ost::seq::alg Namespace Reference

Namespaces

namespace  mat
namespace  renumber

Data Structures

struct  AlignmentOpts
 options for local and global sequence alignment algorithms More...
struct  ContactPredictionScoreResult
struct  ContactWeightMatrix
 matrix to weight pairs of amino-acids. More...
class  InsDel
 get insertions and deletions of an alignment More...
struct  PairSubstWeightMatrix
 position-independet pair substitution weight matrix More...
struct  RefMode
class  SubstWeightMatrix
 position-independet substitution weight matrix More...

Typedefs

typedef boost::shared_ptr
< SubstWeightMatrix > 		SubstWeightMatrixPtr

Functions

std::vector< Real >
DLLEXPORT_OST_SEQ_ALG 		Conservation (const AlignmentHandle &aln, bool assign=true, const String &prop_name="cons", bool ignore_gap=false)
ContactPredictionScoreResult
DLLEXPORT_OST_SEQ_ALG 		CalculateContactScore (const AlignmentHandle &aln, ContactWeightMatrix w=LoadDefaultContactWeightMatrix())
ContactPredictionScoreResult
DLLEXPORT_OST_SEQ_ALG 		CalculateContactSubstitutionScore (const AlignmentHandle &aln, int ref_seq_index=0, PairSubstWeightMatrix w=LoadDefaultPairSubstWeightMatrix())
ContactPredictionScoreResult
DLLEXPORT_OST_SEQ_ALG 		CalculateMutualInformation (const AlignmentHandle &aln, ContactWeightMatrix w=LoadConstantContactWeightMatrix(), bool apc_correction=true, bool zpx_transformation=true, float small_number_correction=0.05)
ContactWeightMatrix
DLLEXPORT_OST_SEQ_ALG 		LoadDefaultContactWeightMatrix ()
ContactWeightMatrix
DLLEXPORT_OST_SEQ_ALG 		LoadConstantContactWeightMatrix ()
std::vector< Real >
DLLEXPORT_OST_SEQ_ALG 		ShannonEntropy (const AlignmentHandle &aln, bool ignore_gaps=true)
AlignmentList DLLEXPORT_OST_SEQ_ALG GlobalAlign (const ConstSequenceHandle &s1, const ConstSequenceHandle &s2, SubstWeightMatrixPtr &subst, int gap_open=-5, int gap_ext=-2)
AlignmentList DLLEXPORT_OST_SEQ_ALG LocalAlign (const ConstSequenceHandle &s1, const ConstSequenceHandle &s2, SubstWeightMatrixPtr &subst, int gap_open=-5, int gap_ext=-2)
AlignmentHandle
DLLEXPORT_OST_SEQ_ALG 		MergePairwiseAlignments (const AlignmentList &pairwise_alns, const ConstSequenceHandle &ref_seq)
PairSubstWeightMatrix DLLIMPORT LoadDefaultPairSubstWeightMatrix ()
AlignmentList DLLIMPORT SemiGlobalAlign (const ConstSequenceHandle &s1, const ConstSequenceHandle &s2, SubstWeightMatrixPtr &subst, int gap_open=-5, int gap_ext=-2)
Real DLLIMPORT SequenceIdentity (const AlignmentHandle &aln, RefMode::Type ref_mode=RefMode::LONGER_SEQUENCE, int seq_a=0, int seq_b=1)
Real DLLIMPORT SequenceSimilarity (const AlignmentHandle &aln, SubstWeightMatrixPtr subst, bool normalize=false, int seq_a=0, int seq_b=1)
def ValidateSEQRESAlignment
def AlignToSEQRES
def AlignmentFromChainView
def PredictContacts

Variables

char RAW_CONTACT_WEIGHT_MATRIX_RES_LIST [21] = {'D', 'E', 'R', 'K', 'H', 'S', 'T', 'N', 'Q', 'G', 'P', 'Y', 'W', 'V', 'I', 'L', 'M', 'F', 'A', 'C','-'}
Real RAW_CONTACT_WEIGHT_MATRIX [21][21]
char RAW_PAIR_SUBST_WEIGHT_MATRIX_RES_LIST [20] = {'D', 'E', 'R', 'K', 'H', 'S', 'T', 'N', 'Q', 'G', 'P', 'Y', 'W', 'V', 'I', 'L', 'M', 'F', 'A', 'C'}
Real RAW_PAIR_SUBST_WEIGHT_MATRIX [20][20][20][20]

Typedef Documentation

typedef boost::shared_ptr<SubstWeightMatrix> SubstWeightMatrixPtr

Definition at line 33 of file subst_weight_matrix.hh.

Function Documentation

def ost::seq::alg::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 
non-ligand peptide-linking residues, the second containing all non-ligand 
peptide-linking residues that are part of the view. 

