Helper object for Contact-score computation
Definition at line 9 of file contact_score.py.
◆ __init__()
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ent, |
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contact_d = 5.0, |
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contact_mode = "aa" |
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◆ _SetupContacts()
◆ _SetupHRInterfaceResidues()
| _SetupHRInterfaceResidues |
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◆ _SetupInterfaceResidues()
| _SetupInterfaceResidues |
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◆ chain_names()
Chain names in :attr:`~view`
Names are sorted
:type: :class:`list` of :class:`str`
Definition at line 96 of file contact_score.py.
◆ contact_d()
Pairwise distance of residues to be considered as contacts
Given at :class:`ContactScorer` construction
:type: :class:`float`
Definition at line 86 of file contact_score.py.
◆ contact_mode()
The contact mode
Can either be "aa", meaning that all atoms are considered to identify
contacts, or "repr" which only considers distances between
representative atoms. For peptides thats CB (CA for GLY), for
nucleotides thats C3'.
:type: :class:`str`
Definition at line 73 of file contact_score.py.
◆ contacts()
Interchain contacts
Organized as :class:`dict` with key (cname1, cname2) and values being
a set of tuples with the respective residue indices.
cname1 < cname2 evaluates to True.
Definition at line 118 of file contact_score.py.
◆ GetChain()
| GetChain |
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chain_name |
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Get chain by name
:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`
Definition at line 165 of file contact_score.py.
◆ GetSequence()
| GetSequence |
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chain_name |
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Get sequence of chain
Returns sequence of specified chain as raw :class:`str`
:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`
Definition at line 176 of file contact_score.py.
◆ hr_contacts()
Human readable interchain contacts
Human readable version of :attr:`~contacts`. Simple list with tuples
containing two strings specifying the residues in contact. Format:
<cname>.<rnum>.<ins_code>
Definition at line 130 of file contact_score.py.
◆ hr_interface_residues()
| hr_interface_residues |
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Human readable interface residues
Human readable version of :attr:`interface_residues`. :class:`list` of
strings specifying the interface residues in format:
<cname>.<rnum>.<ins_code>
Definition at line 154 of file contact_score.py.
◆ interacting_chains()
| interacting_chains |
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Pairs of chains in :attr:`~view` with at least one contact
:type: :class:`list` of :class:`tuples`
Definition at line 108 of file contact_score.py.
◆ interface_residues()
| interface_residues |
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Interface residues
Residues in each chain that are in contact with any other chain.
Organized as :class:`dict` with key cname and values the respective
residue indices in a :class:`set`.
Definition at line 142 of file contact_score.py.
◆ view()
The structure depending on *contact_mode*
Full view in case of "aa", view that only contains representative
atoms in case of "repr".
:type: :class:`ost.mol.EntityView`
Definition at line 62 of file contact_score.py.
◆ _chain_names
◆ _contact_d
◆ _contact_mode
◆ _contacts
◆ _hr_contacts
◆ _hr_interface_residues
◆ _interacting_chains
◆ _interface_residues
◆ _sequence
◆ _view
◆ chain_names
◆ contact_mode
The documentation for this class was generated from the following file:
