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 aSettings
object. Note, that theEntityHandle
is passed by reference and gets altered by rebuilding bonds, adding hydrogens and modification of terminal residues based on the information given by theSettings
/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 theTopology
. Note, that you can override theForcefield
parametrization if you add this particularInteraction
in a parameterized form in theBuildingBlock
Rename entity back to PDB naming if flag is set accordingly in settings
- Parameters:
entity (
ost.mol.EntityHandle
) – Entity for which to createTopology
- Raises:
RuntimeError
if settings has noForcefield
assigned- Raises:
RuntimeError
if there is a residue with no appropriateBuildingBlock
in theForcefield
- Raises:
RuntimeError
if there is aResidueHandle
not matching theBuildingBlock
definition in theForcefield
- Raises:
RuntimeError
if there is an interaction that has no parameters in the forcefield. ThisRuntimeError
can be supressed by setting the appropriate flag in theSettings
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 actualTopology
containing n particles, the indexing of the otherTopology
gets altered by adding n everywhere.- Parameters:
other (
Topology
) – Topology to merge in- Raises:
RuntimeError
if fudge parameters are not consistent- Raises:
RuntimeError
if currentTopology
contains charges but the other not- Raises:
RuntimeError
if currentTopology
contains sigmas but the other not- Raises:
RuntimeError
if currentTopology
contains epsilons but the other not- Raises:
RuntimeError
if currentTopology
contains GBSA Radii but the other not- Raises:
RuntimeError
if currentTopology
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 actualTopology
contains n particles, the indexing of the otherTopology
gets altered by adding n everywhere. This version of the Merge function assumes the current topology describes theEntityHandle
ent and the otherTopology
describes theEntityHandle
other_ent. During merging, all chains, residues, atoms and bonds from other_ent are pulled into ent in a way, that the currentTopology
is consistent with theEntityHandle
ent.- Parameters:
ent (
ost.mol.EntityHandle
) – Entity consistent with current topologyother (
Topology
) – Topology to merge inother_ent (
ost.mol.EntityHandle
) – Entity consistent with other
- Raises:
RuntimeError
if fudge parameters are not consistent- Raises:
RuntimeError
if currentTopology
contains charges but the other not- Raises:
RuntimeError
if currentTopology
contains sigmas but the other not- Raises:
RuntimeError
if currentTopology
contains epsilons but the other not- Raises:
RuntimeError
if currentTopology
contains GBSA Radii but the other not- Raises:
RuntimeError
if currentTopology
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 1index_two (
int
) – Index of particle 2bond_length (
float
) – Bond length in nmforce_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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3angle (
float
) – Angle in radiansforce_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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3angle (
float
) – Angle in radiansangle_force_constant (
float
) – Angle force constant kJ/mol/radian^2bond_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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4multiplicity (
int
) – Multiplicityphase (
float
) – Phase in radiansforce_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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4multiplicity (
int
) – Multiplicityphase (
float
) – Phase in radiansforce_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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4angle (
float
) – Angle in radiansforce_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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4index_five (
int
) – Index of particle 5dimension (
int
) – Dimension of CMapvalues (
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 1index_two (
int
) – Index of particle 2sigma (
float
) – Sigma in nmepsilon – 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 1index_two (
int
) – Index of particle 2distance (
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 1index_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 constrainedreference_pos (
ost.geom.Vec3
) – Reference position in Aforce_constant (
float
) – Force constant in kJ/mol/nm^2x_scale (
float
) – X-scaley_scale (
float
) – Y-scalez_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 1index_two (
int
) – Index of particle 2length (
float
) – Restraint length in nmforce_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 nmsigma (
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 particleepsilon (
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 particleradius (
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 particlecharge (
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 particlemass (
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 bondbond_length (
float
) – New bond length in nmforce_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 angleangle (
float
) – New angle in radiansforce_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 angleangle (
float
) – New angle in radiansangle_force_constant (
float
) – New angle force constant in kJ/mol/radian^2bond_length (
float
) – New bond length in nmbond_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 dihedralmultiplicity (
int
) – New periodicityphase (
float
) – New phase in radiansforce_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 impropermultiplicity (
int
) – New multiplicityphase (
float
) – New phase in radiansforce_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 improperangle (
float
) – New angle in radiansforce_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 CMapdimension (
int
) – New dimensionmap (
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 pairsigma (
float
) – New sigma in nmepsilon (
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 constraintdistance (
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 constraintref_position (
ost.geom.Vec3
) – New reference position in nmk (
float
) – New force constant in kJ/mol/nm^2x_scale (
float
) – New x-scaley_scale (
float
) – New y-scalez_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 restraintlength (
float
) – New restraint distance in nmk (
float
) – New force constant in kJ/mol/nm^2
- Raises:
RuntimeError
when index exceeds number of set harmonic distance restraints
- GetSigmas()¶
- Returns:
list
offloat
with previously set sigmas
- GetEpsilons()¶
- Returns:
list
offloat
with previously set epsilons
- GetGBSARadii()¶
- Returns:
list
offloat
with previously set GBSA radii
- GetOBCScalings()¶
- Returns:
list
offloat
with previously set OBC scalings
- GetCharges()¶
- Returns:
list
offloat
with previously set charges
- GetMasses()¶
- Returns:
list
offloat
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 1index_one – Index of particle 2
- Returns:
list
ofint
- 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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3
- Returns:
list
ofint
- 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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3
- Returns:
list
ofint
- 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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4
- Returns:
list
ofint
- 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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4
- Returns:
list
ofint
- 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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4
- Returns:
list
ofint
- 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 1index_two (
int
) – Index of particle 2index_three (
int
) – Index of particle 3index_four (
int
) – Index of particle 4index_five (
int
) – Index of particle 5
- Returns:
list
ofint
- 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 1index_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 1index_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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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
ofint
- 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