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homelette

A Python package offering a unified interface to different software for generating and evaluating homology models. This enables users to easily assemble custom homology modelling pipelines. homelette is extensively documented, lightweight and easily extendable.

For more information, please check out our online documentation.

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Citing

If you use homelette in your research, please cite the following article:

Philipp Junk, Christina Kiel, HOMELETTE: a unified interface to homology modelling software, Bioinformatics, 2021;, btab866, https://doi.org/10.1093/bioinformatics/btab866

Installation

The simplest way to use homelette is to access it through our prepared docker container. For more information, please check homelette/docker or the documentation.

homelette can also be installed from PIP.

python3 -m pip install homelette

Instructions on how to install homology modelling and evaluation dependencies can be found in our documentation.

Examples

There is a series of eight tutorials available demonstrating the use and extension of our homology modelling interface. Tutorials are available on our documentation webpage or as interactive Jupyter Notebooks in our Docker image or in homelette/examples.

License

homelette is freely available under the MIT license.

homelette's People

Contributors

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Forkers

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homelette's Issues

Could not match sequence in alignment to sequence from structure

Hi,

Sorry to bother again. I used the following code to do template search:

import homelette as hm
print("####read fasta file#####")
gen = hm.alignment.AlignmentGenerator_hhblits.from_fasta("fasta/CD19.fa")
print("#####search template######")
gen.get_suggestion(database_dir="/home/hhsuite_dbs/", n_threads=4)
temp = gen.show_suggestion()
target = "CD19"
gen.select_templates(list(temp.template)[0:9])

gen.alignment.print_clustal(70)

CD19        DIQMTQTTSSLSASLGDRVTISCRASQDIS----KYLNWYQQKPDGTVKLLIYHTSRLHSGVPSRFSGSG
6LFW_A      -IQMTQTASSLSASLGDRVTISCRASQYIN----NYLNWYQQKPDGTVTLLIYYTSILHSGVPSRFIGSG
6LFX_A      -IQMTQTASSLSASLGDRVTISCRASQYIN----NYLNWYQQKPDGTVTLLIYYTSILHSGVPSRFIGSG
3ESU_F      --VLIQSTSSLSASLGDRVTISCRASQDIR----NYLNWYQQKPDGTVKLLIYYTSRLQSGVPSRFSGSG
3ESV_G      --QMTQTTSSLSASLGDRVTVSCRASQDIR----NYLNWYQQKPDGTVKFLIYYTSRLQPGVPSRFSGSG
3AUV_D      --QMTQSPSSLSASVGDRVTITCRASQDVS----TAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSG
3AUV_E      --QMTQSPSSLSASVGDRVTITCRASQDVS----TAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSG
6TCS_A      -IQLTQSPSSLSASVGDRVTITCRASQSVDYDGDSYMNWYQQKPGKAPKLLIYAASYLESGVPSRFSGSG
5OGI_B      -IVMTQSPSSLSASVGDRVTITCKASQSVT----NDAAWYQKKPGKAPKLLIYQASTRYTGVPSRFSGSG
6EQC_D      -IVMTQSPSSLSASVGDRVTITCKASQSVT----NDAAWYQKKPGKAPKLLIYQASTRYTGVPSRFSGSG


CD19        SGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEITGSTSGSGKPGS-----GEGSTKGEVKLQE
6LFW_A      SGTDYSLTISNLDQEDIATYFCQQGYTLPLTFGAGTKLELKRPGGGGSGGGGSG---GGGS-VDEVKLVE
6LFX_A      SGTDYSLTISNLDQEDIATYFCQQGYTLPLTFGAGTKLELKRPGGGGSGGGGSG---GGGS-VDEVKLVE
3ESU_F      SGTDYSLTISNLEQEDIGTYFCQQGNTLPWTFGGGTKLEIRRGGGGSGGGGSGGGG-SGGG-GSEVQLQQ
3ESV_G      SGTDYSLTINNLEQEDIGTYFCQQGNTPPWTFGGGTKLEIKRGGGGSGGGGSGGGG-SGGG-GSEVQLQQ
3AUV_D      SGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGCGTKVEIKGGGGGSIEGR------SGGG-GSEVQLVE
3AUV_E      SGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGCGTKVEIKGGGGGSIEGR------SGGG-GSEVQLVE
6TCS_A      SGTDFTLTISSLQPEDFATYYCQQSHEDPYTFGCGTKVEIKRTGGGGSGGGGSGGGGSGGG-GSEVQLVE
5OGI_B      YGTDFTLTISSLQPEDFATYFCHQDYSSPLTFGQGTKVEIKRGGGGSGGGG------SGGG-GSQVQLVQ
6EQC_D      YGTDFTLTISSLQPEDFATYFCHQDYSSPLTFGQGTKVEIKRGGGGSGGGG------SGGG-GSQVQLVQ


