diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index a5796db6aad75b0cf6b4ddd8328a50c460b98ded..e702b49ac3e4d7ea0819b85cc768d10bf8a3c39f 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -636,6 +636,11 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:returns: true if the residue names are the same, false otherwise
+Superposing structures
+--------------------------------------------------------------------------------
+
+.. autofunction:: Superpose
+
.. autofunction:: ParseAtomNames
.. autofunction:: MatchResidueByNum
@@ -646,7 +651,99 @@ The following function detects steric clashes in atomic structures. Two atoms ar
.. autofunction:: MatchResidueByGlobalAln
-.. autofunction:: Superpose
+.. class:: SuperpositionResult
+
+ .. attribute:: rmsd
+
+ RMSD of the superposed entities.
+
+ .. attribute:: view1
+ view2
+
+ Two :class:`~ost.mol.EntityView` used in superposition (not set if methods
+ with :class:`~ost.geom.Vec3List` used).
+
+ .. attribute:: transformation
+
+ Transformation (:class:`~ost.geom.Mat4`) used to map :attr:`view1` onto
+ :attr:`view2`.
+
+ .. attribute:: fraction_superposed
+ rmsd_superposed_atoms
+ ncycles
+
+ For iterative superposition (:func:`IterativeSuperposeSVD`): fraction and
+ RMSD of atoms that were superposed with a distance below the given
+ threshold and the number of iteration cycles performed.
+
+.. method:: SuperposeSVD(view1, view2, apply_transform=True)
+ SuperposeSVD(list1, list2)
+
+ Superposition of two sets of atoms minimizing RMSD using a classic SVD based
+ algorithm.
+
+ Note that the atom positions in the view are taken blindly in the order in
+ which the atoms appear.
+
+ :param view1: View on the model entity
+ :type view1: :class:`~ost.mol.EntityView`
+ :param view2: View on the reference entity
+ :type view2: :class:`~ost.mol.EntityView`
+ :param list1: List of atom positions for model entity
+ :type list1: :class:`~ost.geom.Vec3List`
+ :param list2: List of atom positions for reference entity
+ :type list2: :class:`~ost.geom.Vec3List`
+ :param apply_transform: If True, the superposition transform is applied to
+ the (full!) entity handle linked to *view1*.
+ :type apply_transform: :class:`bool`
+
+ :return: An instance of :class:`SuperpositionResult`.
+
+.. method:: IterativeSuperposeSVD(view1, view2, max_iterations=5, \
+ distance_threshold=3.0, apply_transform=True)
+ IterativeSuperposeSVD(list1, list2, max_iterations=5, \
+ distance_threshold=3.0)
+
+ Iterative superposition of two sets of atoms. In each iteration cycle, we
+ keep a fraction of atoms with distances below *distance_threshold* and get
+ the superposition considering only those atoms.
+
+ Note that the atom positions in the view are taken blindly in the order in
+ which the atoms appear.
+
+ :param view1: View on the model entity
+ :type view1: :class:`~ost.mol.EntityView`
+ :param view2: View on the reference entity
+ :type view2: :class:`~ost.mol.EntityView`
+ :param list1: List of atom positions for model entity
+ :type list1: :class:`~ost.geom.Vec3List`
+ :param list2: List of atom positions for reference entity
+ :type list2: :class:`~ost.geom.Vec3List`
+ :param max_iterations: Max. number of iterations to be performed
+ :type max_iterations: :class:`int`
+ :param distance_threshold: Distance threshold defining superposed atoms
+ :type distance_threshold: :class:`float`
+ :param apply_transform: If True, the superposition transform is applied to
+ the (full!) entity handle linked to *view1*.
+ :type apply_transform: :class:`bool`
+
+ :return: An instance of :class:`SuperpositionResult`.
+
+ :raises: Exception if atom counts do not match or if less than 3 atoms.
+
+.. method:: CalculateRMSD(view1, view2, transformation=geom.Mat4())
+
+ :return: RMSD of atom positions (taken blindly in the order in which the
+ atoms appear) in the two given views.
+ :rtype: :class:`float`
+
+ :param view1: View on the model entity
+ :type view1: :class:`~ost.mol.EntityView`
+ :param view2: View on the reference entity
+ :type view2: :class:`~ost.mol.EntityView`
+ :param transformation: Optional transformation to apply on each atom position
+ of *view1*.
