topology describes the EntityHandle other_ent. During merging, all chains, residues, atoms and bonds from other_ent are pulled into ent in a way, that the current Topology is consistent with the EntityHandle ent.

Parameters:
Raises:

RuntimeError if fudge parameters are not consistent

Raises:

RuntimeError if current Topology contains charges but the other not

Raises:

RuntimeError if current Topology contains sigmas but the other not

Raises:

RuntimeError if current Topology contains epsilons but the other not

Raises:

RuntimeError if current Topology contains GBSA Radii but the other not

Raises:

RuntimeError if current Topology contains OBC scalings but the other not

Raises:

RuntimeError if the number of atoms in one of the entities is not consistent with their related topologies.

Raises:

RuntimeError other_ent contains a chain with a name already present in ent.

AddHarmonicBond(index_one, index_two, bond_length, force_constant)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • bond_length (float) – Bond length in nm
  • force_constant (float) – Force constant in kJ/mol/nm^2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

AddHarmonicAngle(index_one, index_two, index_three, angle, force_constant)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • angle (float) – Angle in radians
  • force_constant (float) – Force constant in kJ/mol/radian^2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

AddUreyBradleyAngle(index_one, index_two, index_three, angle, angle_force_constant, bond_length, bond_force_constant)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • angle (float) – Angle in radians
  • angle_force_constant (float) – Angle force constant kJ/mol/radian^2
  • bond_length – Bond length in nm
  • bond_force_constant (float) – Bond force constant kJ/mol/nm^2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

AddPeriodicDihedral(index_one, index_two, index_three, index_four, multiplicity, phase, force_constant)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
  • multiplicity (int) – Multiplicity
  • phase (float) – Phase in radians
  • force_constant (float) – Force constant in kJ/mol/radian^2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

AddPeriodicImproper(index_one, index_two, index_three, index_four, multiplicity, phase, force_constant)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
  • multiplicity (int) – Multiplicity
  • phase (float) – Phase in radians
  • force_constant (float) – Force constant in kJ/mol/radian^2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

AddHarmonicImproper(index_one, index_two, index_three, index_four, angle, force_constant)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
  • angle (float) – Angle in radians
  • force_constant (float) – Force constant kJ/mol/radian^2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

AddCMap(index_one, index_two, index_three, index_four, index_five, dimension, values)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
  • index_five (int) – Index of particle 5
  • dimension (int) – Dimension of CMap
  • values (list) – Map of size dimension * dimension describing the correction map in kJ/mol. The values have to be ordered like (phi1,psi1),(phi1,psi2)...(phi1,psin), (phi2,psi1),(phi2,psi2)...(phi2,psin), ...(phin,psin). the range for phi and psi are [-pi,pi[
Returns:

int index of added interaction

Raises:

RuntimeError when size of values is not dimension * dimension or index exceeds number of particles.

AddLJPair(index_one, index_two, sigma, epsilon)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • sigma (float) – Sigma in nm
  • epsilon – Epsilon in kJ/mol
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles or when particular LJPair is already parameterized

AddDistanceConstraint(index_one, index_two, distance)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • distance (float) – Constraint distance in nm
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles or when particular distance constraint is already parameterized

AddExclusion(index_one, index_two)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles or when particular exclusion is already set

AddPositionConstraint(index)
Parameters:index (int) – Index of particle to be constrained
Raises:RuntimeError when index exceeds number of particles
AddHarmonicPositionRestraint(index, reference_pos, force_constant, x_scale=1.0, y_scale=1.0, z_scale=1.0)

Adds a harmonic position restraint for a particle in the form: force_constant*(x_scale*(x-x0)^2+y_scale*(y-y0)^2+z_scale*(z-z0)^2)

Parameters:
  • index (int) – Index of particle to be constrained
  • reference_pos (ost.geom.Vec3) – Reference position in A
  • force_constant (float) – Force constant in kJ/mol/nm^2
  • x_scale (float) – X-scale
  • y_scale (float) – Y-scale
  • z_scale (float) – Z-scale
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

AddHarmonicDistanceRestraint(index_one, index_two, length, force_constant)

Adds a force between two particles in the form: force_constant * (b-b0)^2

Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • length (float) – Restraint length in nm
  • force_constant (float) – Force constant in kJ/mol/nm^2
Returns:

int index of added interaction

Raises:

