Namespaces
	aaindex

	mat

	renumber

Data Structures
struct	AlignmentOpts

struct	ContactPredictionScoreResult

struct	ContactWeightMatrix

struct	Distances

class	DistanceMap

class	ContextProfile

class	ContextProfileDB

class	InsDel

struct	PairSubstWeightMatrix

struct	RefMode

class	SubstWeightMatrix

class	VarianceMap

class	Dist2Mean

class	MeanlDDT

Typedefs
typedef boost::shared_ptr< DistanceMap >	DistanceMapPtr

typedef boost::shared_ptr< ContextProfileDB >	ContextProfileDBPtr

typedef boost::shared_ptr< SubstWeightMatrix >	SubstWeightMatrixPtr

typedef boost::shared_ptr< VarianceMap >	VarianceMapPtr

typedef boost::shared_ptr< Dist2Mean >	Dist2MeanPtr

typedef boost::shared_ptr< MeanlDDT >	MeanlDDTPtr

Functions
int DLLEXPORT_OST_SEQ_ALG	ClipAlignment (AlignmentHandle &aln, uint n_seq_thresh=2, bool set_offset=true, bool remove_empty=true)

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 ()

DistanceMapPtr DLLEXPORT_OST_SEQ_ALG	CreateDistanceMap (const seq::AlignmentHandle &alignment)

std::vector< Real > DLLIMPORT	ShannonEntropy (const AlignmentHandle &aln, bool ignore_gaps=true)

AlignmentList DLLIMPORT	GlobalAlign (const ConstSequenceHandle &s1, const ConstSequenceHandle &s2, SubstWeightMatrixPtr &subst, int gap_open=-5, int gap_ext=-2)

void	AddTransitionPseudoCounts (ost::seq::ProfileHandle &profile, Real gapb=1.0, Real gabd=0.15, Real gape=1.0)

void	AddAAPseudoCounts (ost::seq::ProfileHandle &profile, Real a=1.0, Real b=1.5, Real c=1.0)

void	AddAAPseudoCounts (ost::seq::ProfileHandle &profile, const ContextProfileDB &db, Real a=0.9, Real b=4.0, Real c=1.0)

void	AddNullPseudoCounts (ost::seq::ProfileHandle &profile)

Real	HMMScore (const ost::seq::ProfileHandle &profile_0, const ost::seq::ProfileHandle &profile_1, const ost::seq::AlignmentHandle &aln, int seq_0_idx, int seq_1_idx, Real match_score_offset=-0.03, Real correl_score_weight=0.1, Real del_start_penalty_factor=0.6, Real del_extend_penalty_factor=0.6, Real ins_start_penalty_factor=0.6, Real ins_extend_penalty_factor=0.6)

AlignmentList DLLIMPORT	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 DLLEXPORT_OST_SEQ_ALG	LoadDefaultPairSubstWeightMatrix ()

AlignmentList DLLIMPORT	SemiGlobalAlign (const ConstSequenceHandle &s1, const ConstSequenceHandle &s2, SubstWeightMatrixPtr &subst, int gap_open=-5, int gap_ext=-2)

Real DLLEXPORT_OST_SEQ_ALG	SequenceIdentity (const AlignmentHandle &aln, RefMode::Type ref_mode=RefMode::LONGER_SEQUENCE, int seq_a=0, int seq_b=1)

Real DLLEXPORT_OST_SEQ_ALG	SequenceSimilarity (const AlignmentHandle &aln, SubstWeightMatrixPtr subst, bool normalize=false, int seq_a=0, int seq_b=1)

VarianceMapPtr DLLEXPORT_OST_SEQ_ALG	CreateVarianceMap (const DistanceMapPtr dmap, Real sigma=25)

Dist2MeanPtr DLLEXPORT_OST_SEQ_ALG	CreateDist2Mean (const DistanceMapPtr dmap)

MeanlDDTPtr DLLEXPORT_OST_SEQ_ALG	CreateMeanlDDTHA (const DistanceMapPtr dmap)

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

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

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

bool	ParasailAvailable ()

def	ValidateSEQRESAlignment (aln, chain=None)

def	AlignToSEQRES (chain, seqres, try_resnum_first=False, validate=True)

def	AlignmentFromChainView (chain, handle_seq_name='handle', view_seq_name='view')

def	PredictContacts (ali)

def	CalculateContactProbability (cpred_res, method)

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

◆ ContextProfileDBPtr

typedef boost::shared_ptr<ContextProfileDB> ContextProfileDBPtr

Definition at line 29 of file hmm_pseudo_counts.hh.

