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 boost::shared_ptr<SubstWeightMatrix> SubstWeightMatrixPtr |
Definition at line 33 of file subst_weight_matrix.hh.
| 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.
| 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
| 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 |
| 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
| seq_a | is the index of the first sequence | |
| seq_b | is the index of the second sequence | |
| aln | is the sequence alignment |
| 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.
| Real RAW_CONTACT_WEIGHT_MATRIX[21][21] |
{
{ 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.
1.6.1