:param chain: A valid chain
:type chain: :class:`~ost.mol.ChainView`

:param handle_seq_name: Name of the handle sequence in the output alignment
:param view_seq_name: Name of the view sequence in the output alignment
:returns: The alignment
:rtype: :class:`~ost.seq.AlignmentHandle`

Definition at line 135 of file __init__.py.

def ost::seq::alg::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 non-ligand, peptide-linking 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
:func:`~ost.seq.alg.ValidateSEQRESAlignment`.

:param chain: Source of the sequence
:type chain: :class:`~ost.mol.ChainHandle`
:param seqres: SEQRES sequence
:type seqres: :class:`str`
:param try_resnum_first: Try to align by residue number
:type try_resnum_first: :class:`bool`
:param validate: Validate alignment by
                 :func:`~ost.seq.alg.ValidateSEQRESAlignment`
:type validate: :class:`bool`

:returns: The alignment of the residues in the chain and the SEQRES entries.
:rtype: :class:`~ost.seq.AlignmentHandle`

Definition at line 58 of file __init__.py.

ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CalculateContactScore ( const AlignmentHandle &  aln,
ContactWeightMatrix  w = LoadDefaultContactWeightMatrix() 
)
ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CalculateContactSubstitutionScore ( const AlignmentHandle &  aln,
int  ref_seq_index = 0,
PairSubstWeightMatrix  w = LoadDefaultPairSubstWeightMatrix() 
)
ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CalculateMutualInformation ( const AlignmentHandle &  aln,
ContactWeightMatrix  w = LoadConstantContactWeightMatrix(),
bool  apc_correction = true,
bool  zpx_transformation = true,
float  small_number_correction = 0.05 
)
std::vector<Real> DLLEXPORT_OST_SEQ_ALG ost::seq::alg::Conservation ( const AlignmentHandle &  aln,
bool  assign = true,
const String &  prop_name = "cons",
bool  ignore_gap = false 
)

Calculates conservation scores for each column in the alignment.

The conservation score is a value between 0 and 1. The bigger the number the more conserved the aligned residues are.

assign If true, the conservation scores are assigned to attached residues. The name of the property can be changed with the prop_name parameter. Useful when coloring entities based on sequence conservation. prop_name The property name for assigning the conservation to attached residues. Defaults to 'cons'. ignore_gap If true, the dissimilarity between two gaps is increased to 6.0 instead of 0.5 as defined in the original version. Without this, a stretch where in the alignment there is only one sequence which is aligned to only gaps, is considered highly conserved (depending on the number of gap sequences).

AlignmentList DLLEXPORT_OST_SEQ_ALG ost::seq::alg::GlobalAlign ( const ConstSequenceHandle &  s1,
const ConstSequenceHandle &  s2,
SubstWeightMatrixPtr &  subst,
int  gap_open = -5,
int  gap_ext = -2 
)
ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG ost::seq::alg::LoadConstantContactWeightMatrix (  ) 

weight of 1 for all amino-acid pairs and 0 for gaps.

ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG ost::seq::alg::LoadDefaultContactWeightMatrix (  ) 

statistical potential matrix containing interaction pseudo energies

PairSubstWeightMatrix DLLIMPORT ost::seq::alg::LoadDefaultPairSubstWeightMatrix (  ) 
AlignmentList DLLEXPORT_OST_SEQ_ALG ost::seq::alg::LocalAlign ( const ConstSequenceHandle &  s1,
const ConstSequenceHandle &  s2,
SubstWeightMatrixPtr &  subst,
int  gap_open = -5,
int  gap_ext = -2 
)
AlignmentHandle DLLEXPORT_OST_SEQ_ALG ost::seq::alg::MergePairwiseAlignments ( const AlignmentList &  pairwise_alns,
const ConstSequenceHandle &  ref_seq 
)

merge a list of pairwise alignments into one multiple sequence alignment

All sequences in the pairwise sequence alignments are a realigned to the reference sequence. This is useful to merge the results of a BLAST or HMM database search into one multiple sequence alignment.

The method does not produce the optimal multiple sequence alignemnt for all the sequences.

Parameters:
pairwise_alns is a list of AlignmentHandles, each containing two sequences
ref_seq is the reference sequence. The reference sequence must not contain any gaps.
def ost::seq::alg::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 Z-scores. 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(1-CoEvoSc(i,j))    if *(i,j)* <0

:param ali: The multiple sequence alignment
:type ali: :class:`~ost.seq.AlignmentHandle`

Definition at line 172 of file __init__.py.