+ :type transformation: :class:`~ost.geom.Mat4`
.. _traj-analysis:
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index 9af62d7fa38d37d6f4adc31ba5801ef862bf11a4..e41942d57a01a627ed6e71391118c2b2abc36c50 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -275,28 +275,25 @@ def MatchResidueByGlobalAln(ent_a, ent_b, atoms='all'):
def Superpose(ent_a, ent_b, match='number', atoms='all', iterative=False, max_iterations=5, distance_threshold=3.0):
"""
Superposes the model entity onto the reference. To do so, two views are
- created, returned with the result. **atoms** describes what goes into these
- views and **match** the selection method. For superposition,
- :func:`~ost.mol.alg.SuperposeSVD` is called. For matching, the following methods
- are recognised:
+ created, returned with the result. *atoms* describes what goes into these
+ views and *match* the selection method. For superposition,
+ :func:`SuperposeSVD` or :func:`IterativeSuperposeSVD` are called (depending on
+ *iterative*). For matching, the following methods are recognised:
- * ``number`` - select residues by residue number, includes **atoms**, calls
- :func:`~ost.mol.alg.MatchResidueByNum`
+ * ``number`` - select residues by residue number, includes *atoms*, calls
+ :func:`MatchResidueByNum`
- * ``index`` - select residues by index in chain, includes **atoms**, calls
- :func:`~ost.mol.alg.MatchResidueByIdx`
+ * ``index`` - select residues by index in chain, includes *atoms*, calls
+ :func:`MatchResidueByIdx`
* ``local-aln`` - select residues from a Smith/Waterman alignment, includes
- **atoms**, calls :func:`~ost.mol.alg.MatchResidueByLocalAln`
+ *atoms*, calls :func:`MatchResidueByLocalAln`
* ``global-aln`` - select residues from a Needleman/Wunsch alignment, includes
- **atoms**, calls :func:`~ost.mol.alg.MatchResidueByGlobalAln`
+ *atoms*, calls :func:`MatchResidueByGlobalAln`
- There is also an option to use **iterative** matching which allows for an
- iterative approach to superposing two structures. **iterative** takes two
- additional parameters, **max_iteration** and **distance_threshold**.
-
- :param ent_a: The model entity
+ :param ent_a: The model entity (superposition transform is applied on full
+ entity handle here)
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param ent_b: The reference entity
@@ -308,40 +305,39 @@ def Superpose(ent_a, ent_b, match='number', atoms='all', iterative=False, max_it
:param atoms: The subset of atoms to be used in the superposition
:type atoms: :class:`str`, :class:`list`, :class:`set`
- :param max_iterations: They number of iterations that will be run during
- iterative superposition
+ :param iterative: Whether or not to use iterative superpositon.
+ :type iterative: :class:`bool`
+
+ :param max_iterations: Max. number of iterations for
+ :func:`IterativeSuperposeSVD`
+ (only if *iterative* = True)
:type max_iterations: :class:`int`
- :param distance_threshold: The distance threshold between which two atoms
- that will be used in the next superposition
- iteration
+ :param distance_threshold: Distance threshold for
+ :func:`IterativeSuperposeSVD`
+ (only if *iterative* = True)
:type distance_threshold: :class:`float`
- :returns: An instance of :class:`SuperpositionResult`, containing members
-
- * ``rmsd`` - RMSD of the superposed entities
-
- * ``view1`` - First :class:`~ost.mol.EntityView` used
-
- * ``view2`` - Second :class:`~ost.mol.EntityView` used
+ :returns: An instance of :class:`SuperpositionResult`.
"""
- not_supported="Superpose called with unsupported matching request."
+ not_supported = "Superpose called with unsupported matching request."
