class jade.basic.sequence.PDBConsensusInfo.PDBConsensusInfo(resinfo_list)[source]

Class to compute frequency and probability from an array of PDBInfo classes. The sequences within PDBInfo do not necessarily need to be the same length. A given sequence position is identified and stored in the data maps by its [pdb_num, chain, and icode] -> Use get_position_from_residue(residue) to get this position from a Residue instance.

compute_stats()[source]

Compute frequency and probability (0-1) for each position for each amino acid

get_all_sorted_positions()[source]
get_consensus(residue)[source]
get_consensus_for_position(position)[source]
get_consensus_for_residues(residue_list)[source]

Get the consensus for an ORDERED list of Residues

get_consensus_sequence()[source]
get_frequency(residue, aa)[source]
get_frequency_for_position(position, aa)[source]
get_position_from_residue(residue)[source]
get_probability(residue, aa)[source]

Get probability of the current position (starting from 0) and aa

get_probability_for_position(position, aa)[source]
init_data_map()[source]

Sets all probabilities 0 and appends each map to the stats vector

output_seqlogo_bt_residues(outdir, outname, res1, res2, chain)[source]
output_seqlogo_for_regions(regions, outdir, outname, chain)[source]

Regions is an array of Regions classes. Basically start/stop points

return_initialized_total_map()[source]
set_sequences(pdb_info_list)[source]

Set a sequence list