CD19        SGPGLVAPSQSLSVTCTVSGVSLPD-YGVSWIRQPPRKGLEWLGVIWGS-ETTYYNSALKSRLTIIKDNS
6LFW_A      SGGGLVKPGGSLKLSCAASGFTFST-YGMSWVRQTPEKRLEWVASISGG-GDTYYTDIVKGRVTISRDND
6LFX_A      SGGGLVKPGGSLKLSCAASGFTFST-YGMSWVRQTPEKRLEWVASISGG-GDTYYTDIVKGRVTISRDND
3ESU_F      SGPELVKPGASVKISCKDSGYAFSS-SWMNWVKQRPGQGPEWIGRIYPGDGDTNYNGKFKGKATLTADKS
3ESV_G      SGPELVKPGASVKISCKDSGYAFNS-SWMNWVKQRPGQGLEWIGRIYPGDGDSNYNGKFEGKAILTADKS
3AUV_D      SGGGLVQPGGSLRLSCAASGFTISD-YWIHWVRQAPGKCLEWVAGITPAGGYTYYADSVKGRFTISADTS
3AUV_E      SGGGLVQPGGSLRLSCAASGFTISD-YWIHWVRQAPGKCLEWVAGITPAGGYTYYADSVKGRFTISADTS
6TCS_A      SGGGLVQPGGSLRLSCAVSGYSITSGYSWNWIRQAPGKCLEWVASITYD-GSTNYNPSVKGRITISRDDS
5OGI_B      SGAEDKKPGASVKVSCKVSGFSLGR-YGVHWVRQAPGQGLEWMGVIWRG-GTTDYNAKFQGRVTITKDDS
6EQC_D      SGAEDKKPGASVKVSCKVSGFSLGR-YGVHWVRQAPGQGLEWMGVIWRG-GTTDYNAKFQGRVTITKDDS


CD19        KSQVFLKMNSLQTDDTAIYYCAKHYYYGG--SYAMDYWGQGTSVTVSS
6LFW_A      RNILYLQMSSLRSEDTAMYHCTRGALVRLPHYYSMDYWGQGTSVTVS-
6LFX_A      RNILYLQMSSLRSEDTAMYHCTRGALVRLPHYYSMDYWGQGTSVTVS-
3ESU_F      SSTAYMQLSSLTSVDSAVYFCARSGLLR----YAMDYWGQGTSVTVSS
3ESV_G      SSTAYMQLSSLTSVDSAVYFCARSGLLR----YAMDYWGQGTSVTVSS
3AUV_D      KNTAYLQMNSLRAEDTAVYYCARFVFFLP---YAMDYWGQGTLVTVS-
3AUV_E      KNTAYLQMNSLRAEDTAVYYCARFVFFLP---YAMDYWGQGTLVTVS-
6TCS_A      KNTFYLQMNSLRAEDTAVYYCARGSHYFG--HWHFAVWGQGTLVTVS-
5OGI_B      KSTVYMELSSLRSEDTAVYYCARQGSN-----FPLAYWGQGTLVTVS-
6EQC_D      KSTVYMELSSLRSEDTAVYYCARQGSN-----FPLAYWGQGTLVTVS-

When I got PDB, it show warning and the 6TCS_A was lost:

gen.get_pdbs(pdb_format="polymer_entity_instance")

Checking template dir...
Template dir found!

