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)

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

scalar_score¶

float – The raw_score scaled according to its average

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