AlignmentList DLLIMPORT ost::seq::alg::SemiGlobalAlign ( const ConstSequenceHandle &  s1,
const ConstSequenceHandle &  s2,
SubstWeightMatrixPtr &  subst,
int  gap_open = -5,
int  gap_ext = -2 
)
Real DLLIMPORT ost::seq::alg::SequenceIdentity ( const AlignmentHandle &  aln,
RefMode::Type  ref_mode = RefMode::LONGER_SEQUENCE,
int  seq_a = 0,
int  seq_b = 1 
)

calculate sequence identity for two sequences in an alignment

Parameters:
ref_mode influences the way the sequence identity is calculated. When set to LONGER_SEQUENCE, the sequence identity is calculated as the number of matches divided by the length of the longer sequence. If set to ALIGNMENT, the sequence identity is calculated as the number of matches divided by the number of aligned residues.
seq_a is the index of the first sequence
seq_b is the index of the second sequence
aln is the sequence alignment
Returns:
sequence identity in the range 0 to 100
Real DLLIMPORT ost::seq::alg::SequenceSimilarity ( const AlignmentHandle &  aln,
SubstWeightMatrixPtr  subst,
bool  normalize = false,
int  seq_a = 0,
int  seq_b = 1 
)

calculate sequence similarity for two sequences in an alignment

Parameters:
seq_a is the index of the first sequence
seq_b is the index of the second sequence
aln is the sequence alignment
Returns:
sequence similarity
std::vector<Real> DLLEXPORT_OST_SEQ_ALG ost::seq::alg::ShannonEntropy ( const AlignmentHandle &  aln,
bool  ignore_gaps = true 
)

calculates the Shannon entropy for each column in the alignment

def ost::seq::alg::ValidateSEQRESAlignment (   aln,
  chain = None 
) 
Checks a sequence aligned to a SEQRES sequence to be free of strand breaks.
Residues divided by gaps are not considered as breakage but may also not be
connected.

:param aln: Alignment
:type aln: :class:`~ost.seq.AlignmentHandle`
:param chain: Source of the sequence
:type chain: :class:`~ost.mol.ChainHandle`

:returns: True if all residues (beside gapped ones) are connected, False
          otherwise.

Definition at line 4 of file __init__.py.