Processing templates:

6LFW downloading from PDB...
6LFW downloaded!
6LFW_A: Chain extracted!
6LFW_A: Alignment updated!
6LFW_A: PDB processed!
6LFX downloading from PDB...
6LFX downloaded!
6LFX_A: Chain extracted!
6LFX_A: Alignment updated!
6LFX_A: PDB processed!
3AUV downloading from PDB...
3AUV downloaded!
3AUV_A: Chain extracted!
3AUV_A: Alignment updated!
3AUV_A: PDB processed!
3AUV_B: Chain extracted!
3AUV_B: Alignment updated!
3AUV_B: PDB processed!
3AUV_C: Chain extracted!
3AUV_C: Alignment updated!
3AUV_C: PDB processed!
3AUV_D: Chain extracted!
3AUV_D: Alignment updated!
3AUV_D: PDB processed!
3AUV_E: Chain extracted!
3AUV_E: Alignment updated!
3AUV_E: PDB processed!
3AUV_F: Chain extracted!
3AUV_F: Alignment updated!
3AUV_F: PDB processed!
6TCS downloading from PDB...
6TCS downloaded!
6TCS_A: Chain extracted!
5OGI downloading from PDB...
/usr/local/src/homelette-1.3/homelette/alignment.py:1973: UserWarning: 6TCS_A: Could not match sequence in alignment to sequence from structure.
  warnings.warn(msg)
5OGI downloaded!
5OGI_B: Chain extracted!
5OGI_B: Alignment updated!
5OGI_B: PDB processed!
6EQC downloading from PDB...
6EQC downloaded!
6EQC_D: Chain extracted!
6EQC_D: Alignment updated!
6EQC_D: PDB processed!
6EQC_E: Chain extracted!
6EQC_E: Alignment updated!
6EQC_E: PDB processed!
6EQC_F: Chain extracted!
6EQC_F: Alignment updated!
6EQC_F: PDB processed!

Finishing... All templates successfully
downloaded and processed!
Templates can be found in
"/home/templates".

gen.show_suggestion() ##not have 6TCS_A
template	coverage	identity
1	6LFX_A	94.69	62.86
0	6LFW_A	92.24	62.45
5	3AUV_D	91.02	55.51
2	3AUV_A	90.61	55.51
3	3AUV_B	90.20	55.10
4	3AUV_C	90.20	55.10
6	3AUV_E	90.20	55.10
7	3AUV_F	89.80	54.69
8	5OGI_B	91.02	51.43
9	6EQC_D	91.02	51.43
10	6EQC_E	91.02	51.43
11	6EQC_F	91.02	51.43

How to handle this problem (I want to include the 6TCS_A).
Thanks.

Jupyter lab can not find hhblits

Hi,
I have use the docker of homelette, and installed the hh-suite, downloaded the database. But when I run the code:

import homelette as hm
gen = hm.alignment.AlignmentGenerator_hhblits.from_fasta('test.fa')
gen.get_suggestion(database_dir='/home/hhsuite_dbs/')

It shows:

Performing PDB database search...
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
/tmp/ipykernel_2443/1608178073.py in <module>
----> 1 gen.get_suggestion(database_dir='/home/hhsuite_dbs/')

/usr/local/src/homelette-1.3/homelette/alignment.py in get_suggestion(self, database_dir, use_uniref, evalue_cutoff, iterations, n_threads, neffmax, verbose)
   2702             '-n', str(iterations), '-cpu', str(n_threads), '-neffmax',
   2703             str(neffmax), '-v', '1']
-> 2704         subprocess.run(command, stdout=None, check=True, shell=False)
   2705         vprint('PDB database search completed!')
   2706 

/usr/lib/python3.8/subprocess.py in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    491         kwargs['stderr'] = PIPE
    492 
--> 493     with Popen(*popenargs, **kwargs) as process:
    494         try:
    495             stdout, stderr = process.communicate(input, timeout=timeout)

/usr/lib/python3.8/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors, text)
    856                             encoding=encoding, errors=errors)
    857 
--> 858             self._execute_child(args, executable, preexec_fn, close_fds,
    859                                 pass_fds, cwd, env,
    860                                 startupinfo, creationflags, shell,

/usr/lib/python3.8/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
   1702                     if errno_num != 0:
   1703                         err_msg = os.strerror(errno_num)
-> 1704                     raise child_exception_type(errno_num, err_msg, err_filename)
   1705                 raise child_exception_type(err_msg)
   1706 

FileNotFoundError: [Errno 2] No such file or directory: 'hhblits'

While the hhblits was added in the PATH:

root@e72bf4885a75:~# which hhblits
/home/hh-suite/build/bin/hhblits

Sequence name of fasta file can not exceed 14 character

Hi,

It seems that the sequence name of fasta file can not exceed 15 character.

