Topology
================================================================================
.. currentmodule:: ost.mol.mm
The :class:`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
:class:`Topology` gets internally translated to a molecular mechanics system
as soon as a :class:`Simulation` is set up. To make setting up a
:class:`Topology` more convenient, the :class:`TopologyCreator` class allows
to create a :class:`Topology` based on an mm :class:`Settings` object,
that should suffice for most needs.
Automatically create topologies
--------------------------------------------------------------------------------
.. class:: TopologyCreator
.. method:: Create(entity, settings)
Creates a topology given an :class:`EntityHandle` and a :class:`Settings`
object. Note, that the :class:`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
:class:`Settings`/:class:`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 :class:`BuildingBlock`
#. Add Parametrization from :class:`Forcefield` to the :class:`Topology`. Note, that you can override the :class:`Forcefield` parametrization if you add this particular :class:`Interaction` in a parameterized form in the :class:`BuildingBlock`
#. Rename entity back to PDB naming if flag is set accordingly in **settings**
:param entity: Entity for which to create :class:`Topology`
:param settings: Settings to control :class:`Topology` buildup
:type entity: :class:`ost.mol.EntityHandle`
:type settings: :class:`Settings`
:raises: :class:`RuntimeError` if settings has no
:class:`Forcefield` assigned
:raises: :class:`RuntimeError` if there is a residue with no
appropriate :class:`BuildingBlock` in the
:class:`Forcefield`
:raises: :class:`RuntimeError` if there is a
:class:`ResidueHandle` not matching the
:class:`BuildingBlock` definition in the
:class:`Forcefield`
:raises: :class:`RuntimeError` if there is an interaction
that has no parameters in the forcefield. This
:class:`RuntimeError` can be supressed by setting the
appropriate flag in the :class:`Settings` object.
The Topology Class
--------------------------------------------------------------------------------
.. class:: Topology(masses)
:param masses: :class:`list` of the particles'masses
.. method:: Save(filename)
Dump Toplogy into binary file
:param filename: Name of file
:type filename: :class:`str`
.. method:: Load(filename)
Load binary topology from disk
:param filename: Name of file
:type filename: :class:`str`
:returns: loaded :class:`Topology`
:raises: :class:`RuntimeError` when file can't be found
.. method:: Merge(other)
Merges in another :class:`Topology` and adds all their particles and interactions.
Assuming the actual :class:`Topology` containing n particles, the indexing of the
other :class:`Topology` gets altered by adding n everywhere.
:param other: Topology to merge in
:type other: :class:`Topology`
:raises: :class:`RuntimeError` if fudge parameters are not consistent
:raises: :class:`RuntimeError` if current :class:`Topology`
contains charges but the **other** not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains sigmas but the **other** not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains epsilons but the **other** not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains GBSA Radii but the **other** not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains OBC scalings but the **other** not
.. method:: Merge(ent, other, other_ent)
Merges in another :class:`Topology` and adds all their particles and
interactions. Assuming the actual :class:`Topology` contains n particles,
the indexing of the other :class:`Topology` gets altered by adding n
everywhere. This version of the Merge function assumes the current topology
describes the :class:`EntityHandle` ent and the other :class:`Topology`
describes the :class:`EntityHandle` other_ent. During merging, all
chains, residues, atoms and bonds from **other_ent** are pulled into **ent** in
a way, that the current :class:`Topology` is consistent with the
:class:`EntityHandle` **ent**.
:param ent: Entity consistent with current topology
:param other: Topology to merge in
:param other_ent: Entity consistent with **other**
:type ent: :class:`ost.mol.EntityHandle`
:type other: :class:`Topology`
:type other_ent: :class:`ost.mol.EntityHandle`
:raises: :class:`RuntimeError` if fudge parameters are not consistent
:raises: :class:`RuntimeError` if current :class:`Topology`
contains charges but the other not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains sigmas but the other not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains epsilons but the other not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains GBSA Radii but the other not
:raises: :class:`RuntimeError` if current :class:`Topology`
contains OBC scalings but the other not
:raises: :class:`RuntimeError` if the number of atoms in one
of the entities is not consistent with their related
topologies.
:raises: :class:`RuntimeError` other_ent contains a chain with
a name already present in **ent**.
