Modules
		operator os re string

Classes
		__builtin__.object alignment clustal_alignment fasta_alignment pir_alignment generic_alignment_parser clustal_alignment_parser sequential_alignment_parser generic_sequence_parser midline sequence fasta_sequence pir_sequence   class alignment(__builtin__.object)     Alignment     Methods defined here: __init__(self, alignments, names, gap='-') identity_count(self) identity_fraction(self) midline(self) sequence_strings(self) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class clustal_alignment(alignment)     Clustal alignment     Method resolution order: clustal_alignment alignment __builtin__.object Methods defined here: __init__(self, alignments, names, program, version, gap='-') __str__(self) format(self, aln_width, caption_width) make_aln_info(self, caption, alignment, aln_width) Methods inherited from alignment: identity_count(self) identity_fraction(self) midline(self) sequence_strings(self) Data descriptors inherited from alignment: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class clustal_alignment_parser(generic_alignment_parser)     Specific for Clustal alignments     Method resolution order: clustal_alignment_parser generic_alignment_parser __builtin__.object Methods defined here: parse(self, text) Data and other attributes defined here: regex = <_sre.SRE_Pattern object at 0x33e1ea0> Methods inherited from generic_alignment_parser: __call__(self, text) assess_parsing_results(self, data_dict, text) extract(self, text) fail(self, text) valid_alignments(self, alignments) Data descriptors inherited from generic_alignment_parser: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class fasta_alignment(alignment)     Fasta alignment     Method resolution order: fasta_alignment alignment __builtin__.object Methods defined here: __init__(self, alignments, names, descriptions, gap='-') __str__(self) format(self, width) Methods inherited from alignment: identity_count(self) identity_fraction(self) midline(self) sequence_strings(self) Data descriptors inherited from alignment: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class fasta_sequence(sequence)     Fasta sequence     Method resolution order: fasta_sequence sequence __builtin__.object Methods defined here: __init__(self, sequence, name, description) __str__(self) format(self, width) Methods inherited from sequence: __eq__(self, other) __len__(self) __ne__(self, other) Data descriptors inherited from sequence: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class generic_alignment_parser(__builtin__.object)     General purpose alignment parser     Methods defined here: __call__(self, text) assess_parsing_results(self, data_dict, text) extract(self, text) fail(self, text) valid_alignments(self, alignments) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class generic_sequence_parser(__builtin__.object)     General-purpose sequence parser     Methods defined here: __call__(self, text) __init__(self, regex, type) parse(self, text) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class midline(__builtin__.object)     Alignment midline     Methods defined here: __init__(self, identical='*', conserved=':', semi='.', differ=' ') compare(self, alignments, gap='-') conservation_code(self, residues) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class pir_alignment(alignment)     Pir alignment     Method resolution order: pir_alignment alignment __builtin__.object Methods defined here: __init__(self, alignments, names, types, descriptions, gap='-') __str__(self) format(self, width) Methods inherited from alignment: identity_count(self) identity_fraction(self) midline(self) sequence_strings(self) Data descriptors inherited from alignment: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class pir_sequence(sequence)     Pir sequence     Method resolution order: pir_sequence sequence __builtin__.object Methods defined here: __init__(self, sequence, name, type, description) __str__(self) format(self, width) Methods inherited from sequence: __eq__(self, other) __len__(self) __ne__(self, other) Data descriptors inherited from sequence: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class sequence(__builtin__.object)     Sequence     Methods defined here: __eq__(self, other) __init__(self, sequence, name) __len__(self) __ne__(self, other) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class sequential_alignment_parser(generic_alignment_parser)     Specific for sequential format alignments     Method resolution order: sequential_alignment_parser generic_alignment_parser __builtin__.object Methods defined here: __init__(self, regex, type) parse(self, text) Methods inherited from generic_alignment_parser: __call__(self, text) assess_parsing_results(self, data_dict, text) extract(self, text) fail(self, text) valid_alignments(self, alignments) Data descriptors inherited from generic_alignment_parser: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)

Functions
		alignment_parser_for(file_name) known_alignment_formats() known_sequence_formats() sequence_parser_for(file_name) wrap(text, width) # Wrap lines that are longer than 'width'

Data
		ali_alignment_parse = <mmtbx.bioinformatics.sequential_alignment_parser object at 0x33b87d0> clustal_alignment_parse = <mmtbx.bioinformatics.clustal_alignment_parser object at 0x33b8710> fasta_alignment_parse = <mmtbx.bioinformatics.sequential_alignment_parser object at 0x33b8790> fasta_sequence_parse = <mmtbx.bioinformatics.generic_sequence_parser object at 0x33b85d0> pir_alignment_parse = <mmtbx.bioinformatics.sequential_alignment_parser object at 0x33b8750> pir_sequence_parse = <mmtbx.bioinformatics.generic_sequence_parser object at 0x33b8610> seq_sequence_parse = <mmtbx.bioinformatics.generic_sequence_parser object at 0x33b8590>