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
- settings (
Settings
) – Settings to controlTopology
buildup
Raises: RuntimeError
if settings has noForcefield
assignedRaises: 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 fileReturns: 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 inRaises: RuntimeError
if fudge parameters are not consistentRaises: RuntimeError
if currentTopology
contains charges but the other notRaises: RuntimeError
if currentTopology
contains sigmas but the other notRaises: RuntimeError
if currentTopology
contains epsilons but the other notRaises: RuntimeError
if currentTopology
contains GBSA Radii but the other notRaises: 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 topology - other (
Topology
) – Topology to merge in - other_ent (
ost.mol.EntityHandle
) – Entity consistent with other
Raises: RuntimeError
if fudge parameters are not consistentRaises: RuntimeError
if currentTopology
contains charges but the other notRaises: RuntimeError
if currentTopology
contains sigmas but the other notRaises: RuntimeError
if currentTopology
contains epsilons but the other notRaises: RuntimeError
if currentTopology
contains GBSA Radii but the other notRaises: RuntimeError
if currentTopology
contains OBC scalings but the other notRaises: 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.- 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 interactionRaises: RuntimeError
when index exceeds number of particles- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles- index_one (
-
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 interactionRaises: RuntimeError
when size of values is not dimension * dimension or index exceeds number of particles.- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles or when particular LJPair is already parameterized- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles or when particular distance constraint is already parameterized- index_one (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles or when particular exclusion is already set- index_one (
-
AddPositionConstraint
(index)¶ Parameters: index ( int
) – Index of particle to be constrainedRaises: 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 nm - 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 interactionRaises: RuntimeError
when index exceeds number of particles- index (
-
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 interactionRaises: RuntimeError
when index exceeds number of particles- index_one (
-
ResetPositionConstraints
()¶ Removes all position constraints
-
ResetExclusions
()¶ Removes all set exclusions
-
SetSigmas
(sigmas)¶ Parameters: sigmas ( list
(float
)) – Sigma parameters for all particles in nmRaises: 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- index (
-
SetEpsilons
(epsilons)¶ Parameters: epsilons ( list
(float
)) – Epsilon parameters for all particles in kJ/molRaises: 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- index (
-
SetGBSARadii
(radii)¶ Parameters: radii ( list
(float
)) – GBSA radii for all particles in nmRaises: 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- index (
-
SetOBCScalings
(scalings)¶ Parameters: scalings ( list
(float
)) – OBC scaling factors for all particlesRaises: 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 particlesRaises: 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- index (
-
SetMasses
(masses)¶ Parameters: masses ( list
(float
)) – Masses for all particlesRaises: 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- index (
-
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 bondReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set harmonic bonds
-
GetHarmonicAngleParameters
(index)¶ Parameters: index ( int
) – Index of harmonic angleReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set harmonic angles
-
GetUreyBradleyAngleParameters
(index)¶ Parameters: index ( int
) – Index of Urey-Bradley angleReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set Urey-Bradley angles
-
GetPeriodicDiheralParameters
(index)¶ Parameters: index ( int
) – Index of periodic dihedralReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set periodic dihedrals
-
GetPeriodicImproperParameters
(index)¶ Parameters: index ( int
) – Index of periodic improperReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set periodic impropers
-
GetHarmonicImproperParameters
(index)¶ Parameters: index ( int
) – Index of harmonic improperReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set harmonic impropers
-
GetCMapParameters
(index)¶ Parameters: index ( int
) – Index of CMapReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set cmaps
-
GetLJPairParameters
(index)¶ Parameters: index ( int
) – Index of LJ pairReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set lj pairs
-
GetDistanceConstraintParameters
(index)¶ Parameters: index ( int
) – Index of distance constraintReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set distance constraints
-
GetHarmonicPositionRestraintParameters
(index)¶ Parameters: index ( int
) – Index of harmonic position restraintReturns: tuple
containing the indices of the involved particles and the set parametersRaises: RuntimeError
when index exceeds number of set harmonic position restraints
-
GetHarmonicDistanceRestraintParameters
(index)¶ Parameters: index ( int
) – Index of harmonic distance restraintReturns: tuple
containing the indices of the involved particles and the set parametersRaises: 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- index (
-
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- index (
-
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- index (
-
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- index (
-
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- index (
-
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- index (
-
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- index (
-
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- index (
-
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- index (
-
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- index (
-
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- index (
-
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 particleReturns: 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 particleReturns: 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 particleReturns: 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 particleReturns: 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 particleReturns: 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 particleReturns: 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
ofint
- Indices of all harmonic bonds acting on given particle pairRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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
ofint
- Indices of all harmonic angles acting on given particlesRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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
ofint
- Indices of all Urey-Bradley angles acting on given particlesRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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
ofint
- Indices of all periodic dihedrals acting on given particlesRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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
ofint
- Indices of all periodic impropers acting on given particlesRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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
ofint
- Indices of all harmonic impropers acting on given particlesRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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
ofint
- Indices of all cmaps acting on given particlesRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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 noneRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
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 noneRaises: RuntimeError
when an index exceeds number of particles in topology- index_one (
-
GetHarmonicBondIndices
(index) Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all harmonic bonds this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetHarmonicAngleIndices
(index) Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all harmonic angles this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetUreyBradleyAngleIndices
(index) Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all Urey-Bradley angles this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetPeriodicDihedralIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all periodic dihedrals this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetPeriodicImproperIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all periodic impropers this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetHarmonicImproperIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all harmonic impropers this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetCMapIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all cmaps this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetLJPairIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all LJ pairs this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetDistanceConstraintIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all distance constraints this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetHarmonicPositionRestraintIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all harmonic position restraints this particular particle is involved inRaises: RuntimeError
when index exceeds number of particles in topology
-
GetHarmonicDistanceRestraintIndices
(index)¶ Parameters: index ( int
) – Index of particleReturns: list
ofint
- Indices of all harmonic distance restraints this particular particle is involved inRaises: 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
-