You are reading the documentation for version 1.9 of OpenStructure. You may also want to read the documentation for:
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.7.1
1.8
devel

Parameters: 


Returns:  True if all residues (beside gapped ones) are connected, False otherwise. 
AlignToSEQRES
(chain, seqres, try_resnum_first=False, validate=True)¶Aligns the residues of chain to the SEQRES sequence, inserting gaps where needed. The function uses the connectivity of the protein backbone to find consecutive peptide fragments. These fragments are then aligned to the SEQRES sequence.
All the nonligand, peptidelinking residues of the chain must be listed in SEQRES. If there are any additional residues in the chain, the function raises a ValueError.
If ‘try_resnum_first’ is set, building the alignment following residue numbers is tried first.
If ‘validate’ is set (default), the alignment is checked using
ValidateSEQRESAlignment()
.
Parameters: 


Returns:  The alignment of the residues in the chain and the SEQRES entries. 
Return type: 
AlignmentFromChainView
(chain, handle_seq_name='handle', view_seq_name='view')¶Creates and returns the sequence alignment of the given chain view to the chain handle. The alignment contains two sequences, the first containing all nonligand peptidelinking residues, the second containing all nonligand peptidelinking residues that are part of the view.
Parameters: 


Returns:  The alignment 
Return type: 
Conservation
(aln, assign=true, prop_name="cons", ignore_gap=false)¶Calculates conservation scores for each column in the alignment, according to the ConSurf method (Armon et al., J. Mol. Biol. (2001) 307, 447463).
The conservation score is a value between 0 and 1. The bigger the number the more conserved the aligned residues are.
Parameters: 


LocalAlign
(seq1, seq2, subst_weight, gap_open=5, gap_ext=2)¶Performs a Smith/Waterman local alignment of seq1 and seq2 and returns the bestscoring alignments as a list of pairwise alignments.
Example:
seq_a = seq.CreateSequence('A', 'acdefghiklmn')
seq_b = seq.CreateSequence('B', 'acdhiklmn')
alns = seq.alg.LocalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
print alns[0].ToString(80)
# >>> A acdefghiklmn
# >>> B acdhiklmn
Parameters: 


Returns:  A list of bestscoring, nonoverlapping alignments of seq1 and seq2. Since alignments always start with a replacement, the start is stored in the sequence offset of the two sequences. 
GlobalAlign
(seq1, seq2, subst_weight, gap_open=5, gap_ext=2)¶Performs a Needleman/Wunsch global alignment of seq1 and seq2 and returns the bestscoring alignment.
Example:
seq_a = seq.CreateSequence('A', 'acdefghiklmn')
seq_b = seq.CreateSequence('B', 'acdhiklmn')
alns = seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
print alns[0].ToString(80)
# >>> A acdefghiklmn
# >>> B acdhiklmn
Parameters: 


Returns:  Bestscoring alignment of seq1 and seq2. 
ShannonEntropy
(aln, ignore_gaps=True)¶Returns the percolumn Shannon entropies of the alignment. The entropy describes how conserved a certain column in the alignment is. The higher the entropy is, the less conserved the column. For a column with no amino aids, the entropy value is set to NAN.
Parameters: 


Returns:  List of column entropies 
SemiGlobalAlign
(seq1, seq2, subst_weight, gap_open=5, gap_ext=2)¶Performs a semiglobal alignment of seq1 and seq2 and returns the best scoring alignment. The algorithm is Needleman/Wunsch same as GlobalAlign, but without any gap penalty for starting or ending gaps. This is prefereble whenever one of the sequences is significantly shorted than the other. This make it also suitable for fragment assembly.
Example:
seq_a=seq.CreateSequence('A', 'abcdefghijklmnok')
seq_b=seq.CreateSequence('B', 'cdehijk')
alns=seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
print alns[0].ToString(80)
# >>> A abcdefghijklmnok
# >>> B cdehijk
Parameters: 