## create views to superpose
if match.upper() == 'NUMBER':
view_a, view_b = MatchResidueByNum(ent_a, ent_b, atoms)
elif match.upper() == 'INDEX':
- view_a, view_b=MatchResidueByIdx(ent_a, ent_b, atoms)
+ view_a, view_b = MatchResidueByIdx(ent_a, ent_b, atoms)
elif match.upper() == 'LOCAL-ALN':
- view_a, view_b=_MatchResidueByAln(ent_a, ent_b, atoms,
- ost.seq.alg.LocalAlign)
+ view_a, view_b = _MatchResidueByAln(ent_a, ent_b, atoms,
+ ost.seq.alg.LocalAlign)
elif match.upper() == 'GLOBAL-ALN':
- view_a, view_b=_MatchResidueByAln(ent_a, ent_b, atoms,
- ost.seq.alg.GlobalAlign)
+ view_a, view_b = _MatchResidueByAln(ent_a, ent_b, atoms,
+ ost.seq.alg.GlobalAlign)
else:
raise ValueError(not_supported)
## action
if iterative:
- res=ost.mol.alg.IterativeSuperposeSVD(view_a, view_b, max_iterations, distance_threshold)
+ res = ost.mol.alg.IterativeSuperposeSVD(view_a, view_b, max_iterations,
+ distance_threshold)
else:
- res=ost.mol.alg.SuperposeSVD(view_a, view_b)
+ res = ost.mol.alg.SuperposeSVD(view_a, view_b)
return res
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 849d37af852ccb285e660c580b659a328687feb5..6fcaf9834be7fa0e877568403ea9923c33265197 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -1582,7 +1582,8 @@ Other Entity-Related Functions
:returns: :class:`EntityView`
-.. function:: CreateEntityFromView(view, include_exlusive_atoms, handle=EntityHandle())
+.. function:: CreateEntityFromView(view, include_exlusive_atoms, \
+ handle=EntityHandle())
This function behaves exactly like :meth:`EntityHandle.Copy`, except that only
atoms, residues, chains and bonds that are present in the view will be
@@ -1596,7 +1597,7 @@ Other Entity-Related Functions
residues, chains, bonds and torsions will be added to handle. This is
useful to combine several entities into one.
- :returns :class:`EntityHandle`
+ :returns: :class:`EntityHandle`
Residue Numbering
diff --git a/modules/seq/alg/pymod/renumber.py b/modules/seq/alg/pymod/renumber.py
index 899ad1e1626816e412b9056379d7c883a361d3bb..9f6dd02d56e9a1ff55c7c2c5e89ed6745f199af5 100644
--- a/modules/seq/alg/pymod/renumber.py
+++ b/modules/seq/alg/pymod/renumber.py
@@ -44,7 +44,9 @@ def Renumber(seq_handle, sequence_number_with_attached_view=1):
sequence and the full-length target sequence. The aligned model sequence or
the alignment itself with an attached view needs to be provided. Upon
succcess, the renumbered entity is returned.
- If an alignment is given, the sequence must
+ If an alignment is given, the first sequence of the alignment is considered
+ the full-length sequence and it must match the model sequence wherever it is
+ aligned (i.e. excluding gaps).
.. code-block:: python
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index f2e1edbf33088e1699b00e999db3d4c9f23b9173..5c6c384111b0f8d06167be582cb9906f07ee2b4b 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -19,7 +19,7 @@ Attaching Structures to Sequences
As OpenStructure is a computational structural biology framework, it is not
surprising that the sequence classes have been designed to work together with
-structural data. Each sequence can have an attached :class:`~mol.EntityView`
+structural data. Each sequence can have an attached :class:`~ost.mol.EntityView`
allowing for fast mapping between residues in the entity view and position in
the sequence.
@@ -45,16 +45,17 @@ sequence offset is 0.
Loading and Saving Sequences and Alignments
--------------------------------------------------------------------------------
-The :mod:`io` module supports input and output of common sequence formats.
-Single sequences can be loaded from disk with :func:`io.LoadSequence`,
-alignments are loaded with :func:`io.LoadAlignment` and lists of sequences are loaded with :func:`io.LoadSequenceList`. In addition to the file based input
-methods, sequences can also be loaded from a string:
+The :mod:`~ost.io` module supports input and output of common sequence formats.
