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:

Rename to the Gromacs standard
Kill all bonds
Build difulfide bonds if flag is set in settings
Rename residues/atoms to the standard defined in the forcefield
Extract the building blocks from the forcefield for every residue
Apply BlockModifiers on termini and reconstruct hydrogens with HydrogenConstructors
Reconnect based on the connectivity definitions in the building blocks
Check, whether the residues match with the building blocks
Extract bonds/angles etc. based on the flags in the settings
Impropers and CMaps get only extracted when they are defined in the BuildingBlock
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
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

Topology¶

Automatically create topologies¶

The Topology Class¶

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