ost.mol.alg.qsscoring Namespace Reference

Data Structures
class	QSscoreError
class	QSscorer
class	QSscoreEntity
class	OligoLDDTScorer
class	MappedLDDTScorer
class	_CachedRMSD

Functions
def	FilterContacts
def	GetContacts

Variables
tuple	__all__

Detailed Description

Scoring of quaternary structures (QS). The QS scoring is according to the paper
by `Bertoni et al. <https://dx.doi.org/10.1038/s41598-017-09654-8>`_.

.. warning::

  The `qsscoring` module is deprecated. Consider using the newer implementation
  in :mod:`~ost.mol.alg.qsscore` instead.

.. note ::

  Requirements for use:

  - A default :class:`compound library <ost.conop.CompoundLib>` must be defined
    and accessible via :func:`~ost.conop.GetDefaultLib`. This is set by default
    when executing scripts with ``ost``. Otherwise, you must set this with
    :func:`~ost.conop.SetDefaultLib`.
  - ClustalW must be installed (unless you provide chain mappings)
  - Python modules `numpy` and `scipy` must be installed and available
    (e.g. use ``pip install scipy numpy``)

Function Documentation

def ost.mol.alg.qsscoring.FilterContacts	(		contacts,
			chain_names
	)

Filter contacts to contain only contacts for chains in *chain_names*.

:param contacts: Connectivity dictionary as produced by :func:`GetContacts`.
:type contacts:  :class:`dict`
:param chain_names: Chain names to keep.
:type chain_names:  :class:`list` or (better) :class:`set`
:return: New connectivity dictionary (format as in :func:`GetContacts`)
:rtype:  :class:`dict`

Definition at line 882 of file qsscoring.py.

def ost.mol.alg.qsscoring.GetContacts	(		entity,
			calpha_only,
			dist_thr = 12.0
	)

Get inter-chain contacts of a macromolecular entity.

Contacts are pairs of residues within a given distance belonging to different
chains. They are stored once per pair and include the CA/CB-CA/CB distance.

:param entity: An entity to check connectivity for.
:type entity:  :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
:param calpha_only: If True, we only consider CA-CA distances. Else, we use CB
                    unless the residue is a GLY.
:type calpha_only:  :class:`bool`
:param dist_thr: Maximal CA/CB-CA/CB distance to be considered in contact.
:type dist_thr:  :class:`float`
:return: A connectivity dictionary. A pair of residues with chain names
         *ch_name1* & *ch_name2* (*ch_name1* < *ch_name2*), residue numbers
         *res_num1* & *res_num2* and distance *dist* (<= *dist_thr*) are
         stored as *result[ch_name1][ch_name2][res_num1][res_num2]* = *dist*.
:rtype:  :class:`dict`

Definition at line 905 of file qsscoring.py.

Variable Documentation

tuple __all__

Initial value:

= ('QSscoreError', 'QSscorer', 'QSscoreEntity', 'FilterContacts',
           'GetContacts', 'OligoLDDTScorer', 'MappedLDDTScorer')

Definition at line 2994 of file qsscoring.py.