RuntimeError when index exceeds number of particles

ResetPositionConstraints()

Removes all position constraints

ResetExclusions()

Removes all set exclusions

SetSigmas(sigmas)
Parameters:sigmas (list (float)) – Sigma parameters for all particles in nm
Raises:RuntimeError when list size is inconsistent with number of particles
SetSigma(index, sigma)
Parameters:
  • index (int) – Index of particle in nm
  • sigma (float) – Sigma
Raises:

RuntimeError when index exceeds number of particles

SetEpsilons(epsilons)
Parameters:epsilons (list (float)) – Epsilon parameters for all particles in kJ/mol
Raises:RuntimeError when list size is inconsistent with number of particles
SetEpsilon(index, epsilon)
Parameters:
  • index (int) – Index of particle
  • epsilon (float) – Epsilon in kJ/mol
Raises:

RuntimeError when index exceeds number of particles

SetGBSARadii(radii)
Parameters:radii (list (float)) – GBSA radii for all particles in nm
Raises:RuntimeError when list size is inconsistent with number of particles
SetGBSARadius(index, radius)
Parameters:
  • index (int) – Index of particle
  • radius (float) – GBSA radius in nm
Raises:

RuntimeError when index exceeds number of particles

SetOBCScalings(scalings)
Parameters:scalings (list (float)) – OBC scaling factors for all particles
Raises:RuntimeError when list size is inconsistent with number of particles
SetOBCScaling(index, scaling)
Parameters:
  • index (Index of particle) – Index of particle
  • scaling (float) – OBC scaling factor
Raises:

RuntimeError when index exceeds number of particles

SetCharges(charges)
Parameters:charges (list (float)) – Charges for all particles
Raises:RuntimeError when list size is inconsistent with number of particles
SetCharge(index, charge)
Parameters:
  • index (int) – Index of particle
  • charge (float) – Charge
Raises:

RuntimeError when index exceeds number of particles

SetMasses(masses)
Parameters:masses (list (float)) – Masses for all particles
Raises:RuntimeError when list size is inconsistent with number of particles
SetMass(index, mass)
Parameters:
  • index (int) – Index of particle
  • mass (float) – Mass
Raises:

RuntimeError when index exceeds number of particles

SetFudgeQQ(fudge)
Parameters:fudge (float) – Dampening factor for electrostatic 1,4 interactions
SetFudgeLJ(fudge)
Parameters:fudge (float) – Dampening factor for LJ 1,4 interactions
GetHarmonicBondParameters(index)
Parameters:index (int) – Index of harmonic bond
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set harmonic bonds
GetHarmonicAngleParameters(index)
Parameters:index (int) – Index of harmonic angle
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set harmonic angles
GetUreyBradleyAngleParameters(index)
Parameters:index (int) – Index of Urey-Bradley angle
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set Urey-Bradley angles
GetPeriodicDiheralParameters(index)
Parameters:index (int) – Index of periodic dihedral
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set periodic dihedrals
GetPeriodicImproperParameters(index)
Parameters:index (int) – Index of periodic improper
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set periodic impropers
GetHarmonicImproperParameters(index)
Parameters:index (int) – Index of harmonic improper
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set harmonic impropers
GetCMapParameters(index)
Parameters:index (int) – Index of CMap
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set cmaps
GetLJPairParameters(index)
Parameters:index (int) – Index of LJ pair
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set lj pairs
GetDistanceConstraintParameters(index)
Parameters:index (int) – Index of distance constraint
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set distance constraints
GetHarmonicPositionRestraintParameters(index)
Parameters:index (int) – Index of harmonic position restraint
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set harmonic position restraints
GetHarmonicDistanceRestraintParameters(index)
Parameters:index (int) – Index of harmonic distance restraint
Returns:tuple containing the indices of the involved particles and the set parameters
Raises:RuntimeError when index exceeds number of set harmonic distance restraints
SetHarmonicBondParameters(index, bond_length, force_constant)

Replaces existing parameters for particular interaction

Parameters:
  • index (int) – Index of harmonic bond
  • bond_length (float) – New bond length in nm
  • force_constant (float) – New force constant in kJ/mol/nm^2
Raises:

