diff --git a/modules/mol/mm/doc/settings.rst b/modules/mol/mm/doc/settings.rst
index 0da2420fb5e47dbd02730c7eb604573bf86a7912..648be8bcc11b04995057433bf2644eedc679a94d 100644
--- a/modules/mol/mm/doc/settings.rst
+++ b/modules/mol/mm/doc/settings.rst
@@ -51,7 +51,7 @@ of the :class:`Simulation` object.
.. attribute:: constrain_hbonds
- Flag, whether bonds involving hydrogens should be constraint
+ Flag, whether bonds involving hydrogens should be constrained
in :class:`TopologyCreator`. default: False
.. attribute:: constrain_bonds
@@ -178,7 +178,7 @@ of the :class:`Simulation` object.
.. attribute:: add_barostat
- Flag, whether an MonteCarlo barostat should be attached when settings up
+ Flag, whether an MonteCarlo barostat should be attached when setting up
the :class:`Simulation`. default: False
.. attribute:: barostat_temperature
diff --git a/modules/mol/mm/doc/topology.rst b/modules/mol/mm/doc/topology.rst
index 621d71cb1d1e5b3c8d843981716c01b06c801d98..421be2fe9cf5d95ea3cd89352994f5e67bdcbbe6 100644
--- a/modules/mol/mm/doc/topology.rst
+++ b/modules/mol/mm/doc/topology.rst
@@ -51,7 +51,7 @@ Automatically create topologies
#. Rename entity back to PDB naming if flag is set accordingly in **settings**
- :param entity: Entity to create :class:`Topology`
+ :param entity: Entity for which to create :class:`Topology`
:param settings: Settings to control :class:`Topology` buildup
:type entity: :class:`ost.mol.EntityHandle`
@@ -81,7 +81,7 @@ The Topology Class
.. class:: Topology(masses)
- :param masses: :class:`list` of the particles masses
+ :param masses: :class:`list` of the particles'masses
.. method:: Save(filename)
@@ -298,14 +298,14 @@ The Topology Class
:param index_two: Index of particle 2
:param index_three: Index of particle 3
:param index_four: Index of particle 4
- :param phase: Phase in radians
+ :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 phase: :class:`float`
+ :type angle: :class:`float`
:type force_constant: :class:`float`
:returns: :class:`int` index of added interaction
@@ -335,7 +335,7 @@ The Topology Class
:type index_two: :class:`int`
:type index_three: :class:`int`
:type index_four: :class:`int`
- :type index_five: :class:`float`
+ :type index_five: :class:`int`
:type dimension: :class:`int`
:type values: :class:`list`
@@ -408,8 +408,7 @@ The Topology Class
.. method:: AddHarmonicPositionRestraint(index, reference_pos, force_constant,
- x_scale=1.0, y_scale=1.0,
- z_scale=1.0)
+ 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)
@@ -434,8 +433,7 @@ The Topology Class
particles
- .. method:: AddHarmonicDistanceRestraint(index_one, index_two, length
- force_constant)
+ .. method:: AddHarmonicDistanceRestraint(index_one, index_two, length, force_constant)
Adds a force between two particles in the form:
force_constant * (b-b0)^2
@@ -470,7 +468,7 @@ The Topology Class
:param sigmas: Sigma parameters for all particles in nm
- :type sigmas: :class:`sigma`
+ :type sigmas: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
@@ -492,7 +490,7 @@ The Topology Class
:param epsilons: Epsilon parameters for all particles in kJ/mol
- :type epsilons: :class:`list`
+ :type epsilons: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
@@ -514,7 +512,7 @@ The Topology Class
:param radii: GBSA radii for all particles in nm
- :type radii: :class:`list`
+ :type radii: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
@@ -536,7 +534,7 @@ The Topology Class
:param scalings: OBC scaling factors for all particles
- :type scalings: :class:`list`
+ :type scalings: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
@@ -558,7 +556,7 @@ The Topology Class
:param charges: Charges for all particles
- :type charges: :class:`list`
+ :type charges: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
@@ -578,7 +576,7 @@ The Topology Class
.. method:: SetMasses(masses)
:param masses: Masses for all particles
- :type masses: :class:`list`
+ :type masses: :class:`list` (:class:`float`)
:raises: :class:`RuntimeError` when list size is inconsistent
with number of particles
@@ -772,11 +770,13 @@ The Topology Class
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`
@@ -836,7 +836,7 @@ The Topology Class
.. method:: SetCMapParameters(index, dimension, map)
- Replaces existing parameters a for particular interaction
+ Replaces existing parameters for a particular interaction
:param index: Index of CMap
:param dimension: New dimension
@@ -880,9 +880,8 @@ The Topology Class
set distance constraints
- .. method:: SetHarmonicPositionRestraintParameters(index, ref_position, k,[,]
- x_scale=1.0, y_scale=1.0,
- z_scale=1.0])
+ .. 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
