#!/usr/bin/env python
# coding: utf-8

# # AbNumber Usage Examples

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from abnumber import Chain
import pandas as pd

pd.options.display.max_columns = 200


# ## Creating a chain

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seq = 'EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSSAKTTAPSVYPLA'
chain = Chain(seq, scheme='imgt')
chain


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chain.print(numbering=True)


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chain.seq


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chain.tail


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chain.cdr3_seq


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chain.print_tall()


# ## Separate CDR definitions

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Chain(seq, scheme='imgt', cdr_definition='chothia')


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Chain(seq, scheme='imgt', cdr_definition='north')


# ## Renumbering

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# Use Chothia numbering and CDR definitions
chain.renumber('chothia').print_tall(6)


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# Keep IMGT numbering, use Chothia CDR definitions
chain.renumber(cdr_definition='chothia').print_tall(6)


# ## Chain properties

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chain.scheme


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chain.chain_type


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chain.is_heavy_chain()


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len(chain)


# ## Chain indexing and slicing

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chain['112']


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chain.raw[112]


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chain[:'30']


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chain['120':]


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chain.raw[114:]


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chain.raw[-10:]


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chain.raw[-10:]


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chain['111A':'112A'].print_tall()


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for pos, aa in chain['111A':'112A']:
     print(pos, aa)


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for pos, aa in chain.raw[:10]:
     print(pos, aa)


# ## Alignment

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seq2 = 'QVQLVQSGAELDRPGATVKMSCKASGYTTTRYTMHWVKQRPGQGLDWIGYINPSDRSYTNYNQKFKDKATLTTDKSSSTAYMQKTSLTSEDSAVYYCARYYDDERYDYLDRWGQGTTLTVSSAKTTAP'
chain2 = Chain(seq2, scheme='imgt')
chain2


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alignment = chain.align(chain2)
alignment


# ## Alignment indexing and slicing

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aa, bb = alignment['112A']
print(aa, bb)


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aa, bb = alignment.raw[10]
aa, bb


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for pos, (aa, bb) in alignment['108':'112A']:
    print(pos, aa, bb)


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for pos, (aa, bb) in alignment.raw[:10]:
    print(pos, aa, bb)


# ## CDR grafting

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alignment


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chain.graft_cdrs_onto(chain2).print()


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chain2.graft_cdrs_onto(chain).print()


# # Different numbering schemes

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from IPython.display import display, HTML


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EXAMPLES = [
    'EVQLQQSGAELARPGASVKMSCKASGYTFTSRRYTMHWVKQRPGQGLEWIGYINPSDERGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSSAKTTAPSVYPLA',
    'EIVLTQSPATLSLSPGERATLSCRASKGVSTDLSGYSYLHWYQQKPGQAPRLLIYLGYASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDGTLPLTFGGGTKVEIK',
    'QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGVFGGGTKLTVL'
]


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for chain_seq in EXAMPLES:
    for scheme, cdr_definition in [('imgt', 'imgt'), ('chothia','chothia'), ('kabat','kabat'), ('chothia','north'), ('aho','north')]:
        chain = Chain(chain_seq, scheme=scheme, cdr_definition=cdr_definition)
        scheme_label = scheme + ('-'+cdr_definition if cdr_definition != scheme else '')
        display(HTML(f'<h3>{chain.chain_type} {scheme_label}</h3>'))
        print(chain.format(numbering=True))


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