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Backbone Score Environment
BackboneScoreEnv class

class
promod3.scoring. BackboneScoreEnv (seqres)
The backbone score environment contains and handles all modelspecific data
used by the scorers. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
process with all known data (positions extracted from template, psipred
prediction, etc). All scorers attached to that environment will see that data
and can calculate scores accordingly.
Scoring with this setup is a two step process:
 Set the positions you want to score in the environment to make it available
to all attached scorers
 Call the scorers to get the desired scores
One problem that might occur is that you mess around with the environment and
at some point you want to restore the original state. The
BackboneScoreEnv provides a Stash / Pop mechanism to perform this
task.
To access parts of the environment there are two key arguments to consider:
 chain_idx: Index of chain as it occurs in seqres (0 for single sequence)
 start_resnum: Residue number defining the position in the SEQRES of chain
with index chain_idx. The numbering starts for every chain with the
value 1.

Copy ()


SetInitialEnvironment (env_structure)
Sets structural environment with which loops to be scored interact. If
structural data was already set, all the existing data gets cleared first.
Parameters:  env_structure (ost.mol.EntityHandle ) – Structral data to be set as environment. The chains
in env_structure are expected to be in the same
order as the SEQRES items provided in constructor. 
Raises:  RuntimeError if env is inconsistent with
SEQRES set in constructor. This can be because of corrupt residue
numbers or sequence mismatches. 

SetEnvironment (bb_list, start_resnum, chain_idx=0)
Add/update structural information in environment. If structural data for
specific residues is already set, the data gets resetted for these
positions.
Parameters: 
 bb_list (
BackboneList ) – Structural data to be set as environment.
 start_resnum (
int / ost.mol.ResNum ) – Res. number defining the position in the SEQRES.
 chain_idx (
int ) – Index of chain the structural data belongs to.

Raises:  RuntimeError if sequence of bb_list is
inconsistent with previously SEQRES set in constructor or when
either start_resnum or chain_idx point to invalid positions in
the SEQRES.


ClearEnvironment (start_resnum, num_residues, chain_idx=0)
Clears a stretch of length num_residues in the environment in chain
with idx chain_idx starting from residue number start_resnum
Parameters: 
 start_resnum (
int ) – Start of stretch to clear
 num_residues (
int ) – Length of stretch to clear
 chain_idx (
int ) – Chain the stretch belongs to

Raises:  RuntimeError when either start_resnum or
chain_idx point to invalid positions in the SEQRES.


SetPsipredPrediction (pred)
Set the psipred prediction, which is necessary to calculate some scores.
Parameters:  pred (PsipredPrediction / list of
PsipredPrediction ) – Psipred prediction to set (one per chain). 
Raises:  RuntimeError if the number of predictions is
inconsistent with the number of internal chains or when one of the
predictions’ sizes is inconsistent with the internal SEQRES size. 

AddPairwiseFunction (function, function_type)
Adds a pairwise function that can be used in ApplyPairwiseFunction() .

ApplyPairwiseFunction (chain_idx_one, resnum_one, chain_idx_two, resnum_two, f_idx)
Define two residues to be evaluated with a given pairwise function. This
data can then be used by scorers. Note that the pairs are symmetric and so
there is no need to add them twice with switched residues.
Parameters: 
 chain_idx_one (
int ) – Chain index of first residue
 resnum_one (
int ) – Res. number of first residue
 chain_idx_two (
int ) – Chain index of second residue
 resnum_two (
int ) – Res. number of second residue
 f_idx (
int ) – Index of pairwise function (as returned by
AddPairwiseFunction() )

Raises:  RuntimeError if any of the chain indices or
res. numbers is invalid, the interaction partners are the same
residue or when f_idx is an invalid index.


Stash (start_rnum, num_residues, chain_idx)
FILO style stashing. You can perform up to 100 stash operations to save
the current state of certain stretches in the environment. This state can
be restored by calling Pop() . In one stash operation you can either
stash one stretch by providing integers as input or several stretches by
providing lists of integers.
Parameters: 
 start_rnum (
int / list of int ) – start rnum of stretch to stash
 num_residues (
int / list of int ) – length of stretch to stash
 chain_idx (
int / list of int ) – chain idx of stretch to stash


Pop ()
Remove and apply the the last stash operation.

GetSeqres ()
Returns:  SEQRES that was set in constructor (one sequence per chain). 
Return type:  ost.seq.SequenceList 
Pairwise function classes

class
promod3.scoring. PairwiseFunctionType
Enumerates the pairwise function types. Possible values:
 CA_PAIRWISE_FUNCTION  Evaluate CA atoms distances.
 CB_PAIRWISE_FUNCTION  Evaluate CB atoms distances.

class
promod3.scoring. PairwiseFunction
Base class for any pairwise function.

Score (distance)
Returns:  Score for a given pairwise distance 
Return type:  float 
Parameters:  distance (float ) – Pairwise distance 

class
promod3.scoring. ConstraintFunction (min_dist, max_dist, values)
Inherits all functionality of PairwiseFunction .
Defines a constraint function. The score for a distance between min_dist and
max_dist is determined by linear interpolation assuming the first and last
value exactly lying on min_dist and max_dist. For distances outside the
range defined by min_dist and max_dist, the returned score is 0.0.
Parameters: 
 min_dist (
float ) – Minimal distance to be considered
 max_dist (
float ) – Maximal distance to be considered
 values (
list of float ) – The possible values that get returned when the distance is
between min_dist and max_dist

Raises:  RuntimeError if min_dist >= max_dist or when
min_dist or max_dist are negative or when values contains no
elements


class
promod3.scoring. ContactFunction (max_dist, score)
Inherits all functionality of PairwiseFunction .
Defines a simple contact function. The score value is score if
distance < max_dist and 0.0 otherwise.
Parameters: 
 max_dist (
float ) – Maximal distance to be in contact
 score (
float ) – Value that gets returned if in contact

Convenient construction of pairwise functions

class
promod3.scoring. DiscoContainer (seqres[, function_type = CA_PAIRWISE_FUNCTION])
A container collecting structural information until it can be added in form
of ConstraintFunction to a BackboneScoreEnv .
The constraint functions are built after the principle of QMEANDisCo.

AddStructuralInfo (aln)
Parameters:  aln (ost.seq.AlignmentHandle ) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached. 
Raises:  RuntimeError if number of sequences in aln is
not two, the SEQRES does not match or when the second sequence in
aln has no view attached. 

AttachConstraints (env, chain_indices[, cluster_thresh = 0.5, gamma = 70.0])
Generates distance constraints and adds it to env.
It first clusters the added sequences with a pairwise normalised sequence
similarity based on BLOSUM62. It’s a hierarchical clustering with with an
average distance metric and cluster_thresh as threshold to merge two
clusters. Constraint functions are built for every cluster and finally
merged. The influence of the per cluster constraint functions to the overall
function depends on the clusters average sequence similarity to the
target SEQRES. How fast this influence vanishes gets controlled by gamma.
The higher it is, the faster vanishes the influence of structural info
from distant clusters. The final pairwise cluster functions get then
directly added to the scoring env.
Parameters: 
 env (
BackboneScoreEnv ) – The scoring env to which the constraint
should be added
 chain_indices (
list of int ) – Indices of chains for which the constraints should
be added
 cluster_thresh (
float ) – Controls the clustering behaviour at the initial
stage of constraint construction
 gamma (
float ) – Controls how fast the influence of constraint
functions of distant clusters vanishes

Raises:  RuntimeError if one of the chain_indices is
invalid or the SEQRES set in env for specified chain is
inconsistent with SEQRES you initialized the DiscoContainer with


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