+Single sequences can be loaded from disk with :func:`~ost.io.LoadSequence`,
+alignments are loaded with :func:`~ost.io.LoadAlignment` and lists of sequences
+are loaded with :func:`~ost.io.LoadSequenceList`. In addition to the file based
+input methods, sequences can also be loaded from a string:
.. code-block:: python
- seq_string='''>sequence
+ seq_string = '''>sequence
abcdefghiklmnop'''
- s=io.SequenceFromString(seq_string, 'fasta')
+ s = io.SequenceFromString(seq_string, 'fasta')
print s.name, s # will print "sequence abcdefghiklmnop"
Note that, in that case specifying the format is mandatory.
@@ -62,21 +63,24 @@ Note that, in that case specifying the format is mandatory.
The SequenceHandle
--------------------------------------------------------------------------------
-.. function:: CreateSequence(name, sequence)
+.. function:: CreateSequence(name, sequence, role="UNKNOWN")
Create a new :class:`SequenceHandle` with the given name and sequence.
- :param name: name of the sequence
- :type name: str
+ :param name: Name of the sequence
+ :type name: :class:`str`
:param sequence: String of characters representing the sequence. Only
'word' characters (no digits), '?', '-' and '.' are allowed. In an
upcoming release, '?' and '.' will also be forbidden so its best to
translate those to 'X' or '-'.
- :type sequence: str
+ :type sequence: :class:`str`
+ :param role: Role of the sequence (optional)
+ :type role: :class:`str`
:raises InvalidSequence: When the sequence string contains forbidden
characters. In the future, '?' and '.' will also raise this exception.
.. class:: SequenceHandle
+ ConstSequenceHandle
Represents a sequence. New instances are created with :func:`CreateSequence`.
@@ -130,7 +134,7 @@ The SequenceHandle
sequence, or, a sequence only consisting of hyphens, -1 is returned.
.. method:: AttachView(view)
- AttachView(view, [chain_name])
+ AttachView(view, chain_name)
Attach an :class:`~mol.EntityView` to sequence. The first signature requires
that the view contains one chain. If not, an :exc:`IntegrityError` is
@@ -176,6 +180,14 @@ The SequenceHandle
.. method:: SetName()
Set name of the sequence. Also available as the property :attr:`name`.
+
+ .. method:: GetOneLetterCode(pos)
+ __getitem__(pos)
+ __getitem__(slice)
+
+ :return: Character at position *pos* of sequence (also supports pythonic
+ slicing with [] operator)
+ :rtype: :class:`str`
.. attribute:: gapless_string
@@ -193,13 +205,29 @@ The SequenceHandle
Shorthand for :meth:`GetOffset`/:meth:`SetOffset`
+ .. attribute:: role
+
+ Role of this sequence.
+
+ :type: :class:`str`
+
.. method:: __len__()
- Returns the length of the sequence (including insertions and deletions)
+ :return: The length of the sequence (including insertions and deletions)
.. method:: __str__()
- Returns the sequence as a string.
+ :return: The sequence as a string.
+
+.. function:: SequenceFromChain(name, chain)
+
+ :return: Sequence extracted from one letter codes in given *chain* with a
+ view to the chain attached to it
+ :rtype: :class:`SequenceHandle`
+ :param name: Name of the sequence
+ :type name: :class:`str`
+ :param chain: Chain from which to extract sequence
+ :type chain: :class:`~ost.mol.ChainHandle` / :class:`~ost.mol.ChainView`
.. function:: Match(s1, s2)
@@ -212,16 +240,57 @@ The SequenceHandle
case-insensitive comparison of the two sequences. The character 'X' is
interpreted as a wild card character that always matches the other sequence.
-The SequenceList
+The SequenceList
--------------------------------------------------------------------------------
+.. function:: CreateSequenceList()
+
+ Creates and returns a new :class:`SequenceList` with no sequences.
+
.. class:: SequenceList
+ ConstSequenceList
+
+ Represents a list of sequences. The class provides a row-based interface.
+
+ .. method:: GetCount()
+ __len__()
+
+ :return: Number of sequences in the list.
+ :rtype: :class:`int`
+
+ .. method:: AddSequence(sequence)
+
+ Append a sequence to the list.
+
+ .. method:: GetMinLength()
+ GetMaxLength()
+
+ :return: Minimal / maximal length of the sequences in this list.
+ :rtype: :class:`int`
+
+ .. method:: FindSequence(name)
+
+ Find sequence with given *name*. If the alignment contains several sequences
+ with the same name, the first sequence is returned.