Returns:  bestscoring alignment of seq1 and seq2. 
Renumber
(seq_handle, sequence_number_with_attached_view=1)¶Function to renumber an entity according to an alignment between the model sequence and the fulllength target sequence. The aligned model sequence or the alignment itself with an attached view needs to be provided. Upon succcess, the renumbered entity is returned. If an alignment is given, the first sequence of the alignment is considered the fulllength sequence and it must match the model sequence wherever it is aligned (i.e. excluding gaps).
from ost.seq.alg import renumber
from ost.bindings.clustalw import *
ent = io.LoadPDB("path_to_model")
s = io.LoadSequence("path_to_full_length_fasta_seqeunce")
pdb_seq = seq.SequenceFromChain("model", ent.chains[0])
aln = ClustalW(s, pdb_seq)
aln.AttachView(1, ent.chains[0].Select(""))
e = Renumber(aln.sequences[1])
io.SavePDB(e, "renum.pdb")
Parameters: 


Raises: 

This is a set of functions for predicting pairwise contacts from a multiple sequence alignment (MSA). The core method here is mutual information which uses coevolution to predict contacts. Mutual information is complemented by two other methods which score pairs of columns of a MSA from the likelyhood of certain amino acid pairs to form contacts (statistical potential) and the likelyhood of finding certain substitutions of aminioacid pairs in columns of the MSA corresponding to interacting residues.
ContactPredictionScoreResult
¶Object containing the results form a contact prediction.
matrix
¶An NxN FloatMatrix
where N is the length of the alignment.
The element i,j corresponds to the score of the corresponding
columns of the MSA. High scores correspond to high likelyhood of
a contact.
sorted_indices
¶List of all indices pairs i,j, containing (N*N1)/2 elements, as the matrix is symmetrical and elements in the diagonal are ignored. The indices are sorted from the pair most likely to form a contact to the least likely one.
GetScore
(i, j)¶returns matrix(i,j)
Parameters: 


SetScore
(i, j, score)¶Sets matrix(i,j) to score
Parameters: 


PredictContacts
(ali)¶Predicts contacts from a multiple sequence alignment using a combination of Mutual Information (MI) and the Contact Substitution Score (CoEvoSc). MI is calculated with the APC and small number corrections as well as with a transformation into Zscores. The CoEvoSc is calculated using the default PairSubstWeightMatrix (see seq.alg.LoadDefaultPairSubstWeightMatrix). The final score for a pair of columns (i,j) of ali is obtained from:
Sc(i,j)=MI(i,j)exp(CoEvoSc(i,j)) if (i,j) >=0
Sc(i,j)=MI(i,j)exp(1CoEvoSc(i,j)) if (i,j) <0
Parameters:  ali (AlignmentHandle ) – The multiple sequence alignment 

CalculateMutualInformation
(aln, weights=LoadConstantContactWeightMatrix(), apc_correction=true, zpx_transformation=true, small_number_correction=0.05)¶Calculates the mutual information (MI) from a multiple sequence alignemnt. Contributions of each pair of aminoacids are weighted using the matrix weights (weighted mutual information). The average product correction (apc_correction) correction and transformation into Zscores (zpx_transofrmation) increase prediciton accuracy by reducing the effect of phylogeny and other noise sources. The small number correction reduces noise for alignments with small number of sequences of low diversity.
Parameters: 


CalculateContactScore
(aln, weights=LoadDefaultContactWeightMatrix())¶Calculates the Contact Score (CoSc) from a multiple sequence alignment. For each pair of residues (i,j) (pair of columns in the MSA), CoSc(i,j) is the average over the values of the weights corresponding to the amino acid pairs in the columns.
Parameters: 


CalculateContactSubstitutionScore
(aln, ref_seq_index=0, weights=LoadDefaultPairSubstWeightMatrix())¶Calculates the Contact Substitution Score (CoEvoSc) from a multiple sequence alignment. For each pair of residues (i,j) (pair of columns in the MSA), CoEvoSc(i,j) is the average over the values of the weights corresponding to substituting the amino acid pair in the reference sequence (given by ref_seq_index) with all other pairs in columns (i,j) of the aln.
Parameters: 


LoadDefaultContactWeightMatrix
()¶Returns:  CPE, a ContactWeightMatrix that was calculated from a large (>15000) set of
high quality crystal structures as CPE=log(CF(a,b)/NCF(a,b)) and then normalised so that all its elements are comprised between 0 and 1. CF(a,b) is the frequency of amino acids a and b for pairs of contacting residues and NCF(a,b) is the frequency of amino acids a and b for pairs of noncontacting residues. Apart from weights for the standard amino acids, this matrix gives a weight of 0 to all pairs for which at least one aminoacid is a gap. 