.. method:: AddHarmonicBond(index_one, index_two, bond_length, force_constant)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param bond_length: Bond length in nm
:param force_constant: Force constant in kJ/mol/nm^2
:type index_one: :class:`int`
:type index_two: :class:`int`
:type bond_length: :class:`float`
:type force_constant: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: AddHarmonicAngle(index_one, index_two, index_three, angle, \
force_constant)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param angle: Angle in radians
:param force_constant: Force constant in kJ/mol/radian^2
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type angle: :class:`float`
:type force_constant: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: AddUreyBradleyAngle(index_one, index_two, index_three, \
angle, angle_force_constant, \
bond_length, bond_force_constant)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param angle: Angle in radians
:param angle_force_constant: Angle force constant kJ/mol/radian^2
:param bond_length: Bond length in nm
:param bond_force_constant: Bond force constant kJ/mol/nm^2
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type angle: :class:`float`
:type angle_force_constant: :class:`float`
:type bond: :class:`float`
:type bond_force_constant: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: AddPeriodicDihedral(index_one, index_two, index_three, \
index_four, multiplicity, phase, \
force_constant)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:param multiplicity: Multiplicity
:param phase: Phase in radians
:param force_constant: Force constant in kJ/mol/radian^2
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:type multiplicity: :class:`int`
:type phase: :class:`float`
:type force_constant: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: AddPeriodicImproper(index_one, index_two, index_three, \
index_four, multiplicity, phase, \
force_constant)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:param multiplicity: Multiplicity
:param phase: Phase in radians
:param force_constant: Force constant in kJ/mol/radian^2
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:type multiplicity: :class:`int`
:type phase: :class:`float`
:type force_constant: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: AddHarmonicImproper(index_one, index_two, index_three, \
index_four, angle, force_constant)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:param angle: Angle in radians
:param force_constant: Force constant kJ/mol/radian^2
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:type angle: :class:`float`
:type force_constant: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: AddCMap(index_one, index_two, index_three, index_four, \
index_five, dimension, values)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:param index_five: Index of particle 5
:param dimension: Dimension of CMap
:param values: 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[
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:type index_five: :class:`int`
:type dimension: :class:`int`
:type values: :class:`list`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when size of values is not
**dimension** * **dimension** or index exceeds number of
particles.
.. method:: AddLJPair(index_one, index_two, sigma, epsilon)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param sigma: Sigma in nm
:param epsilon: Epsilon in kJ/mol
:type index_one: :class:`int`
:type index_two: :class:`int`
:type sigma: :class:`float`
:type epsiolon: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles or when particular LJPair is already
parameterized
.. method:: AddDistanceConstraint(index_one, index_two, distance)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param distance: Constraint distance in nm
:type index_one: :class:`int`
:type index_two: :class:`int`
:type distance: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles or when particular distance constraint
is already parameterized
.. method:: AddExclusion(index_one, index_two)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:type index_one: :class:`int`
:type index_two: :class:`int`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles or when particular exclusion is already set
.. method:: AddPositionConstraint(index)
:param index: Index of particle to be constrained
:type index: :class:`int`
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: 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)
:param index: Index of particle to be constrained
:param reference_pos: Reference position in A
:param force_constant: Force constant in kJ/mol/nm^2
:param x_scale: X-scale
:param y_scale: Y-scale
:param z_scale: Z-scale
:type index: :class:`int`
:type reference_pos: :class:`ost.geom.Vec3`
:type force_constant: :class:`float`
:type x_scale: :class:`float`
:type y_scale: :class:`float`
:type z_scale: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: AddHarmonicDistanceRestraint(index_one, index_two, length, \
force_constant)
Adds a force between two particles in the form:
force_constant * (b-b0)^2
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param length: Restraint length in nm
:param force_constant: Force constant in kJ/mol/nm^2
:type index_one: :class:`int`
:type index_two: :class:`int`
:type length: :class:`float`
:type force_constant: :class:`float`
:returns: :class:`int` index of added interaction
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: ResetPositionConstraints()
Removes all position constraints
.. method:: ResetExclusions()
Removes all set exclusions
.. method:: SetSigmas(sigmas)
:param sigmas: Sigma parameters for all particles in nm
:type sigmas: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
.. method:: SetSigma(index, sigma)
:param index: Index of particle in nm
:param sigma: Sigma
:type index: :class:`int`
:type sigma: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: SetEpsilons(epsilons)
:param epsilons: Epsilon parameters for all particles in kJ/mol
:type epsilons: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
.. method:: SetEpsilon(index, epsilon)
:param index: Index of particle
:param epsilon: Epsilon in kJ/mol
:type index: :class:`int`
:type epsilon: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: SetGBSARadii(radii)
:param radii: GBSA radii for all particles in nm
:type radii: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
