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schwede
ProMod3
Commits
14139e3c
Commit
14139e3c
authored
10 years ago
by
Bienchen
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Removed loop part from meld
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meld/doc/CMakeLists.txt
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meld/doc/CMakeLists.txt
meld/doc/index.rst
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meld/doc/index.rst
meld/doc/loop.rst
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meld/doc/loop.rst
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meld/doc/CMakeLists.txt
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MELD_RST
index.rst
loop.rst
rawmodel.rst
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meld/doc/index.rst
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.. module:: promod3.meld
:synopsis: Coordinate modeling and sampling
This module contains functions and classes to model protein structures from sequence.
This module contains functions and classes to build raw-models for protein
structures from templates.
.. toctree::
:maxdepth: 2
loop
rawmodel
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meld/doc/loop.rst
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Loop Modeling
================================================================================
.. currentmodule:: sm.meld
Loop Modeling API
--------------------------------------------------------------------------------
.. class:: LoopCandidate(gap, bb_list)
A loop candidate holds the coordinates of the four backbone atoms for a given
peptide fragment as well as the sequence.
:param gap: The structural gap
:type gap: :class:`StructuralGap`
:param bb_list: List of peptide backbone coordinates
:type bb_list: :class:`BackboneList`
.. method:: InsertInto(entity)
Inserts the loop candidate into the given entity. This honours the start and
end point stored in the gap. Missing residues and atoms will be inserted
into the structure.
:param entity:
:type entity: :class:`~ost.mol.EntityHandle`
:returns: True on success, false if the insertion failed
:rtype: bool
.. method:: RmsdTo(entity)
Calculates the RMSD to the corresponding backbone fragment in *entity*.
Raises a RuntimeError if not all backbone atoms exist.
:param entity:
:type entity: :class:`~ost.mol.EntityHandle`
:rtype: float
.. method:: ToEntity()
Returns an entity holding this backbone fragment. Residue numbers go from
gap.start to gap.end.
:rtype: :class:`~ost.mol.EntityHandle`
.. attribute:: allatom_score
If set, the allatom_score of this fragment
.. attribute:: clash_bb_score
The clash score of the loop candidate with sidechain atoms
.. attribute:: clash_score
The sum of backbone and sidechain clash scores
.. attribute:: clash_sc_score
Clash score with sidechain atoms
.. attribute:: coords
Access to the actual coordinates
:type: :class:`BackboneList`
.. attribute:: correl
Correlation with density
.. attribute:: gap
The structural gap
.. attribute:: packing_score
Packing score of this loop candidate
.. attribute:: reduced_score
Reduced score
.. attribute:: score
Total score of this loop candidate.
.. attribute:: torsion_score
Torsion score of this loop candidate
.. class:: LoopCandidates(model)
A list of loop candidates with a few helper methods to make your life easier.
The candidates are supposed to be loop candidates for the same gap. However,
they are not required to have the same start and end position, e.g. due to
extension of the gap.
:param model: The model the candidates are for.
:type model: :class:`~ost.mol.EntityHandle`
.. method:: Add(candidate)
Add a new candidate
:param candidate:
:type candidate: :class:`LoopCandidate`
.. method:: SortByCorrel([, increasing])
Sort loop candidates by correlation score
:param increasing: If true, the candidates are sorted in increasing order
:type increasing: bool
.. method:: SortByScore([, increasing])
Sort loop canditates by total score
:param increasing: If true, the candidates are sorted in increasing order
:type increasing: bool
.. attribute:: model
The model the candidates are for
:type: :class:`~ost.mol.EntityHandle`
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