+
+ .. method:: SequencesHaveEqualLength()
+
+ :return: True if all sequences have same length.
+
+ .. method:: Take(n)
+
+ :return: First *n* (or last *-n* if *n* negative) sequences.
- Represents a list of sequences. The class provides a row-based interface. New
- instances are created with :func:`CreateSequenceList`.
+ .. method:: Slice(first, n)
+ :return: *n* sequences starting from *first*.
-The AlignmentHandle
+ .. method:: __getitem__(key)
+
+ :return: Access sequence(s) *key* (also supports pythonic slicing).
+
+
+The AlignmentHandle
--------------------------------------------------------------------------------
The :class:`AlignmentHandle` represents a list of aligned sequences. In
@@ -231,7 +300,7 @@ the same length. New instances of alignments are created with
Typically sequence alignments are used column-based, i.e by looking at an
aligned columns in the sequence alignment. To get a row-based (sequence) view
-on the sequence list, use :meth:`GetSequences()`.
+on the sequence list, use :meth:`~AlignmentHandle.GetSequences()`.
All functions that operate on an alignment will again produce a valid alignment.
This mean that it is not possible to change the length of one sequence, without
@@ -266,34 +335,35 @@ an alignment:
.. class:: AlignmentHandle
- .. note::
-
- Several of these methods just forward calls to the sequence. For more
- detailed information, have a look at the :class:`SequenceHandle`
- documentation.
-
.. method:: GetSequence(index)
- Returns the sequence at the given index, raising an IndexError when trying
- to access an inexistent sequence.
+ :return: Sequence at the given index, raising an IndexError when trying
+ to access an inexistent sequence.
+ :rtype: :class:`ConstSequenceHandle`
.. method:: GetSequences()
- Returns a list of all sequence of the alignment.
+ :return: List of all sequence of the alignment. Also available as
+ :attr:`sequences`.
+ :rtype: :class:`ConstSequenceList`
.. method:: GetLength()
+ __len__()
- Returns the length of the alignment.
+ :return: Length of the alignment.
+ :rtype: :class:`int`
.. method:: GetCount()
- Returns the number of sequences in the alignment.
-
+ :return: Number of sequences in the alignment. Also available as
+ :attr:`sequence_count`.
+ :rtype: :class:`int`
.. method:: ToString(width=80)
- Returns a formatted string version of the alignment. The sequences are
- split into smaller parts to fit into the number columns specified.
+ :return: Formatted string version of the alignment. The sequences are
+ split into smaller parts to fit into the number columns specified.
+ :rtype: :class:`str`
.. code-block:: python
@@ -310,16 +380,13 @@ an alignment:
.. method:: FindSequence(name)
- Find sequence with given name. If the alignment contains several sequences
- with the same name, the first sequence is returned.
+ :return: Sequence with given *name*. If the alignment contains several
+ sequences with the same name, the first sequence is returned.
.. method:: SetSequenceName(seq_index, name)
- Set the name of the sequence at index `seq_index` to name
-
- .. method:: SetSequenceOffset(seq_index, offset)
-
- Set the sequence offset of sequence at index `seq_index`
+ Set the name of the sequence at index `seq_index` to `name`
+ (see :attr:`SequenceHandle.name`).
.. method:: Copy()
@@ -327,18 +394,24 @@ an alignment:
.. method:: GetPos(seq_index, res_index)
- Get position of residue with index equal to `res_index` in sequence at index
- `seq_index`.
+ :return: Position of residue with index equal to `res_index` in sequence at
+ index `seq_index` (see :meth:`SequenceHandle.GetPos`)
.. method:: GetResidueIndex(seq_index, pos)
- Get residue index of residue at position `pos` in sequence at index
- `seq_index`.
+ :return: Residue index of residue at position `pos` in sequence at index
+ `seq_index` (see :meth:`SequenceHandle.GetResidueIndex`)
+
+ .. method:: GetResidue(seq_index, pos)
+
+ :return: Attached residue at position `pos` in sequence at index `seq_index`
+ (see :meth:`SequenceHandle.GetResidue`).
.. method:: AttachView(seq_index, view)
AttachView(seq_index, view, chain_name)
- Attach the given view to the sequence at index `seq_index`.
