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Unverified Commit fb6ca470 authored by Xavier Robin's avatar Xavier Robin
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doc: cleanup and make things more consistent.

The breadcrumbs now correctly indicate the module hierarchy and can be
used to determine imports. All the documentation for ost.* is now rooted
on the base `ost` module for more clarity.
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:mod:`mol.alg.trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more
:mod:`~ost.mol.alg.trajectory_analysis` -- DRMSD, Pairwise Distances and More
---------------------------------------------------------------------------------------------------------------
.. automodule:: ost.mol.alg.trajectory_analysis
......
......@@ -8,6 +8,7 @@
The mol module implements data structures to work with molecular datasets. At its heart lie the :class:`EntityHandle` and :class:`EntityView` classes which represent molecular structures such as proteins, DNA, RNA and small molecules. There are also classes to deal with molecular surfaces.
.. toctree::
:maxdepth: 2
entity
editors
......@@ -15,13 +16,4 @@ The mol module implements data structures to work with molecular datasets. At it
surface
traj
../alg/molalg
../alg/chain_mapping
../alg/contact_score
../alg/dockq
../alg/helix_kinks
../alg/ligand_scoring
../alg/qsscore
../alg/scoring
../alg/stereochemistry
../alg/structure_analysis
../alg/trajectory_analysis
\ No newline at end of file
../mm/molmm
\ No newline at end of file
:mod:`~ost.mol.mm.antechamber` -- Generating forcefields with Antechamber
--------------------------------------------------------------------------------
The antechamber submodule of mol.mm defines functions to use Antechamber (from
AmberTools) to automatically generate force field parameters and load the
results into :class:`~ost.mol.mm.Forcefield` objects.
**Example usage**:
.. code-block:: python
from ost.mol import mm
# create parameters for RVP using PDB's component dictionary
mm.antechamber.RunAntechamber('RVP', 'components.cif', base_out_dir='ligands')
# create force field
ff = mm.Forcefield()
ff = mm.antechamber.AddFromPath(ff, 'ligands/RVP')
# equivalent: ff = mm.antechamber.AddFromFiles(ff, 'ligands/RVP/frcmod',
# 'ligands/RVP/out.mpdb')
# since Antechamber cannot deal with ions, you can do it manually
ff = mm.antechamber.AddIon(ff, 'CL', 'CL', 35.45, -1.0, 0.4401, 0.4184)
# save it
ff.Save('ligands/ff.dat')
**Functions**:
.. automodule:: ost.mol.mm.antechamber
:members:
\ No newline at end of file
......@@ -139,33 +139,9 @@ Reading forcefields
Generating forcefields with Antechamber
--------------------------------------------------------------------------------
The antechamber submodule of mol.mm defines functions to use Antechamber (from
AmberTools) to automatically generate force field parameters and load the
results into :class:`~ost.mol.mm.Forcefield` objects.
**Example usage**:
.. code-block:: python
from ost.mol import mm
# create parameters for RVP using PDB's component dictionary
mm.antechamber.RunAntechamber('RVP', 'components.cif', base_out_dir='ligands')
# create force field
ff = mm.Forcefield()
ff = mm.antechamber.AddFromPath(ff, 'ligands/RVP')
# equivalent: ff = mm.antechamber.AddFromFiles(ff, 'ligands/RVP/frcmod',
# 'ligands/RVP/out.mpdb')
# since Antechamber cannot deal with ions, you can do it manually
ff = mm.antechamber.AddIon(ff, 'CL', 'CL', 35.45, -1.0, 0.4401, 0.4184)
# save it
ff.Save('ligands/ff.dat')
**Functions**:
.. automodule:: ost.mol.mm.antechamber
:members:
The :doc:`antechamber <antechamber>` submodule of mol.mm defines functions to use
Antechamber (from AmberTools) to automatically generate force field parameters
and load the results into :class:`~ost.mol.mm.Forcefield` objects.
The Forcefield Class
--------------------------------------------------------------------------------
......@@ -707,8 +683,3 @@ The Forcefield Class
:returns: :class:`BlockModifier` for this name, invalid if it can't
be found
The mm Module
:mod:`~ost.mol.mm` - The mm Module
================================================================================
.. module:: ost.mol.mm
......@@ -79,6 +79,7 @@ Documentation
interaction
buildingblock
forcefield
antechamber
settings
topology
observers
......
:mod:`seq.alg.aaindex <ost.seq.alg.aaindex>` -- AAIndex annotations
:mod:`~ost.seq.alg.aaindex` -- AAIndex annotations
--------------------------------------------------------------------------------
.. module:: ost.seq.alg.aaindex
......
:mod:`seq.alg.renumber <ost.seq.alg.renumber>` -- Renumber entities
:mod:`~ost.seq.alg.renumber` -- Renumber entities
--------------------------------------------------------------------
.. module:: ost.seq.alg.renumber
......
:mod:`seq.alg <ost.seq.alg>` -- Algorithms for Sequences
:mod:`~ost.seq.alg` -- Algorithms for Sequences
================================================================================
.. module:: ost.seq.alg
......@@ -7,8 +7,11 @@
Submodules
--------------------------------------------------------------------------------
* :doc:`aaindex – AAIndex annotations <aaindex>`
* :doc:`renumber – Renumber entities <renumber>`
.. toctree::
:maxdepth: 1
aaindex
renumber
Algorithms for Alignments
--------------------------------------------------------------------------------
......
......@@ -863,3 +863,9 @@ probabilities between Match, Insertion or Deletion states or neff values
:returns: A nonsorted list of the names of all :class:`ProfileHandle`
objects in the database
.. toctree::
:maxdepth: 2
:hidden:
../alg/seqalg
\ No newline at end of file
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