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:

• entity (ost.mol.EntityHandle) – Entity for which to create Topology

• settings (Settings) – Settings to control Topology buildup

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:

masses – list 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:

• ent (ost.mol.EntityHandle) – Entity consistent with current topology

• other (Topology) – Topology to merge in

• other_ent (ost.mol.EntityHandle) – Entity consistent with other

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