mmtbx.msa
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/msa.py

 
Modules
       
libtbx.easy_run
libtbx
os
sys

 
Classes
       
__builtin__.object
align_pdb_residues

 
class align_pdb_residues(__builtin__.object)
    Provides mapping between original residue numbers or IDs and a reference
numbering, via multiple sequence alignment.  Depending on whether or not
the insertion code was used in the original PDB files, it can use either
the resseq or the resid as the lookup key.
 
  Methods defined here:
__init__(self, pdb_sequences, pdb_names, pdb_offsets=None, pdb_resids=None, reference_sequence=None, reference_sequence_name='reference_seq', reference_sequence_offset=0, reference_sequence_resids=None, reference_index=None, substitute_names=False, out=None)
build_lookup_table(self)
# I am not proud of this.
convert_resid(self, pdb_name, resid)
convert_residue_number(self, pdb_name, resseq)
get_alignment_size(self)
get_all_resids_at_index(self, index)
get_name_index(self, pdb_name)
get_reference_resid(self, index)
get_resid_array_index(self, pdb_name, resid)
get_residue_position(self, pdb_name, resseq=None, resid=None)
run_alignment(self, out=None)
write_file(self, file_name)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
align_pdb_hierarchies(hierarchies, hierarchy_names, reference_hierarchy=None, substitute_names=True, log=None)
Convenience function: takes a collection of *single-model, single-chain* PDB
hierarchies, plus optional reference hierarchy, extracts sequences and
resseq offsets or resids, and generates alignment object.  By default, if
any of the hierarchies contain atoms with insertion codes, the resid mapping
will be used automatically.
get_muscle_alignment(fasta_sequences, group_sequences=True, out=None)
get_muscle_alignment_ordered(sequences)
run(args=(), params=None, out=<open file '<stdout>', mode 'w'>)
run_muscle(fasta_sequences, group_sequences=True)
validate_params(params)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
master_phil = <libtbx.phil.scope object>