@@ -1031,8 +1030,8 @@ The Topology Class
:type index_one: :class:`int`
:type index_one: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
- bonds acting on given particles
+ :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
@@ -1048,7 +1047,7 @@ The Topology Class
:type index_two: :class:`int`
:type index_three: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
angles acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
@@ -1065,7 +1064,7 @@ The Topology Class
:type index_two: :class:`int`
:type index_three: :class:`int`
- :returns: :class:`list` of :class:`int` describing all
+ :returns: :class:`list` of :class:`int` - Indices of all
Urey-Bradley angles acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
@@ -1085,7 +1084,7 @@ The Topology Class
:type index_three: :class:`int`
:type index_four: :class:`int`
- :returns: :class:`list` of :class:`int` describing all periodic
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
dihedrals acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
@@ -1105,7 +1104,7 @@ The Topology Class
:type index_three: :class:`int`
:type index_four: :class:`int`
- :returns: :class:`list` of :class:`int` describing all periodic
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
impropers acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
@@ -1125,7 +1124,7 @@ The Topology Class
:type index_three: :class:`int`
:type index_four: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
impropers acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
@@ -1147,7 +1146,7 @@ The Topology Class
:type index_four: :class:`int`
:type index_five: :class:`int`
- :returns: :class:`list` of :class:`int` describing all cmaps
+ :returns: :class:`list` of :class:`int` - Indices of all cmaps
acting on given particles
:raises: :class:`RuntimeError` when an index exceeds
@@ -1157,12 +1156,12 @@ The Topology Class
.. method:: GetLJPairIndex(index_one, index_two)
:param index_one: Index of particle 1
- :param index_one: Index of particle 2
+ :param index_two: Index of particle 2
:type index_one: :class:`int`
- :type index_one: :class:`int`
+ :type index_two: :class:`int`
- :returns: :class:`int` describing LJPair acting on particles,
+ :returns: :class:`int` Index of LJPair acting on particles,
-1 if there is none
:raises: :class:`RuntimeError` when an index exceeds
@@ -1177,7 +1176,7 @@ The Topology Class
:type index_one: :class:`int`
:type index_one: :class:`int`
- :returns: :class:`int` describing distance constraint acting on
+ :returns: :class:`int` - Index of distance constraint acting on
particles, -1 if there is none
:raises: :class:`RuntimeError` when an index exceeds
@@ -1189,7 +1188,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
bonds this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1201,7 +1200,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
angles this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1213,7 +1212,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all
+ :returns: :class:`list` of :class:`int` - Indices of all
Urey-Bradley angles this particular particle
is involved in
@@ -1226,7 +1225,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all periodic
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
dihedrals this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1238,7 +1237,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all periodic
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
impropers this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1249,7 +1248,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
impropers this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1261,7 +1260,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all cmaps
+ :returns: :class:`list` of :class:`int` - Indices of all cmaps
this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1273,7 +1272,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all LJ pairs
+ :returns: :class:`list` of :class:`int` - Indices of all LJ pairs
this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1285,7 +1284,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all distance
+ :returns: :class:`list` of :class:`int` - Indices of all distance
constraints this particular particle is involved in
:raises: :class:`RuntimeError` when index exceeds
@@ -1297,7 +1296,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
position restraints this particular particle is
involved in
@@ -1310,7 +1309,7 @@ The Topology Class
:param index: Index of particle
:type index: :class:`int`
- :returns: :class:`list` of :class:`int` describing all harmonic
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
distance restraints this particular particle is
involved in