LoadConstantContactWeightMatrix
()¶Returns:  A ContactWeightMatrix . This matrix gives a weight of one to all pairs of
standard aminoacids and a weight of 0 to pairs for which at least one aminoacid is a gap. 

LoadDefaultPairSubstWeightMatrix
()¶Returns:  CRPE, a PairSubstWeightMatrix that was calculated from a large (>15000) set of
high quality crystal structures as CRPE=log(CRF(ab>cd)/NCRF(ab>cd)) and then normalised so that all its elements are comprised between 0 and 1. CRF(ab>cd) is the frequency of replacement of a pair of amino acids a and b by a pair c and d in columns of the MSA corresponding to contacting residues and NCRF(ab>cd) is the frequency of replacement of a pair of amino acids a and b by a pair c and d in columns of the MSA corresponding to noncontacting residues. Apart from weights for the standard amino acids, this matrix gives a weight of 0 to all pair substitutions for which at least one aminoacid is a gap. 

PairSubstWeightMatrix
(weights, aa_list)¶This class is used to associate a weight to any substitution from one aminoacid pair (a,b) to any other pair (c,d).
weights
¶A FloatMatrix4
of size NxNxNxN, where N=len(aa_list)
aa_list
¶A CharList
of one letter codes of the amino acids for which weights are found in the weights matrix.
Given a multiple sequence alignment between a reference sequence (first sequence in alignment) and a list of structures (remaining sequences in alignment with an attached view to the structure), this set of functions can be used to analyze differences between the structures.
Example:
# SETUP: aln is multiple sequence alignment, where first sequence is the
# reference sequence and all others have a structure attached
# clip alignment to only have parts with at least 3 sequences (incl. ref.)
# > aln will be cut and clip_start is 1st column of aln that was kept
clip_start = seq.alg.ClipAlignment(aln, 3)
# get variance measure and distance to mean for each residue pair
d_map = seq.alg.CreateDistanceMap(aln)
var_map = seq.alg.CreateVarianceMap(d_map)
dist_to_mean = seq.alg.CreateDist2Mean(d_map)
# report min. and max. variances
print "MINMAX:", var_map.Min(), "", var_map.Max()
# get data and jsonstrings for further processing
var_map_data = var_map.GetData()
var_map_json = var_map.GetJsonString()
dist_to_mean_data = dist_to_mean.GetData()
dist_to_mean_json = dist_to_mean.GetJsonString()
ClipAlignment
(aln, n_seq_thresh=2, set_offset=true, remove_empty=true)¶Clips alignment so that first and last column have at least the desired number of structures.
Parameters: 


Returns:  Starting column (0indexed), where cut region starts (w.r.t. original aln). 1, if there is no region in the alignment with at least the desired number of structures. 
Return type: 

CreateDistanceMap
(aln)¶Create distance map from a multiple sequence alignment.
The algorithm requires that the sequence alignment consists of at least two
sequences. The sequence at index 0 serves as a frame of reference. All the
other sequences must have an attached view and a properly set sequence offset
(see SetSequenceOffset()
).
For each of the attached views, the Calpha distance pairs are extracted and mapped onto the corresponding Calpha distances in the reference sequence.
Parameters:  aln (AlignmentHandle ) – Multiple sequence alignment. 

Returns:  Distance map. 
Return type:  DistanceMap 
Raises:  Exception if aln has less than 2 sequences or any sequence (apart from index 0) is lacking an attached view. 
CreateVarianceMap
(d_map, sigma=25)¶Returns:  Variance measure for each entry in d_map. 

Return type:  
Parameters: 

Raises:  Exception if d_map has no entries. 
CreateDist2Mean
(d_map)¶Returns:  Distances to mean for each structure in d_map. Structures are in the same order as passed when creating d_map. 

Return type:  Dist2Mean 
Parameters:  d_map (DistanceMap ) – Distance map as created with CreateDistanceMap() . 
Raises:  Exception if d_map has no entries. 
Distances
¶Container used by DistanceMap
to store a pair wise distance for each
structure. Each structure is identified by its index in the originally used
alignment (see CreateDistanceMap()
).
GetDataSize
()¶Returns:  Number of pairwise distances. 

Return type:  int 
GetAverage
()¶Returns:  Average of all distances. 