The name of first fasta file is 14 character long:

>AAAAAAAAAAAAAA
DIELTQSPTTLSVTPGDRVSLSCRASQSISDYLHWYQQQSHESPRLLIKYASQSISGIPSRFSGSGSGSDFTLSINSVEPEDVGVYYCQNGHSFPLTFGAGTKLELKGGGGSGGGGSGGGGSQVQLQQSGAELVQPGASVKLSCKASGYTFTNYDINWVRQRPEQGLEWIGWIFPGDGSTQYNEKFQGKATLTTDTSSSTAYMQLSRLTSEDSAVYFCARQTTATWFAYWGQGTTVTVSS

Code can run normal:

print("####read fasta file#####")
gen = hm.alignment.AlignmentGenerator_hhblits.from_fasta("fasta/B7-H3_8H9_10_kq.fa",template_location="templates/B7-H3_8H9_10_kq/")
print("#####search template######")
gen.get_suggestion(database_dir="hhsuite_dbs/", n_threads=3)

gen.select_templates(list(temp.template)[0:10])
gen.alignment.sequences["AAAAAAAAAAAAAA"].sequence

'DIELTQSPTTLSVTPGDRVSLSCRASQ-----S-----I------S----DYLHWYQQQSHESPRLLIKYASQSISGIPSRFSGSGSGSDFTLSINSVEPEDVGVYYCQNGHSFPLTFGAGTKLELKGGGGSGGGG---------SGGGGSQVQLQQSGAELVQPGASVKLSCKASGYTFTNYDINWVRQRPEQGLEWIGWIFPGDGSTQYNEKFQGKATLTTDTSSSTAYMQLSRLTSEDSAVYFCARQTTAT-----WFAYWGQGTTVTVSS'

gen.alignment.print_clustal(70)

AAAAAAAAAA  DIELTQSPTTLSVTPGDRVSLSCRASQ-----S-----I------S----DYLHWYQQQSHESPRLLIKY
6EJG_C      -IVLTQSPASLSVSLGQRATISCRASK-----S-----V------STSIYSYMHWYQQKPGQPPKLLIKY
3WBD_B      -VVMTQTPLSLPVSLGDQASISCRSSQ-----SLVHSNG------N----TYLYWYLQKPGQSPKPLIYR
5F3J_C      ---ITQDELSNPVTSGESVSISCRSSK-----SLLYQDG------K----TYLNWFLQRPGQSPQLLIYL
1H8O_B      --VLTQSHKFMSTSVGDRVSITCKASQ-----D-----V------G----TAVAWYQQKPGQSPKLLIYW
1H8N_A      --VLTQSHKFMSTSVGDRVSITCKASQ-----D-----V------G----TAVAWYQQKPGQSPKLLIYW
5KVE_L      -IVMSQSPSSLAVSVGEKITMSCKSSQ-----S-----LLYSNNEK----NYLAWYQQKPGQSPKLLIYW
3ESU_F      --VLIQSTSSLSASLGDRVTISCRASQ-----D-----I------R----NYLNWYQQKPDGTVKLLIYY
1KTR_L      -ILMTQTPSSLPVSLGDQASISCRSSQSIVHSN-----G------N----TYLEWYLQKPGQSPKLLIYK
3ESV_G      --QMTQTTSSLSASLGDRVTVSCRASQ-----D-----I------R----NYLNWYQQKPDGTVKFLIYY
4F9L_C      -IVLTQSPSSLSASLGDTITITCHASQ-----N-----I------N----LWLSWYQQRPGNIPKLLIYR


