# conkit.core.contact module¶

Contact container used throughout ConKit

class Contact(res1_seq, res2_seq, raw_score, distance_bound=(0, 8))[source]

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