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| ChemicalShiftSequence () |
| ctors More...
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| ChemicalShiftSequence (FileName const &fn) |
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| ChemicalShiftSequence (utility::vector1< utility::vector1< core::Real > > cs_prof, std::string const &seq, std::string const &ident, Size start_idx=1) |
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| ChemicalShiftSequence (ChemicalShiftSequence const &src) |
| copy ctor More...
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ChemicalShiftSequence & | operator= (ChemicalShiftSequence const &rhs) |
| assignment operator. More...
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virtual | ~ChemicalShiftSequence () |
| dtor More...
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virtual SequenceOP | clone () const |
| Returns an owning pointer to a new ChemicalShiftSequence object, with data that is a deep copy of the information in this object. More...
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void | read_from_file (FileName const &fn) |
| Read an profile matrix from the given filename using the 2nd_inCS.tab format. More...
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utility::vector1< std::string > | alphabet () const |
| Return the alphabet used by this sequence profile. This is an N-dimensional vector1 where N is the width of the profile, and the ith entry of any row in the profile represents the probability of ith character at that row in the sequence. More...
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void | alphabet (utility::vector1< std::string > new_alphabet) |
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Real | sigma (Size, Size idx) |
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| SequenceProfile () |
| ctors More...
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| SequenceProfile (FileName const &fn) |
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| SequenceProfile (utility::vector1< utility::vector1< core::Real > > prof, std::string const &sequence, std::string const &id, Size start=1, bool negative_better=false) |
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| SequenceProfile (SequenceProfile const &src) |
| copy ctor More...
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SequenceProfile & | operator= (SequenceProfile const &rhs) |
| assignment operator. More...
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| ~SequenceProfile () |
| dtor More...
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virtual void | generate_from_sequence (Sequence const &seq, std::string matrix="BLOSUM62") |
| Generate the profile matrix from a sequence and a given substitution matrix. More...
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void | rescale (core::Real factor=1) |
| Multiply all profile weights by factor. More...
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void | convert_profile_to_probs (core::Real temp=1.0) |
| Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 ) More...
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void | global_auto_rescale () |
| Use linear rescaling (with a fixed zero) to fit the values within the range -1.0 to 1.0. More...
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void | read_from_checkpoint (FileName const &fn, bool negative_better=true) |
| Read profile matrix from the given filename using the NNMAKE .checkpoint format. For compatability, negative_better defaults to true. Set manually if necessary. More...
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void | read_from_binary_chk (FileName const &fn) |
| Read profile matrix from the given filename in the legacy BLAST binary format. More...
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utility::vector1
< utility::vector1< Real >
> const & | profile () const |
| Returns the 2D vector1 of Real values representing this profile. More...
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utility::vector1
< utility::vector1< Real >
> const & | occurrence_data () const |
| Returns the 2D vector1 of Real values of the probabilties of each aa. More...
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void | profile (utility::vector1< utility::vector1< Real > > const &new_profile) |
| Sets the 2D vector1 of Real values representing this profile. More...
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void | occurrence_data (utility::vector1< utility::vector1< Real > > const &new_occurrence_data) |
| Sets the 2D vector1 of Real values of the probabilties of each aa. More...
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virtual void | insert_char (core::Size pos, char new_char) |
| Inserts a character at the given position. More...
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virtual void | delete_position (core::Size pos) |
| Deletes the given position from the Sequence and shifts everything else back by one. More...
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virtual std::string | type () const |
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Size | width () const |
| Returns the number of distinct values at each position in this profile. More...
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utility::vector1< Real > const & | prof_row (Size pos) const |
| Returns the vector1 of values at this position. More...
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utility::vector1< Real > const & | probability_row (Size pos) const |
| Returns the vector1 of values at this position. More...
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void | prof_row (utility::vector1< Real > const &new_prof_row, core::Size pos) |
| Sets the 1D vector1 of Real values representing this profile at pos X. More...
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void | probabilty_row (utility::vector1< Real > const &new_prob_row, core::Size pos) |
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Size | size () const |
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bool | negative_better () const |
| Returns true if negative values are better identities. More...
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void | negative_better (bool negbet) |
| Set whether negative identities are better. More...
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core::Real | temp () const |
| returns the temperature used in computing profile probabilities More...
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utility::vector1< std::string > | alphabet () const |
| Return the alphabet used by this sequence profile. This is an N-dimensional vector1 where N is the width of the profile, and the ith entry of any row in the profile represents the probability of ith character at that row in the sequence. More...
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void | alphabet (utility::vector1< std::string > new_alphabet) |
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| Sequence () |
| ctor More...
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| Sequence (std::string seq, std::string id, core::Size start=1) |
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| Sequence (core::pose::Pose const &pose) |
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| Sequence (Sequence const &src) |
| copy constructor. More...
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virtual | ~Sequence () |
| dtor More...
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virtual core::Size | length () const |
| Returns the number of characters in this object. More...
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virtual std::string | to_string () const |
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void | sequence (std::string sequence) |
| sets sequence to the given value. More...
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void | id (std::string new_id) |
| sets id to the given value. More...
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void | start (core::Size new_start) |
| sets starting index to the given value. More...
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void | gap_char (char gap_char) |
| sets gap_char to the given value. More...
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core::Size | ungapped_length () const |
| Returns the number of characters in this object, ignoring gaps. More...
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core::Size | start () const |
| Returns the start of this object. More...
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std::string | id () const |
| Returns the id of this object. More...
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char | gap_char () const |
| Returns the character used to represent a gap for this object. More...
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std::string | ungapped_sequence () const |
| Returns the string representing this sequence without gaps. More...
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std::string | sequence () const |
| Returns the full sequence, which may include gaps. More...
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Sequence & | operator= (Sequence const &rhs) |
| assignment operator. More...
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bool | operator< (const Sequence &s) const |
| Returns true if this Sequence object's id is lexicographically less than the given Sequence object's id, returns false otherwise. Uses C++ string < operator to compare this Sequence object's id() to the given Sequence object's id(). More...
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bool | operator== (const Sequence &s) const |
| Returns true if the given Sequence object is equal to this Sequence object. Tests for string equality of id(), start(), and sequence(), and returns false if any of these are not equal. More...
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char | operator[] (core::Size pos) const |
| Returns the character at the given sequence position. More...
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char | at (core::Size pos) const |
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void | insert_gap (core::Size pos) |
| Inserts a gap at the given position, where insert_gap( 0 ) inserts the character at the beginning of the sequence, and insert_gap( length() ) inserts the character at the end of the sequence. More...
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void | append_char (char new_char) |
| Append a character. More...
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void | append_gap () |
| Append a gap. More...
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bool | is_gap (core::Size pos) const |
| Returns true if this position in the sequence represents a gap, returns false otherwise. More...
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void | read_data (std::istream &in) |
| Initializes the information in this sequence from the given std::istream. The istream should yield three pieces of information in the following order: More...
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core::Size | resnum (core::Size idx) const |
| Returns the index of the given sequence position, which is the position in the sequence minus any gaps that occur earlier in the sequence. For example, if the sequence is —AT, resnum(5) will return 2. Returns 0 for unaligned positions. More...
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