some more documentation

modules/mol/mm/doc/topology.rst

+Topology
+================================================================================
+
+.. currentmodule:: ost.mol
+
+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 most needs.
+
+.. 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 adding hydrogens and modification of terminal residues
+    based on the information given by the :class:`Settings`/:class:`Forcefield`.
+
+    :param entity:      :class:`EntityHandle`
+    :param settings:    :class:`Settings`
+
+
+.. class:: Topology
+
+
+  .. method:: Save(filename)
+
+    Dump Toplogy into binary file
+
+    :param filename:    :class:`str`
+
+
+  .. method:: Load(filename)
+
+    Load binary topology from disk
+
+    :param 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:       :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` containing 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 
+    to describe the :class:`EntityHandle` ent and the other :class:`Topology`
+    to describe 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:         :class:`EntityHandle`
+
+    :param other:       :class:`Topology`
+
+    :param other_ent:   :class:`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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param bond_length: :class:`float`
+
+    :param 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, bond_length, 
+                               force_constant)
+
+    :param index_one:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param angle:       :class:`float`
+
+    :param 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param angle:       :class:`float`
+
+    :param angle_force_constant: :class:`float`
+
+    :param bond_length: :class:`float`
+
+    :param 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :param multiplicity: :class:`int`
+
+    :param phase:       :class:`float`
+
+    :param 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :param multiplicity: :class:`int`
+
+    :param phase:       :class:`float`
+
+    :param 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :param angle:       :class:`float`
+
+    :param 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :param index_five:  :class:`int`
+
+    :param dimension:   :class:`int`
+
+    :param values:      :class:`list` of :class:`float` of size 
+                        dimension*dimension describing the correction
+                        map. 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:           :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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param sigma:       :class:`float`
+
+    :param epsilon:     :class:`float`
+
+    :returns:           :class:`int` index of added interaction
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         particles or when particular LJPair is already 
+                         parametrized
+
+
+  .. method:: AddDistanceConstraint(index_one, index_two, distance)
+
+    :param index_one:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param 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 parametrized
+
+
+  .. method:: AddExclusion(index_one, index_two)
+
+    :param index_one:   :class:`int`
+
+    :param 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:       :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 of the form:
+    force_constant*(x_scale*(x-x0)^2+y_scale*(y-y0)^2+z_scale*(z-z0)^2)
+
+    :param index:       :class:`int`
+
+    :param reference_pos: :class:`ost.geom.Vec3` reference_position
+
+    :param force_constant: :class:`float`
+
+    :param x_scale: :class:`float`
+
+    :param y_scale: :class:`float`
+
+    :param 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 of the form:
+    force_constant * (b-b0)^2
+
+    :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:      :class:`list` of :class:`float` defining sigma params
+   
+    :raises:            :class:`RuntimeError` when list size is inconsistent
+                        with number of particles
+
+
+  .. method:: SetSigma(index, sigma)
+
+    :param index:       :class:`int`
+
+    :parm sigma:        :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         particles
+
+
+  .. method:: SetEpsilons(epsilons)
+
+    :param epsilons:    :class:`list` of :class:`float` defining epsilon params
+   
+    :raises:            :class:`RuntimeError` when list size is inconsistent
+                        with number of particles
+
+
+  .. method:: SetEpsilon(index, epsilon)
+
+    :param index:       :class:`int`
+
+    :parm epsilon:        :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         particles
+
+
+  .. method:: SetGBSARadii(radii)
+
+    :param radii:      :class:`list` of :class:`float` defining radii
+   
+    :raises:            :class:`RuntimeError` when list size is inconsistent
+                        with number of particles
+
+
+  .. method:: SetGBSARadii(index, radius)
+
+    :param index:       :class:`int`
+
+    :parm radius:       :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         particles
+
+
+  .. method:: SetOBCScalings(scalings)
+
+    :param scalings:    :class:`list` of :class:`float` defining scaling params
+   
+    :raises:            :class:`RuntimeError` when list size is inconsistent
+                        with number of particles
+
+
+  .. method:: SetOBCScaling(index, scaling)
+
+    :param index:       :class:`int`
+
+    :parm scaling:      :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         particles
+
+
+  .. method:: SetCharges(charges)
+
+    :param charges:     :class:`list` of :class:`float` defining charge params
+   
+    :raises:            :class:`RuntimeError` when list size is inconsistent
+                        with number of particles
+
+
+  .. method:: SetCharge(index, charge)
+
+    :param index:       :class:`int`
+
+    :parm charge:       :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         particles
+
+  .. method:: SetMasses(masses)
+
+    :param masses:      :class:`list` of :class:`float` defining mass params
+   
+    :raises:            :class:`RuntimeError` when list size is inconsistent
+                        with number of particles
+
+
+  .. method:: SetMass(index, mass)
+
+    :param index:       :class:`int`
+
+    :parm mass:         :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         particles
+
+
+  .. method:: SetFudgeQQ(fudge)
+