◆ Dist2MeanPtr

typedef boost::shared_ptr<Dist2Mean> Dist2MeanPtr

Definition at line 41 of file variance_map.hh.

◆ DistanceMapPtr

typedef boost::shared_ptr<DistanceMap> DistanceMapPtr

Definition at line 148 of file distance_map.hh.

◆ MeanlDDTPtr

typedef boost::shared_ptr<MeanlDDT> MeanlDDTPtr

Definition at line 42 of file variance_map.hh.

◆ SubstWeightMatrixPtr

typedef boost::shared_ptr<SubstWeightMatrix> SubstWeightMatrixPtr

Definition at line 36 of file subst_weight_matrix.hh.

◆ VarianceMapPtr

typedef boost::shared_ptr<VarianceMap> VarianceMapPtr

Definition at line 40 of file variance_map.hh.

Function Documentation

◆ AddAAPseudoCounts() [1/2]

void ost::seq::alg::AddAAPseudoCounts	(	ost::seq::ProfileHandle &	profile,
		const ContextProfileDB &	db,
		Real	a = `0.9`,
		Real	b = `4.0`,
		Real	c = `1.0`
	)

◆ AddAAPseudoCounts() [2/2]

void ost::seq::alg::AddAAPseudoCounts	(	ost::seq::ProfileHandle &	profile,
		Real	a = `1.0`,
		Real	b = `1.5`,
		Real	c = `1.0`
	)

◆ AddNullPseudoCounts()

void ost::seq::alg::AddNullPseudoCounts ( ost::seq::ProfileHandle & profile )

◆ AddTransitionPseudoCounts()

void ost::seq::alg::AddTransitionPseudoCounts	(	ost::seq::ProfileHandle &	profile,
		Real	gapb = `1.0`,
		Real	gabd = `0.15`,
		Real	gape = `1.0`
	)

◆ AlignmentFromChainView()

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 153 of file __init__.py.

◆ AlignToSEQRES()

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.

:param chain: Source of the sequence
:type chain: :class:`~ost.mol.ChainHandle`
:param seqres: SEQRES sequence
:type seqres: :class:`str`
:param try_resnum_first: If set to True, this first builds an alignment using
                         residue numbers and checks if the one-letter-codes
                         match. If they all match, this alignment is used
                         (and possibly validated). Otherwise, it displays a
                         warning and falls back to the connectivity-based
                         alignment.
:type try_resnum_first: :class:`bool`
:param validate: If set to True, the alignment is additionally checked by
                 :func:`~ost.seq.alg.ValidateSEQRESAlignment` and raises
                 a ValueError if the validation failed.
: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 60 of file __init__.py.

◆ CalculateContactProbability()

def ost.seq.alg.CalculateContactProbability	(	cpred_res,
		method
	)

Calculate the probability of a predicted contact to be correct.
This simply transforms the score associated with a prediction into a probability.

:param cpred_res: A contact prediction result
:param method: The method which was used for contact prediction. Should be one
 of "MI", "MIp", "MIpz", "cevoMI", "cevo"

:type cpred_res: :class:`ost.seq.alg.ContactPredictionScoreResult`
:type method: :class:`str`

Definition at line 223 of file __init__.py.

◆ CalculateContactScore()

ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CalculateContactScore	(	const AlignmentHandle &	aln,
		ContactWeightMatrix	w = `LoadDefaultContactWeightMatrix()`
	)

◆ CalculateContactSubstitutionScore()

ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CalculateContactSubstitutionScore	(	const AlignmentHandle &	aln,
		int	ref_seq_index = `0`,
		PairSubstWeightMatrix	w = `LoadDefaultPairSubstWeightMatrix()`
	)

◆ CalculateMutualInformation()

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`
	)

◆ ClipAlignment()

int DLLEXPORT_OST_SEQ_ALG ost::seq::alg::ClipAlignment	(	AlignmentHandle &	aln,
		uint	n_seq_thresh = `2`,
		bool	set_offset = `true`,
		bool	remove_empty = `true`
	)

Clips alignment so that first and last column have at least the desired number of structures.