Return type:  float 
Raises:  Exception if there are no distances. 
GetMin
()¶GetMax
()¶Returns:  Minimal/maximal distance. 

Return type:  tuple (distance (float ), index (int )) 
Raises:  Exception if there are no distances. 
GetDataElement
(index)¶Returns:  Element at given index. 

Return type:  tuple (distance (float ), index (int )) 
Parameters:  index (int ) – Index within list of distances (must be < GetDataSize() ). 
Raises:  Exception if there are no distances or index out of bounds. 
GetStdDev
()¶Returns:  Standard deviation of all distances. 

Return type:  float 
Raises:  Exception if there are no distances. 
GetWeightedStdDev
(sigma)¶Returns:  Standard deviation of all distances multiplied by
exp( GetAverage() / (2*sigma) ). 

Return type:  float 
Parameters:  sigma (float ) – Defines weight. 
Raises:  Exception if there are no distances. 
GetNormStdDev
()¶Returns:  Standard deviation of all distances divided by GetAverage() . 

Return type:  float 
Raises:  Exception if there are no distances. 
DistanceMap
¶Container returned by CreateDistanceMap()
.
Essentially a symmetric GetSize()
x GetSize()
matrix containing
up to GetNumStructures()
distances (list stored as Distances
).
Indexing of residues starts at 0 and corresponds to the positions in the
originally used alignment (see CreateDistanceMap()
).
GetDistances
(i_res1, i_res2)¶Returns:  List of distances for given pair of residue indices. 

Return type:  
Parameters: 

GetSize
()¶Returns:  Number of residues in map. 

Return type:  int 
GetNumStructures
()¶Returns:  Number of structures originally used when creating the map
(see CreateDistanceMap() ). 

Return type:  int 
VarianceMap
¶Container returned by CreateVarianceMap()
.
Like DistanceMap
, it is a symmetric GetSize()
x GetSize()
matrix containing variance measures.
Indexing of residues is as in DistanceMap
.
Get
(i_res1, i_res2)¶Returns:  Variance measure for given pair of residue indices. 

Return type: 

Parameters: 

GetSize
()¶Returns:  Number of residues in map. 

Return type:  int 
ExportDat
(file_name)¶ExportCsv
(file_name)¶ExportJson
(file_name)¶Write all variance measures into a file. The possible formats are:
GetJsonString()
)Parameters:  file_name (str ) – Path to file to be created. 

Raises:  Exception if the file cannot be opened for writing. 
GetJsonString
()¶Returns:  A JSON formatted list of GetSize() lists with
GetSize() variances 

Return type:  str 
GetData
()¶Gets all the data in this map at once. Note that this is much faster (10x
speedup observed) than parsing GetJsonString()
or using Get()
on each element.
Returns:  A list of GetSize() lists with GetSize() variances. 

Return type:  list of list of float 
Dist2Mean
¶Container returned by CreateDist2Mean()
.
Stores distances to mean for GetNumResidues()
residues of
GetNumStructures()
structures.
Indexing of residues is as in DistanceMap
.
Indexing of structures goes from 0 to GetNumStructures()
 1 and is in
the same order as the structures in the originally used alignment.
Get
(i_res, i_str)¶Returns:  Distance to mean for given residue and structure indices. 

Return type: 

Parameters: 

GetNumResidues
()¶Returns:  Number of residues. 

Return type:  int 
GetNumStructures
()¶Returns:  Number of structures. 

Return type:  int 
ExportDat
(file_name)¶ExportCsv
(file_name)¶ExportJson
(file_name)¶Write all distance measures into a file. The possible formats are:
GetJsonString()
)Parameters:  file_name (str ) – Path to file to be created. 

Raises:  Exception if the file cannot be opened for writing. 
GetJsonString
()¶Returns:  A JSON formatted list of GetNumResidues() lists with
GetNumStructures() distances. 

Return type:  str 
GetData
()¶Gets all the data in this map at once. Note that this is much faster (10x
speedup observed) than parsing GetJsonString()
or using Get()
on each element.
Returns:  A list of GetNumResidues() lists with
GetNumStructures() distances. 

Return type:  list of list of float 
Enter search terms or a module, class or function name.
seq
– Sequences and Alignments
bindings
– Interfacing external programs
seq.alg
– Algorithms for Sequences