Variable Documentation

Real RAW_CONTACT_WEIGHT_MATRIX[21][21]
Initial value:
    {
      { 0.0168, 0.0000, 0.4730, 0.3602, 0.3627, 0.1650, 0.1716, 0.2177, 0.2272, 0.0770, 0.0733, 0.3501, 0.3262, 0.1228, 0.1393, 0.1263, 0.1792, 0.2105, 0.0757, 0.1801, 0.0000},
      { 0.0000, 0.0676, 0.4996, 0.3966, 0.3357, 0.1594, 0.1866, 0.1958, 0.2390, 0.0333, 0.0945, 0.3699, 0.3719, 0.1753, 0.1948, 0.1866, 0.2057, 0.2506, 0.1179, 0.1688, 0.0000},
      { 0.4730, 0.4996, 0.3499, 0.1961, 0.3666, 0.2970, 0.3204, 0.3266, 0.3599, 0.2218, 0.2777, 0.5060, 0.5262, 0.3196, 0.3532, 0.3577, 0.3560, 0.4251, 0.2489, 0.3517, 0.0000},
      { 0.3602, 0.3966, 0.1961, 0.1128, 0.2100, 0.1731, 0.2061, 0.2093, 0.2493, 0.0799, 0.0802, 0.3928, 0.3725, 0.2150, 0.2331, 0.2226, 0.2164, 0.2845, 0.1383, 0.2104, 0.0000},
      { 0.3627, 0.3357, 0.3666, 0.2100, 0.5496, 0.3269, 0.3494, 0.3122, 0.3180, 0.2106, 0.2629, 0.5362, 0.5588, 0.3475, 0.3754, 0.3618, 0.4193, 0.4679, 0.2361, 0.4789, 0.0000},
      { 0.1650, 0.1594, 0.2970, 0.1731, 0.3269, 0.1866, 0.2143, 0.2210, 0.2315, 0.1203, 0.1250, 0.3501, 0.3960, 0.2381, 0.2586, 0.2358, 0.2758, 0.3335, 0.1628, 0.3010, 0.0000},
      { 0.1716, 0.1866, 0.3204, 0.2061, 0.3494, 0.2143, 0.2894, 0.2553, 0.2783, 0.1418, 0.1529, 0.3962, 0.4310, 0.3452, 0.3660, 0.3237, 0.3417, 0.3951, 0.2073, 0.3458, 0.0000},
      { 0.2177, 0.1958, 0.3266, 0.2093, 0.3122, 0.2210, 0.2553, 0.3119, 0.2868, 0.1666, 0.1810, 0.3706, 0.3994, 0.2195, 0.2391, 0.2168, 0.2834, 0.3160, 0.1618, 0.2983, 0.0000},
      { 0.2272, 0.2390, 0.3599, 0.2493, 0.3180, 0.2315, 0.2783, 0.2868, 0.3159, 0.1473, 0.2187, 0.4208, 0.4769, 0.2727, 0.3014, 0.2989, 0.3234, 0.3733, 0.2010, 0.2982, 0.0000},
      { 0.0770, 0.0333, 0.2218, 0.0799, 0.2106, 0.1203, 0.1418, 0.1666, 0.1473, 0.0990, 0.0727, 0.3054, 0.3354, 0.1831, 0.1984, 0.1959, 0.2488, 0.2887, 0.1321, 0.2889, 0.0000},
      { 0.0733, 0.0945, 0.2777, 0.0802, 0.2629, 0.1250, 0.1529, 0.1810, 0.2187, 0.0727, 0.1358, 0.4454, 0.4871, 0.1879, 0.2176, 0.2163, 0.2738, 0.3492, 0.1143, 0.2611, 0.0000},
      { 0.3501, 0.3699, 0.5060, 0.3928, 0.5362, 0.3501, 0.3962, 0.3706, 0.4208, 0.3054, 0.4454, 0.6013, 0.6686, 0.5248, 0.5702, 0.5625, 0.5797, 0.6506, 0.3876, 0.5335, 0.0000},
      { 0.3262, 0.3719, 0.5262, 0.3725, 0.5588, 0.3960, 0.4310, 0.3994, 0.4769, 0.3354, 0.4871, 0.6686, 0.7438, 0.5554, 0.6133, 0.6157, 0.6450, 0.7208, 0.4170, 0.6399, 0.0000},
      { 0.1228, 0.1753, 0.3196, 0.2150, 0.3475, 0.2381, 0.3452, 0.2195, 0.2727, 0.1831, 0.1879, 0.5248, 0.5554, 0.5436, 0.5726, 0.5340, 0.4934, 0.5834, 0.3537, 0.4786, 0.0000},
      { 0.1393, 0.1948, 0.3532, 0.2331, 0.3754, 0.2586, 0.3660, 0.2391, 0.3014, 0.1984, 0.2176, 0.5702, 0.6133, 0.5726, 0.6365, 0.5952, 0.5478, 0.6388, 0.3921, 0.5096, 0.0000},
      { 0.1263, 0.1866, 0.3577, 0.2226, 0.3618, 0.2358, 0.3237, 0.2168, 0.2989, 0.1959, 0.2163, 0.5625, 0.6157, 0.5340, 0.5952, 0.5835, 0.5272, 0.6279, 0.3691, 0.4760, 0.0000},
      { 0.1792, 0.2057, 0.3560, 0.2164, 0.4193, 0.2758, 0.3417, 0.2834, 0.3234, 0.2488, 0.2738, 0.5797, 0.6450, 0.4934, 0.5478, 0.5272, 0.5920, 0.6433, 0.3527, 0.5070, 0.0000},
      { 0.2105, 0.2506, 0.4251, 0.2845, 0.4679, 0.3335, 0.3951, 0.3160, 0.3733, 0.2887, 0.3492, 0.6506, 0.7208, 0.5834, 0.6388, 0.6279, 0.6433, 0.7323, 0.4201, 0.5920, 0.0000},
      { 0.0757, 0.1179, 0.2489, 0.1383, 0.2361, 0.1628, 0.2073, 0.1618, 0.2010, 0.1321, 0.1143, 0.3876, 0.4170, 0.3537, 0.3921, 0.3691, 0.3527, 0.4201, 0.2846, 0.3407, 0.0000},
      { 0.1801, 0.1688, 0.3517, 0.2104, 0.4789, 0.3010, 0.3458, 0.2983, 0.2982, 0.2889, 0.2611, 0.5335, 0.6399, 0.4786, 0.5096, 0.4760, 0.5070, 0.5920, 0.3407, 1.0000, 0.0000},
      { 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000}}

Definition at line 5 of file default_contact_weight_matrix.hh.

char RAW_CONTACT_WEIGHT_MATRIX_RES_LIST[21] = {'D', 'E', 'R', 'K', 'H', 'S', 'T', 'N', 'Q', 'G', 'P', 'Y', 'W', 'V', 'I', 'L', 'M', 'F', 'A', 'C','-'}

Definition at line 3 of file default_contact_weight_matrix.hh.

Real RAW_PAIR_SUBST_WEIGHT_MATRIX[20][20][20][20]

Definition at line 5 of file default_pair_subst_weight_matrix.hh.

char RAW_PAIR_SUBST_WEIGHT_MATRIX_RES_LIST[20] = {'D', 'E', 'R', 'K', 'H', 'S', 'T', 'N', 'Q', 'G', 'P', 'Y', 'W', 'V', 'I', 'L', 'M', 'F', 'A', 'C'}

Definition at line 3 of file default_pair_subst_weight_matrix.hh.

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