# conkit.core.contact module¶

Contact container used throughout ConKit

class 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
define_match()[source]

Define a contact as matching contact

define_mismatch()[source]

Define a contact as mismatching contact

define_unknown()[source]

Define a contact with unknown status

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

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

class ContactMatchState[source]

Bases: enum.Enum

Enumerated class to store state constants for each contact

matched = 1
mismatched = 2
unknown = 0