Contact container used throughout ConKit
Contact
(res1_seq, res2_seq, raw_score, distance_bound=(0, 8))[source]¶Bases: conkit.core.entity.Entity
A contact pair template to store all associated information
Examples
>>> from conkit.core import Contact
>>> contact = Contact(1, 25, 1.0)
>>> print(contact)
Contact(id="(1, 25)" res1="A" res1_seq=1 res2="A" res2_seq=25 raw_score=1.0)
distance_bound
¶tuple – The lower and upper distance boundary values of a contact pair in Ångstrom [Default: 0-8Å].
id
¶str – A unique identifier
true_positive
¶bool – A boolean status for the contact
true_negative
¶bool – A boolean status for the contact
false_positive
¶bool – A boolean status for the contact
false_negative
¶bool – A boolean status for the contact
status_unknown
¶bool – A boolean status for the contact
lower_bound
¶int – The lower distance boundary value
raw_score
¶float – The prediction score for the contact pair
res1
¶str – The amino acid of residue 1 [default: X]
res2
¶str – The amino acid of residue 2 [default: X]
res1_chain
¶str – The chain for residue 1
res2_chain
¶str – The chain for residue 2
res1_seq
¶int – The residue sequence number of residue 1
res2_seq
¶int – The residue sequence number of residue 2
res1_altseq
¶int – The alternative residue sequence number of residue 1
res2_altseq
¶int – The alternative residue sequence number of residue 2
status
¶int – An indication of the residue status
upper_bound
¶int – The upper distance boundary value
weight
¶float – A separate internal weight factor for the contact pair
define_match
(*args, **kwargs)¶define_mismatch
(*args, **kwargs)¶define_unknown
(*args, **kwargs)¶distance_bound
The lower and upper distance boundary values of a contact pair in Ångstrom [Default – 0-8Å].
false_negative
false_positive
is_match
¶is_mismatch
¶is_unknown
¶lower_bound
The lower distance boundary value
raw_score
res1
The amino acid of residue 1 [default – X]
res1_altseq
The alternative residue sequence number of residue 1
res1_chain
res1_seq
The residue sequence number of residue 1
res2
The amino acid of residue 2 [default – X]
res2_altseq
The alternative residue sequence number of residue 2
res2_chain
res2_seq
The residue sequence number of residue 2
scalar_score
status
An indication of the residue status
status_unknown
true_negative
true_positive
upper_bound
The upper distance boundary value
weight