Modules
		boost mmtbx_alignment_ext scitbx.array_family.flex scitbx sys types

Classes
		__builtin__.object align alignment   class align(__builtin__.object)       Methods defined here: __init__(self, seq_a, seq_b, style='global', gap_opening_penalty=1, gap_extension_penalty=1, similarity_function='identity') endpt(self) extract_alignment(self) gap_cost(self, width) make_matrix(self, m, n) score(self) show_matrices(self, out=None) show_matrix(self, data, label=None, out=None) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class alignment(__builtin__.object)       Methods defined here: __init__(self, similarity_function, a, b, i_seqs_a, i_seqs_b, match_codes) blosum50_matches(self, is_similar_threshold=0) dayhoff_matches(self, is_similar_threshold=0) exact_match_selections(self) identity_matches(self) matches(self, similarity_function=None, is_similar_threshold=0) pretty_print(self, matches=None, out=None, block_size=20, n_block=1, top_name='reference', bottom_name='query', comment=None) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)

Functions
		blosum50(a, b) dayhoff(a, b) exercise() exercise_ext() exercise_similarity_scores() identity(a, b)

Data
		blosum50_similarity_scores = [[5, -2, -1, -2, -1, -3, 0, -2, -1, -1, -2, -1, -1, -1, -1, -2, 1, 0, 0, -3, ...], [-2, 5, -3, 5, 1, -4, -1, 0, -4, 0, -4, -3, 4, -2, 0, -1, 0, 0, -4, -5, ...], [-1, -3, 13, -4, -3, -2, -3, -3, -2, -3, -2, -2, -2, -4, -3, -4, -1, -1, -1, -5, ...], [-2, 5, -4, 8, 2, -5, -1, -1, -4, -1, -4, -4, 2, -1, 0, -2, 0, -1, -4, -5, ...], [-1, 1, -3, 2, 6, -3, -3, 0, -4, 1, -3, -2, 0, -1, 2, 0, -1, -1, -3, -3, ...], [-3, -4, -2, -5, -3, 8, -4, -1, 0, -4, 1, 0, -4, -4, -4, -3, -3, -2, -1, 1, ...], [0, -1, -3, -1, -3, -4, 8, -2, -4, -2, -4, -3, 0, -2, -2, -3, 0, -2, -4, -3, ...], [-2, 0, -3, -1, 0, -1, -2, 10, -4, 0, -3, -1, 1, -2, 1, 0, -1, -2, -4, -3, ...], [-1, -4, -2, -4, -4, 0, -4, -4, 5, -3, 2, 2, -3, -3, -3, -4, -3, -1, 4, -3, ...], [-1, 0, -3, -1, 1, -4, -2, 0, -3, 6, -3, -2, 0, -1, 2, 3, 0, -1, -3, -3, ...], [-2, -4, -2, -4, -3, 1, -4, -3, 2, -3, 5, 3, -4, -4, -2, -3, -3, -1, 1, -2, ...], [-1, -3, -2, -4, -2, 0, -3, -1, 2, -2, 3, 7, -2, -3, 0, -2, -2, -1, 1, -1, ...], [-1, 4, -2, 2, 0, -4, 0, 1, -3, 0, -4, -2, 7, -2, 0, -1, 1, 0, -3, -4, ...], [-1, -2, -4, -1, -1, -4, -2, -2, -3, -1, -4, -3, -2, 10, -1, -3, -1, -1, -3, -4, ...], [-1, 0, -3, 0, 2, -4, -2, 1, -3, 2, -2, 0, 0, -1, 7, 1, 0, -1, -3, -1, ...], [-2, -1, -4, -2, 0, -3, -3, 0, -4, 3, -3, -2, -1, -3, 1, 7, -1, -1, -3, -3, ...], [1, 0, -1, 0, -1, -3, 0, -1, -3, 0, -3, -2, 1, -1, 0, -1, 5, 2, -2, -4, ...], [0, 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5, 0, -3, ...], [0, -4, -1, -4, -3, -1, -4, -4, 4, -3, 1, 1, -3, -3, -3, -3, -2, 0, 5, -3, ...], [-3, -5, -5, -5, -3, 1, -3, -3, -3, -3, -2, -1, -4, -4, -1, -3, -4, -3, -3, 15, ...], ...] dayhoff_mdm78_similarity_scores = [[18, -20, 3, 3, -35, 13, -14, -5, -12, -19, -11, 2, 11, -4, -15, 11, 12, 2, -58, -35], [-20, 119, -51, -53, -43, -34, -34, -23, -54, -60, -52, -36, -28, -54, -36, 0, -22, -19, -78, 3], [3, -51, 39, 34, -56, 6, 7, -24, 1, -40, -26, 21, -10, 16, -13, 3, -1, -21, -68, -43], [3, -53, 34, 38, -54, 2, 7, -20, -1, -34, -21, 14, -6, 25, -11, 0, -4, -18, -70, -43], [-35, -43, -56, -54, 91, -48, -18, 10, -53, 18, 2, -35, -46, -47, -45, -32, -31, -12, 4, 70], [13, -34, 6, 2, -48, 48, -21, -26, -17, -41, -28, 3, -5, -12, -26, 11, 0, -14, -70, -52], [-14, -34, 7, 7, -18, -21, 65, -24, 0, -21, -21, 16, -2, 29, 16, -8, -13, -22, -28, -1], [-5, -23, -24, -20, 10, -26, -24, 45, -19, 24, 22, -18, -20, -20, -20, -14, 1, 37, -51, -9], [-12, -54, 1, -1, -53, -17, 0, -19, 47, -29, 4, 10, -11, 7, 34, -2, 0, -24, -35, -44], [-19, -60, -40, -34, 18, -41, -21, 24, -29, 59, 37, -29, -25, -18, -30, -28, -17, 19, -18, -9], [-11, -52, -26, -21, 2, -28, -21, 22, 4, 37, 64, -17, -21, -10, -4, -16, -6, 18, -42, -24], [2, -36, 21, 14, -35, 3, 16, -18, 10, -29, -17, 20, -5, 8, 0, 7, 4, -17, -42, -21], [11, -28, -10, -6, -46, -5, -2, -20, -11, -25, -21, -5, 59, 2, -2, 9, 3, -12, -56, -49], [-4, -54, 16, 25, -47, -12, 29, -20, 7, -18, -10, 8, 2, 40, 13, -5, -8, -19, -48, -40], [-15, -36, -13, -11, -45, -26, 16, -20, 34, -30, -4, 0, -2, 13, 61, -3, -9, -25, 22, -42], [11, 0, 3, 0, -32, 11, -8, -14, -2, -28, -16, 7, 9, -5, -3, 16, 13, -10, -25, -28], [12, -22, -1, -4, -31, 0, -13, 1, 0, -17, -6, 4, 3, -8, -9, 13, 26, 3, -52, -27], [2, -19, -21, -18, -12, -14, -22, 37, -24, 19, 18, -17, -12, -19, -25, -10, 3, 43, -62, -25], [-58, -78, -68, -70, 4, -70, -28, -51, -35, -18, -42, -42, -56, -48, 22, -25, -52, -62, 173, -2], [-35, 3, -43, -43, 70, -52, -1, -9, -44, -9, -24, -21, -49, -40, -42, -28, -27, -25, -2, 101]]