RuntimeError when index exceeds number of set harmonic bonds

SetHarmonicAngleParameters(index, angle, force_constant)

Replaces existing parameters for particular interaction

Parameters:
  • index (int) – Index of harmonic angle
  • angle (float) – New angle in radians
  • force_constant (float) – New force constant kJ/mol/radian^2
Raises:

RuntimeError when index exceeds number of set harmonic angles

SetUreyBradleyAngleParameters(index, angle, angle_force_constant,
bond_length, bond_force_constant)

Replaces existing parameters for particular interaction

Parameters:
  • index (int) – Index of Urey-Bradley angle
  • angle (float) – New angle in radians
  • angle_force_constant (float) – New angle force constant in kJ/mol/radian^2
  • bond_length (float) – New bond length in nm
  • bond_force_constant (float) – New bond force constant in kJ/mol/nm^2
Raises:

RuntimeError when index exceeds number of set Urey-Bradley angles

SetPeriodicDiheralParameters(index, multiplicity, phase, force_constant)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of periodic dihedral
  • multiplicity (int) – New periodicity
  • phase (float) – New phase in radians
  • force_constant (float) – New force constant in kJ/mol/radian^2
Raises:

RuntimeError when index exceeds number of set periodic dihedrals

SetPeriodicImproperParameters(index, multiplicity, phase, force_constant)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of periodic improper
  • multiplicity (int) – New multiplicity
  • phase (float) – New phase in radians
  • force_constant (float) – New force constant kJ/mol/radian^2
Raises:

RuntimeError when index exceeds number of set periodic impropers

SetHarmonicImproperParameters(index, angle, force_constant)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of harmonic improper
  • angle (float) – New angle in radians
  • force_constant (float) – New force constant kJ/mol/radian^2
Raises:

RuntimeError when index exceeds number of set harmonic impropers

SetCMapParameters(index, dimension, map)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of CMap
  • dimension (int) – New dimension
  • map (list) – New CMap of format described in the AddCMap function.
Raises:

RuntimeError when index exceeds number of set cmaps or size of map is not dimension*dimension

SetLJPairParameters(index, sigma, epsilon)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of LJ pair
  • sigma (float) – New sigma in nm
  • epsilon (float) – New epsilon in kJ/mol
Raises:

RuntimeError when index exceeds number of set lj pairs

SetDistanceConstraintParameters(index, distance)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of distance constraint
  • distance (float) – New constraint distance in nm
Raises:

RuntimeError when index exceeds number of set distance constraints

SetHarmonicPositionRestraintParameters(index, ref_position, k, x_scale=1.0, y_scale=1.0, z_scale=1.0)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of harmonic position constraint
  • ref_position (ost.geom.Vec3) – New reference position in nm
  • k (float) – New force constant in kJ/mol/nm^2
  • x_scale (float) – New x-scale
  • y_scale (float) – New y-scale
  • z_scale (float) – New z-scale
Raises:

RuntimeError when index exceeds number of set harmonic position restraints

SetHarmonicDistanceRestraintParameters(index, length, k)

Replaces existing parameters for a particular interaction

Parameters:
  • index (int) – Index of harmonic distance restraint
  • length (float) – New restraint distance in nm
  • k (float) – New force constant in kJ/mol/nm^2
Raises:

RuntimeError when index exceeds number of set harmonic distance restraints

GetSigmas()
Returns:list of float with previously set sigmas
GetEpsilons()
Returns:list of float with previously set epsilons
GetGBSARadii()
Returns:list of float with previously set GBSA radii
GetOBCScalings()
Returns:list of float with previously set OBC scalings
GetCharges()
Returns:list of float with previously set charges
GetMasses()
Returns:list of float with previously set masses
GetSigma(particle_index)
Parameters:particle_index (int) – Index of particle
Returns:float
Raises:RuntimeError when particle_index exceeds number of particles or sigmas have not been set
GetEpsilon(particle_index)
Parameters:particle_index (int) – Index of particle
Returns:float
Raises:RuntimeError when particle_index exceeds number of particles or epsilons have not been set
GetGBSARadius(particle_index)
Parameters:particle_index (int) – Index of particle
Returns:float
Raises:RuntimeError when particle_index exceeds number of particles or gbsa_radii have not been set
GetOBCScaling(particle_index)
Parameters:particle_index (int) – Index of particle
Returns:float
Raises:RuntimeError when particle_index exceeds number of particles or obc scalings have not been set
GetCharge(particle_index)
Parameters:particle_index (float) – Index of particle
Returns:float
Raises:RuntimeError when particle_index exceeds number of particles or charges have not been set
GetMass(particle_index)
Parameters:particle_index (int) – Index of particle
Returns:float
Raises:RuntimeError when particle_index exceeds number of particles
GetHarmonicBondIndices(index_one, index_two)
Parameters:
  • index_one (int) – Index of particle 1
  • index_one – Index of particle 2
Returns:

list of int - Indices of all harmonic bonds acting on given particle pair

Raises:

RuntimeError when an index exceeds number of particles in topology

GetHarmonicAngleIndices(index_one, index_two, index_three)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
Returns:

list of int - Indices of all harmonic angles acting on given particles

Raises:

RuntimeError when an index exceeds number of particles in topology

GetUreyBradleyAngleIndices(index_one, index_two, index_three)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
Returns:

list of int - Indices of all Urey-Bradley angles acting on given particles

Raises:

RuntimeError when an index exceeds number of particles in topology

GetPeriodicDihedralIndices(index_one, index_two, index_three, index_four)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
Returns:

list of int - Indices of all periodic dihedrals acting on given particles

Raises:

RuntimeError when an index exceeds number of particles in topology

GetPeriodicImpropersIndices(index_one, index_two, index_three, index_four)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
Returns:

list of int - Indices of all periodic impropers acting on given particles

Raises:

RuntimeError when an index exceeds number of particles in topology

GetHarmonicImpropersIndices(index_one, index_two, index_three, index_four)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
Returns:

list of int - Indices of all harmonic impropers acting on given particles

Raises:

RuntimeError when an index exceeds number of particles in topology

GetCMapIndices(index_one, index_two, index_three, index_four, index_five)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
  • index_three (int) – Index of particle 3
  • index_four (int) – Index of particle 4
  • index_five (int) – Index of particle 5
Returns:

list of int - Indices of all cmaps acting on given particles

Raises:

RuntimeError when an index exceeds number of particles in topology

GetLJPairIndex(index_one, index_two)
Parameters:
  • index_one (int) – Index of particle 1
  • index_two (int) – Index of particle 2
Returns:

int Index of LJPair acting on particles, -1 if there is none

Raises:

RuntimeError when an index exceeds number of particles in topology

GetDistanceConstraintIndex(index_one, index_two)
Parameters:
  • index_one (int) – Index of particle 1
  • index_one – Index of particle 2
Returns:

int - Index of distance constraint acting on particles, -1 if there is none

Raises:

RuntimeError when an index exceeds number of particles in topology

GetHarmonicBondIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all harmonic bonds this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetHarmonicAngleIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all harmonic angles this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetUreyBradleyAngleIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all Urey-Bradley angles this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetPeriodicDihedralIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all periodic dihedrals this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetPeriodicImproperIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all periodic impropers this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetHarmonicImproperIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all harmonic impropers this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetCMapIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all cmaps this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetLJPairIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all LJ pairs this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetDistanceConstraintIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all distance constraints this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetHarmonicPositionRestraintIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all harmonic position restraints this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetHarmonicDistanceRestraintIndices(index)
Parameters:index (int) – Index of particle
Returns:list of int - Indices of all harmonic distance restraints this particular particle is involved in
Raises:RuntimeError when index exceeds number of particles in topology
GetNumParticles()
Returns:int
GetNumHarmonicBonds()
Returns:int
GetNumHarmonicAngles()
Returns:int
GetNumUreyBradleyAngles()
Returns:int
GetNumPeriodicDihedrals()
Returns:int
GetNumPeriodicImpropers()
Returns:int
GetNumHarmonicImpropers()
Returns:int
GetNumCMaps()
Returns:int
GetNumLJPairs()
Returns:int
GetNumDistanceConstraints()
Returns:int
GetNumPositionConstraints()
Returns:int
GetNumHarmonicPositionRestraints()
Returns:int
GetNumHarmonicDistanceRestraints()
Returns:int
GetNumExclusions()
Returns:int

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