Storage space for a contact pair
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_false_positive |
A boolean status for the contact |
is_true_positive |
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_false_positive() |
Define a contact as false positive |
define_true_positive() |
Define a contact as true positive |
remove(id) |
Remove a child |
distance_bound¶The lower and upper distance boundary values of a contact pair in Ångstrom [Default: 0-8Å].
is_false_positive¶A boolean status for the contact
| Parameters: | is_false_positive : bool
|
|---|
is_true_positive¶A boolean status for the contact
| Parameters: | is_true_positive : bool
|
|---|
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