.. method:: SetGBSARadius(index, radius)
:param index: Index of particle
:param radius: GBSA radius in nm
:type index: :class:`int`
:type radius: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: SetOBCScalings(scalings)
:param scalings: OBC scaling factors for all particles
:type scalings: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
.. method:: SetOBCScaling(index, scaling)
:param index: Index of particle
:param scaling: OBC scaling factor
:type index: Index of particle
:type scaling: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: SetCharges(charges)
:param charges: Charges for all particles
:type charges: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
.. method:: SetCharge(index, charge)
:param index: Index of particle
:param charge: Charge
:type index: :class:`int`
:type charge: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: SetMasses(masses)
:param masses: Masses for all particles
:type masses: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
.. method:: SetMass(index, mass)
:param index: Index of particle
:param mass: Mass
:type index: :class:`int`
:type mass: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
particles
.. method:: SetFudgeQQ(fudge)
:param fudge: Dampening factor for electrostatic 1,4 interactions
:type fudge: :class:`float`
.. method:: SetFudgeLJ(fudge)
:param fudge: Dampening factor for LJ 1,4 interactions
:type fudge: :class:`float`
.. method:: GetHarmonicBondParameters(index)
:param index: Index of harmonic bond
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic bonds
.. method:: GetHarmonicAngleParameters(index)
:param index: Index of harmonic angle
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic angles
.. method:: GetUreyBradleyAngleParameters(index)
:param index: Index of Urey-Bradley angle
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set Urey-Bradley angles
.. method:: GetPeriodicDiheralParameters(index)
:param index: Index of periodic dihedral
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set periodic dihedrals
.. method:: GetPeriodicImproperParameters(index)
:param index: Index of periodic improper
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set periodic impropers
.. method:: GetHarmonicImproperParameters(index)
:param index: Index of harmonic improper
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic impropers
.. method:: GetCMapParameters(index)
:param index: Index of CMap
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set cmaps
.. method:: GetLJPairParameters(index)
:param index: Index of LJ pair
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set lj pairs
.. method:: GetDistanceConstraintParameters(index)
:param index: Index of distance constraint
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set distance constraints
.. method:: GetHarmonicPositionRestraintParameters(index)
:param index: Index of harmonic position restraint
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic position restraints
.. method:: GetHarmonicDistanceRestraintParameters(index)
:param index: Index of harmonic distance restraint
:type index: :class:`int`
:returns: :class:`tuple` containing the indices of the involved
particles and the set parameters
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic distance restraints
.. method:: SetHarmonicBondParameters(index, bond_length, force_constant)
Replaces existing parameters for particular interaction
:param index: Index of harmonic bond
:param bond_length: New bond length in nm
:param force_constant: New force constant in kJ/mol/nm^2
:type index: :class:`int`
:type bond_length: :class:`float`
:type force_constant: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic bonds
.. method:: SetHarmonicAngleParameters(index, angle, force_constant)
Replaces existing parameters for particular interaction
:param index: Index of harmonic angle
:param angle: New angle in radians
:param force_constant: New force constant kJ/mol/radian^2
:type index: :class:`int`
:type angle: :class:`float`
:type force_constant: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic angles
.. method:: SetUreyBradleyAngleParameters(index, angle, angle_force_constant,
bond_length, bond_force_constant)
Replaces existing parameters for particular interaction
:param index: Index of Urey-Bradley angle
:param angle: New angle in radians
:param angle_force_constant: New angle force constant in kJ/mol/radian^2
:param bond_length: New bond length in nm
:param bond_force_constant: New bond force constant in kJ/mol/nm^2
:type index: :class:`int`
:type angle: :class:`float`
:type angle_force_constant: :class:`float`
:type bond_length: :class:`float`
:type bond_force_constant: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set Urey-Bradley angles
.. method:: SetPeriodicDiheralParameters(index, multiplicity, phase, \
force_constant)
Replaces existing parameters for a particular interaction
:param index: Index of periodic dihedral
:param multiplicity: New periodicity
:param phase: New phase in radians
:param force_constant: New force constant in kJ/mol/radian^2
:type index: :class:`int`
:type multiplicity: :class:`int`
:type phase: :class:`float`
:type force_constant: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set periodic dihedrals
.. method:: SetPeriodicImproperParameters(index, multiplicity, phase, \
force_constant)
Replaces existing parameters for a particular interaction
:param index: Index of periodic improper
:param multiplicity: New multiplicity
:param phase: New phase in radians
:param force_constant: New force constant kJ/mol/radian^2
:type index: :class:`int`
:type multiplicity: :class:`int`
:type phase: :class:`float`
:type force_constant: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set periodic impropers
.. method:: SetHarmonicImproperParameters(index, angle, force_constant)
Replaces existing parameters for a particular interaction
:param index: Index of harmonic improper
:param angle: New angle in radians
:param force_constant: New force constant kJ/mol/radian^2
:type index: :class:`int`
:type angle: :class:`float`
:type force_constant: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic impropers
.. method:: SetCMapParameters(index, dimension, map)
Replaces existing parameters for a particular interaction
:param index: Index of CMap
:param dimension: New dimension
:param map: New CMap of format described in the AddCMap function.
