ost::mol::alg::qsscoring Namespace Reference
Detailed Description
Scoring of quaternary structures as in Martino's 2017 paper.
.. 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``)
Authors: Gerardo Tauriello, Martino Bertoni
Function Documentation
def ost::mol::alg::qsscoring::FilterContacts |
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contacts, |
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chain_names | |
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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 831 of file qsscoring.py.
def ost::mol::alg::qsscoring::GetContacts |
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entity, |
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calpha_only, |
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dist_thr = 12.0 | |
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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 854 of file qsscoring.py.
Variable Documentation
Initial value:('QSscoreError', 'QSscorer', 'QSscoreEntity', 'FilterContacts',
'GetContacts')
Definition at line 2403 of file qsscoring.py.