Parameters

aln	Multiple sequence alignment. Will be cut.
n_seq_thresh	Minimal number of sequences desired.
set_offset	Shall we update offsets for attached views?
remove_empty	Shall we remove sequences with only gaps in cut aln?

Returns: Starting column (0-indexed), 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.

◆ Conservation()

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).

◆ CreateDist2Mean()

Dist2MeanPtr DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CreateDist2Mean ( const DistanceMapPtr dmap )

Returns: Distances to mean for each structure in dmap. Structures are in the same order as passed when creating dmap.

Parameters

dmap	Distance map as created with CreateDistanceMap.

◆ CreateDistanceMap()

DistanceMapPtr DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CreateDistanceMap ( const seq::AlignmentHandle & alignment )

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.

For each of the attached views, the C-alpha distance pairs are extracted and mapped onto the corresponding C-alpha distances in the reference sequence.

◆ CreateMeanlDDTHA()

MeanlDDTPtr DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CreateMeanlDDTHA ( const DistanceMapPtr dmap )

◆ CreateVarianceMap()

VarianceMapPtr DLLEXPORT_OST_SEQ_ALG ost::seq::alg::CreateVarianceMap	(	const DistanceMapPtr	dmap,
		Real	sigma = `25`
	)

Returns: Variance measure for each entry in dmap.

Parameters

dmap	Distance map as created with CreateDistanceMap.
sigma	Used for weighting of variance measure (see Distances::GetWeightedStdDev)

◆ GlobalAlign()

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

◆ HMMScore()

Real ost::seq::alg::HMMScore	(	const ost::seq::ProfileHandle &	profile_0,
		const ost::seq::ProfileHandle &	profile_1,
		const ost::seq::AlignmentHandle &	aln,
		int	seq_0_idx,
		int	seq_1_idx,
		Real	match_score_offset = `-0.03`,
		Real	correl_score_weight = `0.1`,
		Real	del_start_penalty_factor = `0.6`,
		Real	del_extend_penalty_factor = `0.6`,
		Real	ins_start_penalty_factor = `0.6`,
		Real	ins_extend_penalty_factor = `0.6`
	)

◆ LoadConstantContactWeightMatrix()

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

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

◆ LoadDefaultContactWeightMatrix()

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

statistical potential matrix containing interaction pseudo energies

◆ LoadDefaultPairSubstWeightMatrix()

PairSubstWeightMatrix DLLEXPORT_OST_SEQ_ALG ost::seq::alg::LoadDefaultPairSubstWeightMatrix ( )

◆ LocalAlign()

AlignmentList DLLIMPORT ost::seq::alg::LocalAlign	(	const ConstSequenceHandle &	s1,
		const ConstSequenceHandle &	s2,
		SubstWeightMatrixPtr &	subst,
		int	gap_open = `-5`,
		int	gap_ext = `-2`
	)

◆ MergePairwiseAlignments()

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.

◆ ParaGlobalAlign()

ost::seq::AlignmentList ost::seq::alg::ParaGlobalAlign	(	const ost::seq::ConstSequenceHandle &	s1,
		const ost::seq::ConstSequenceHandle &	s2,
		ost::seq::alg::SubstWeightMatrixPtr &	subst,
		int	gap_open = `-5`,
		int	gap_ext = `-2`
	)

◆ ParaLocalAlign()

ost::seq::AlignmentList ost::seq::alg::ParaLocalAlign	(	const ost::seq::ConstSequenceHandle &	s1,
		const ost::seq::ConstSequenceHandle &	s2,
		ost::seq::alg::SubstWeightMatrixPtr &	subst,
		int	gap_open = `-5`,
		int	gap_ext = `-2`
	)

◆ ParasailAvailable()

bool ost::seq::alg::ParasailAvailable ( )

◆ ParaSemiGlobalAlign()

ost::seq::AlignmentList ost::seq::alg::ParaSemiGlobalAlign	(	const ost::seq::ConstSequenceHandle &	s1,
		const ost::seq::ConstSequenceHandle &	s2,
		ost::seq::alg::SubstWeightMatrixPtr &	subst,
		int	gap_open = `-5`,
		int	gap_ext = `-2`
	)

◆ PredictContacts()

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 190 of file __init__.py.