:type index: :class:`int`
:type dimension: :class:`int`
:type map: :class:`list`
:raises: :class:`RuntimeError` when index exceeds number of
set cmaps or size of map is not dimension*dimension
.. method:: SetLJPairParameters(index, sigma, epsilon)
Replaces existing parameters for a particular interaction
:param index: Index of LJ pair
:param sigma: New sigma in nm
:param epsilon: New epsilon in kJ/mol
:type index: :class:`int`
:type sigma: :class:`float`
:type epsilon: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set lj pairs
.. method:: SetDistanceConstraintParameters(index, distance)
Replaces existing parameters for a particular interaction
:param index: Index of distance constraint
:param distance: New constraint distance in nm
:type index: :class:`int`
:type distance: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set distance constraints
.. method:: SetHarmonicPositionRestraintParameters(index, ref_position, k,\
x_scale=1.0, y_scale=1.0,\
z_scale=1.0)
Replaces existing parameters for a particular interaction
:param index: Index of harmonic position constraint
:param ref_position: New reference position in nm
:param k: New force constant in kJ/mol/nm^2
:param x_scale: New x-scale
:param y_scale: New y-scale
:param z_scale: New z-scale
:type index: :class:`int`
:type ref_position: :class:`ost.geom.Vec3`
:type k: :class:`float`
:type x_scale: :class:`float`
:type y_scale: :class:`float`
:type z_scale: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic position restraints
.. method:: SetHarmonicDistanceRestraintParameters(index, length, k)
Replaces existing parameters for a particular interaction
:param index: Index of harmonic distance restraint
:param length: New restraint distance in nm
:param k: New force constant in kJ/mol/nm^2
:type index: :class:`int`
:type length: :class:`float`
:type k: :class:`float`
:raises: :class:`RuntimeError` when index exceeds number of
set harmonic distance restraints
.. method:: GetSigmas()
:returns: :class:`list` of :class:`float` with previously set
sigmas
.. method:: GetEpsilons()
:returns: :class:`list` of :class:`float` with previously set
epsilons
.. method:: GetGBSARadii()
:returns: :class:`list` of :class:`float` with previously set
GBSA radii
.. method:: GetOBCScalings()
:returns: :class:`list` of :class:`float` with previously set
OBC scalings
.. method:: GetCharges()
:returns: :class:`list` of :class:`float` with previously set
charges
.. method:: GetMasses()
:returns: :class:`list` of :class:`float` with previously set
masses
.. method:: GetSigma(particle_index)
:param particle_index: Index of particle
:type particle_index: :class:`int`
:returns: :class:`float`
:raises: :class:`RuntimeError` when particle_index exceeds
number of particles or sigmas have not been set
.. method:: GetEpsilon(particle_index)
:param particle_index: Index of particle
:type particle_index: :class:`int`
:returns: :class:`float`
:raises: :class:`RuntimeError` when particle_index exceeds
number of particles or epsilons have not been set
.. method:: GetGBSARadius(particle_index)
:param particle_index: Index of particle
:type particle_index: :class:`int`
:returns: :class:`float`
:raises: :class:`RuntimeError` when particle_index exceeds
number of particles or gbsa_radii have not been set
.. method:: GetOBCScaling(particle_index)
:param particle_index: Index of particle
:type particle_index: :class:`int`
:returns: :class:`float`
:raises: :class:`RuntimeError` when particle_index exceeds
number of particles or obc scalings have not been set
.. method:: GetCharge(particle_index)
:param particle_index: Index of particle
:type particle_index: :class:`float`
:returns: :class:`float`
:raises: :class:`RuntimeError` when particle_index exceeds
number of particles or charges have not been set
.. method:: GetMass(particle_index)
:param particle_index: Index of particle
:type particle_index: :class:`int`
:returns: :class:`float`
:raises: :class:`RuntimeError` when particle_index exceeds
number of particles
.. method:: GetHarmonicBondIndices(index_one, index_two)
:param index_one: Index of particle 1
:param index_one: Index of particle 2
:type index_one: :class:`int`
:type index_one: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of
all harmonic bonds acting on given particle pair
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetHarmonicAngleIndices(index_one, index_two, index_three)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all harmonic