+    :param fudge:       :class:`fudge`
+
+
+  .. method:: SetFudgeLJ(fudge)
+
+    :param fudge:       :class:`fudge`
+
+
+  .. method:: GetHarmonicBondParameters(index)
+
+    :param 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:       :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:       :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:       :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:       :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:       :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:       :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:       :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:       :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:       :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:       :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:       :class:`int`
+
+    :param bond_length: :class:`float`
+
+    :param 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:       :class:`int`
+
+    :param angle:       :class:`float`
+
+    :param 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:       :class:`int`
+
+    :param angle_force_constant: :class:`float`
+
+    :param bond_length: :class:`float`
+
+    :param 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 particular interaction
+
+    :param index:       :class:`int`
+
+    :param multiplicity: :class:`int`
+
+    :param phase:       :class:`float`
+
+    :param 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 particular interaction
+
+    :param index:       :class:`int`
+
+    :param multiplicity: :class:`int`
+
+    :param phase:       :class:`float`
+
+    :param 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 particular interaction
+
+    :param index:       :class:`int`
+
+    :param angle:       :class:`float`
+
+    :param force_constant: :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         set harmonic impropers
+
+
+  .. method:: SetCMapParameters(index, dimension, map)
+
+    Replaces existing parameters for particular interaction
+
+    :param index:       :class:`int`
+
+    :param dimension:   :class:`int`
+
+    :param map:         :class:`list` of :class:`float` values in the format
+                        described in the AddCMap function.
+
+    :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 particular interaction
+
+    :param index:       :class:`int`
+
+    :param sigma:       :class:`float`
+
+    :param epsilon:     :class:`float`
+
+    :raises:            :class:`RuntimeError` when index exceeds number of 
+                         set lj pairs
+
+
+  .. method:: SetDistanceConstraintParameters(index, distance)
+
+    Replaces existing parameters for particular interaction
+
+    :param index:       :class:`int`
+
+    :param 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 particular interaction
+
+    :param index:       :class:`int`
+
+    :param ref_position: :class:`ost.geom.Vec3`
+
+    :param k:           :class:`float`
+
+    :param x_scale:     :class:`float`
+
+    :param y_scale:     :class:`float`
+
+    :param 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 particular interaction
+
+    :param index:       :class:`int`
+
+    :param length:      :class:`float`
+
+    :param 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 
+                        gbsa charges
+
+
+  .. method:: GetMasses()
+
+    :returns:           :class:`list` of :class:`float` with previously set 
+                        masses
+
+
+  .. method:: GetSigma(particle_index)
+
+    :param 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: :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: :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: :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: :class:`int`
+
+    :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: :class:`int`
+
+    :returns:           :class:`float`
+
+    :raises:            :class:`RuntimeError` when particle_index exceeds
+                        number of particles
+
+
+  .. method:: GetHarmonicBondIndices(index_one, index_two)
+
+    :param index_one:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :returns:           :class:`list` of :class:`int` describing all harmonic
+                        bonds acting on given particles
+
+    :raises:            :class:`RuntimeError` when an index exceeds
+                        number of particles in topology
+
+
+  .. method:: GetHarmonicAngleIndices(index_one, index_two, index_three)
+
+    :param index_one:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :returns:           :class:`list` of :class:`int` describing 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :returns:           :class:`list` of :class:`int` describing 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :returns:           :class:`list` of :class:`int` describing 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :returns:           :class:`list` of :class:`int` describing 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :returns:           :class:`list` of :class:`int` describing 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :param index_three: :class:`int`
+
+    :param index_four:  :class:`int`
+
+    :param index_five:  :class:`int`
+
+    :returns:           :class:`list` of :class:`int` describing 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :returns:           :class:`int` describing 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:   :class:`int`
+
+    :param index_two:   :class:`int`
+
+    :returns:           :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing all cmaps
+                        this particular particle is involved in
+
+    :raises:            :class:`RuntimeError` when index exceeds
+                        number of particles in topology
+
+
+  .. method:: GetLJPairIndices(index)
+
+    :param index:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing all LJPairs
+                        this particular particle is involved in
+
+    :raises:            :class:`RuntimeError` when index exceeds
+                        number of particles in topology
+
+
+  .. method:: GetDistanceConstraintIndices(index)
+
+    :param index:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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:       :class:
+
+    :returns:           :class:`list` of :class:`int` describing 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`
\ No newline at end of file