+ Attach the given view to the sequence at index `seq_index`
+ (see :meth:`SequenceHandle.AttachView`).
.. method:: Cut(start, end)
@@ -396,7 +469,8 @@ an alignment:
.. method:: GetSequenceOffset(index)
SetSequenceOffset(index, offset)
- Get/set the offset for sequence at *index*.
+ Get/set the offset for sequence at *index*
+ (see :attr:`SequenceHandle.offset`).
:param index: The index of the sequence
:type index: :class:`int`
@@ -407,7 +481,8 @@ an alignment:
.. method:: GetSequenceRole(index)
SetSequenceRole(index, role)
- Get/Set the sequence role for sequence at *index*.
+ Get/Set the sequence role for sequence at *index*
+ (see :attr:`SequenceHandle.role`).
:param index: The index of the sequence
:type index: :class:`int`
@@ -426,6 +501,109 @@ an alignment:
.. method:: RemoveSequence(index)
Remove sequence at *index* from the alignment.
+
+ .. attribute:: sequences
+
+ Shorthand for :meth:`GetSequences`
+
+ .. attribute:: sequence_count
+
+ Shorthand for :meth:`GetCount`
+
+ .. method:: __getitem__(pos)
+
+ :return: Column at position *pos* of alignment.
+ :rtype: :class:`AlignedColumn`
+
+ .. method:: __getitem__(slice)
+
+ :return: Columns defined by by pythonic slicing.
+ :rtype: :class:`AlignedRegion`
+
+
+.. class:: AlignedRegion
+
+ Represents a slice of an :class:`AlignmentHandle`.
+
+ .. method:: GetAlignmentHandle()
+
+ :return: Alignment from which we slices.
+ :rtype: :class:`AlignmentHandle`
+
+ .. method:: GetLength()
+ __len__()
+
+ :return: Number of columns in the slice.
+
+ .. method:: __getitem__(pos)
+
+ :return: Column at position *pos* within this slice.
+ :rtype: :class:`AlignedColumn`
+
+ .. attribute:: start
+
+ Starting position in alignment.
+
+ .. attribute:: end
+
+ One after end position in alignment.
+
+
+.. class:: AlignedColumn
+
+ .. method:: GetIndex()
+
+ :return: Position in alignment.
+
+ .. method:: GetRowCount()
+
+ :return: Number of rows in the column.
+
+ .. method:: GetResidue(row)
+
+ :return: Attached residue for sequence at given *row* of this column
+ (see :meth:`AlignmentHandle.GetResidue`).
+
+ .. method:: __getitem__(row)
+
+ :return: Character at given *row* of this column.
+ :rtype: :class:`str`
+
+ .. method:: __str__()
+
+ :return: String representation of column in alignment.
+
+
+Extracting views from sequences
+--------------------------------------------------------------------------------
+
+.. function:: ViewsFromSequences(seq1, seq2)
+
+ Returns a tuple of entity views containing only the atoms of the aligned
+ residues. The order of residues in the two views is guaranteed to be the same
+ but the order of atoms within each residue may differ. If the order of atoms
+ is crucial (e.g. for :func:`~ost.mol.alg.SuperposeSVD`) either prefilter the
+ attached views to include only one atom per residue or use the slower (approx.
+ 50% more runtime) :meth:`AlignmentHandle.GetMatchingBackboneViews`.
+
+ :return: Pair of views including all the aligned residues of the two given
+ sequences. An alignment is
+ :rtype: :class:`tuple` with two :class:`~ost.mol.EntityView`
+
+ :raises: :class:`Exception` if sequence lengths do not match or if any of the
+ sequences is lacking an attached view.
+
+.. function:: ViewsFromAlignment(aln, index1=0, index2=1)
+
+ :return: Pair of views as in :meth:`ViewsFromSequences`.
+ :rtype: :class:`tuple` with two :class:`~ost.mol.EntityView`
+
+ :param aln: Alignment from which to extract sequences.
+ :type aln: :class:`AlignmentHandle`
+ :param index1: Index of first sequence in *aln* to use.
+ :type index1: :class:`int`
+ :param index2: Index of second sequence in *aln* to use.
+ :type index2: :class:`int`
Handling Sequence Profiles