angles acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetUreyBradleyAngleIndices(index_one, index_two, index_three)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all
Urey-Bradley angles acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetPeriodicDihedralIndices(index_one, index_two, index_three, \
index_four)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all periodic
dihedrals acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetPeriodicImpropersIndices(index_one, index_two, index_three, \
index_four)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all periodic
impropers acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetHarmonicImpropersIndices(index_one, index_two, index_three, \
index_four)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all harmonic
impropers acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetCMapIndices(index_one, index_two, index_three, \
index_four, index_five)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
:param index_five: Index of particle 5
:type index_one: :class:`int`
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
:type index_five: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all cmaps
acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetLJPairIndex(index_one, index_two)
:param index_one: Index of particle 1
:param index_two: Index of particle 2
:type index_one: :class:`int`
:type index_two: :class:`int`
:returns: :class:`int` Index of LJPair acting on particles,
-1 if there is none
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetDistanceConstraintIndex(index_one, index_two)
:param index_one: Index of particle 1
:param index_one: Index of particle 2
:type index_one: :class:`int`
:type index_one: :class:`int`
:returns: :class:`int` - Index of distance constraint acting on
particles, -1 if there is none
:raises: :class:`RuntimeError` when an index exceeds
number of particles in topology
.. method:: GetHarmonicBondIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all harmonic
bonds this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetHarmonicAngleIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all harmonic
angles this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetUreyBradleyAngleIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all
Urey-Bradley angles this particular particle
is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetPeriodicDihedralIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all periodic
dihedrals this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetPeriodicImproperIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all periodic
impropers this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetHarmonicImproperIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all harmonic
impropers this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetCMapIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all cmaps
this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetLJPairIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all LJ pairs
this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetDistanceConstraintIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all distance
constraints this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetHarmonicPositionRestraintIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all harmonic
position restraints this particular particle is
involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetHarmonicDistanceRestraintIndices(index)
:param index: Index of particle
:type index: :class:`int`
:returns: :class:`list` of :class:`int` - Indices of all harmonic
distance restraints this particular particle is
involved in
:raises: :class:`RuntimeError` when index exceeds
number of particles in topology
.. method:: GetNumParticles()
:returns: :class:`int`
.. method:: GetNumHarmonicBonds()
:returns: :class:`int`
.. method:: GetNumHarmonicAngles()
:returns: :class:`int`
.. method:: GetNumUreyBradleyAngles()
:returns: :class:`int`
.. method:: GetNumPeriodicDihedrals()
:returns: :class:`int`
.. method:: GetNumPeriodicImpropers()
:returns: :class:`int`
.. method:: GetNumHarmonicImpropers()
:returns: :class:`int`
.. method:: GetNumCMaps()
:returns: :class:`int`
.. method:: GetNumLJPairs()
:returns: :class:`int`
.. method:: GetNumDistanceConstraints()
:returns: :class:`int`
.. method:: GetNumPositionConstraints()
:returns: :class:`int`
.. method:: GetNumHarmonicPositionRestraints()
:returns: :class:`int`
.. method:: GetNumHarmonicDistanceRestraints()
:returns: :class:`int`
.. method:: GetNumExclusions()
:returns: :class:`int`