◆ SemiGlobalAlign()

AlignmentList DLLIMPORT ost::seq::alg::SemiGlobalAlign	(	const ConstSequenceHandle &	s1,
		const ConstSequenceHandle &	s2,
		SubstWeightMatrixPtr &	subst,
		int	gap_open = `-5`,
		int	gap_ext = `-2`
	)

◆ SequenceIdentity()

Real DLLEXPORT_OST_SEQ_ALG 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

◆ SequenceSimilarity()

Real DLLEXPORT_OST_SEQ_ALG 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

◆ ShannonEntropy()

std::vector<Real> DLLIMPORT ost::seq::alg::ShannonEntropy	(	const AlignmentHandle &	aln,
		bool	ignore_gaps = `true`
	)

calculates the Shannon entropy for each column in the alignment

◆ ValidateSEQRESAlignment()

def ost.seq.alg.ValidateSEQRESAlignment	(	aln,
		chain = `None`
	)

Checks if sequence in alignment has same connectivity as residues in chain.
This looks for connected stretches in both the sequence and the chain and
returns False if they don't match. This uses the connectivity of the protein
backbone.

:param aln: Alignment of two sequences with second one expected to map to
            residues in *chain*.
: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

◆ RAW_CONTACT_WEIGHT_MATRIX

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.

◆ RAW_CONTACT_WEIGHT_MATRIX_RES_LIST

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.

◆ RAW_PAIR_SUBST_WEIGHT_MATRIX

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

Definition at line 5 of file default_pair_subst_weight_matrix.hh.

◆ RAW_PAIR_SUBST_WEIGHT_MATRIX_RES_LIST

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.

Namespaces

Data Structures

Typedefs

Functions

Variables

Typedef Documentation

◆ ContextProfileDBPtr

◆ Dist2MeanPtr

◆ DistanceMapPtr

◆ MeanlDDTPtr

◆ SubstWeightMatrixPtr

◆ VarianceMapPtr

Function Documentation

◆ AddAAPseudoCounts() [1/2]

◆ AddAAPseudoCounts() [2/2]

◆ AddNullPseudoCounts()

◆ AddTransitionPseudoCounts()

◆ AlignmentFromChainView()

◆ AlignToSEQRES()

◆ CalculateContactProbability()

◆ CalculateContactScore()

◆ CalculateContactSubstitutionScore()

◆ CalculateMutualInformation()

◆ ClipAlignment()

◆ Conservation()

◆ CreateDist2Mean()

◆ CreateDistanceMap()

◆ CreateMeanlDDTHA()

◆ CreateVarianceMap()

◆ GlobalAlign()

◆ HMMScore()

◆ LoadConstantContactWeightMatrix()

◆ LoadDefaultContactWeightMatrix()

◆ LoadDefaultPairSubstWeightMatrix()

◆ LocalAlign()

◆ MergePairwiseAlignments()

◆ ParaGlobalAlign()

◆ ParaLocalAlign()

◆ ParasailAvailable()

◆ ParaSemiGlobalAlign()

◆ PredictContacts()

◆ SemiGlobalAlign()

◆ SequenceIdentity()

◆ SequenceSimilarity()

◆ ShannonEntropy()

◆ ValidateSEQRESAlignment()

Variable Documentation

◆ RAW_CONTACT_WEIGHT_MATRIX

◆ RAW_CONTACT_WEIGHT_MATRIX_RES_LIST

◆ RAW_PAIR_SUBST_WEIGHT_MATRIX

◆ RAW_PAIR_SUBST_WEIGHT_MATRIX_RES_LIST