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)
Attributes
distance_bound |
The lower and upper distance boundary values of a contact pair in Ångstrom [Default: 0-8Å]. |
id |
The ID of the selected entity |
is_match |
A boolean status for the contact |
is_mismatch |
A boolean status for the contact |
is_unknown |
A boolean status for the contact |
lower_bound |
The lower distance boundary value |
raw_score |
The prediction score for the contact pair |
res1 |
The amino acid of residue 1 [default: X] |
res2 |
The amino acid of residue 2 [default: X] |
res1_chain |
The chain for residue 1 |
res2_chain |
The chain for residue 2 |
res1_seq |
The residue sequence number of residue 1 |
res2_seq |
The residue sequence number of residue 2 |
res1_altseq |
The alternative residue sequence number of residue 1 |
res2_altseq |
The alternative residue sequence number of residue 2 |
scalar_score |
The raw_score scaled according to the average raw_score |
status |
An indication of the residue status, i.e true positive, false positive, or unknown |
upper_bound |
The upper distance boundary value |
weight |
A separate internal weight factor for the contact pair |
Methods
add (entity) |
Add a child to the Entity |
copy () |
Create a shallow copy of Entity |
deepcopy () |
Create a deep copy of Entity |
define_match () |
Define a contact as matching contact |
define_mismatch () |
Define a contact as mismatching contact |
define_unknown () |
Define a contact with unknown status |
remove (id) |
Remove a child |
distance_bound
¶The lower and upper distance boundary values of a contact pair in Ångstrom [Default: 0-8Å].
is_match
¶A boolean status for the contact
is_mismatch
¶A boolean status for the contact
is_unknown
¶A boolean status for the contact
lower_bound
¶The lower distance boundary value
raw_score
¶The prediction score for the contact pair
res1
¶The amino acid of residue 1 [default: X]
res1_altseq
¶The alternative residue sequence number of residue 1
res1_chain
¶The chain for residue 1
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
¶The chain for residue 2
res2_seq
¶The residue sequence number of residue 2
status
¶An indication of the residue status, i.e true positive, false positive, or unknown
upper_bound
¶The upper distance boundary value
weight
¶A separate internal weight factor for the contact pair