AAAAAAAAAA  ASQSISGIPSRFSGSGSGSDFTLSINSVEPEDVGVYYCQNGHSFPLTFGAGTKLELKGGGGSGGGG----
6EJG_C      ASYLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCEHSREFPFTFGTGTKLEIKGGGGSGGGGSGGG
3WBD_B      VSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCFQGTHVPYTFGGGTRLEIKGGGGSGGGG----
5F3J_C      MSTRASGVSDRFSGSGSGTDFTLEISRVEAEDVGVYYCQQLVEYPLTFGAGTKLELKRADGGGGSGGGG-
1H8O_B      ASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGAGTKLELKRGGGGSGGGGSGG
1H8N_A      ASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGAGTKLELKRGGGGSGGGGSGG
5KVE_L      ASARDSGVPDRFTGSGSGTDFTLTISSVKAEDLAVFYCQQYYSYPYTFGGGTKLEIKGGGGSGGGG----
3ESU_F      TSRLQSGVPSRFSGSGSGTDYSLTISNLEQEDIGTYFCQQGNTLPWTFGGGTKLEIRRGGGGSGGGGSGG
1KTR_L      VSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRGGGGSGGGGSGG
3ESV_G      TSRLQPGVPSRFSGSGSGTDYSLTINNLEQEDIGTYFCQQGNTPPWTFGGGTKLEIKRGGGGSGGGGSGG
4F9L_C      ASNLHTGVPSRFSGSGSATGFTLTISSLQPEDIATYYCQQGHSYPYTFGGGTKLDIKRADAGGGGSGGGG


AAAAAAAAAA  -----SGGGGSQVQLQQSGAELVQPGASVKLSCKASGYTFTNYDINWVRQRPEQGLEWIGWIFPGDGSTQ
6EJG_C      G----SGGGGSQVQLQQSGPELVKPGASVKISCKASGYTFSSSWMNWVKQRPGKGLEWIGRIYSGDGDAI
3WBD_B      -----SGGGGSQIQLQQSGPELVRPGASVKISCKASGYTFTDYYIHWVKQRPGEGLEWIGWIYPGSGNTK
5F3J_C      -----SGGGGSQVQLQQSGPELVKPGASVKISCKASGYAFISSWMNWVKQRPGKGLEWIGRIYPGDGDTH
1H8O_B      GG---SGGGGSQVQLQEPGGELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTN
1H8N_A      GG---SGGGGSQVQLQESGGELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTN
5KVE_L      -----SGGGGSQVQLQQPGAELLKPGASVKLSCKASGYSFSNYWMHWVKQRPGQGPEWIGMIHPNSGNTK
3ESU_F      GG---SGGGGSEVQLQQSGPELVKPGASVKISCKDSGYAFSSSWMNWVKQRPGQGPEWIGRIYPGDGDTN
1KTR_L      GG---SGGGGSQVQLQQSGPEDVKPGASVKISCKASGYTFTDYYMNWVKQSPGKGLEWIGDINPNNGGTS
3ESV_G      GG---SGGGGSEVQLQQSGPELVKPGASVKISCKDSGYAFNSSWMNWVKQRPGQGLEWIGRIYPGDGDSN
4F9L_C      SGGGGSGGGGSQVQLQESGAELVKPGASVKLSCKASGYTFTRYYLYWVKQRPGQGLEWIGEINPNNGGTK


AAAAAAAAAA  YNEKFQGKATLTTDTSSSTAYMQLSRLTSEDSAVYFCARQTTAT-----WFAYWGQGTTVTVSS
6EJG_C      YNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREG-KTGDL--LLRSWGQGSALTVSS
3WBD_B      YNEKFKGKATLTVDTSSSTAYMQLSSLTSEDSAVYFCARGG-KF-----AMDYWGQGTSVTVSS
5F3J_C      YNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREE-TAQTG--GFDYWGQGTTLTVS-
1H8O_B      YNQKFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWG-Y----------WGQGTLVTVS-
1H8N_A      YNQKFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWG-Y----------WGQGTLVTV--
5KVE_L      YNEKFKNKATLTVDKSSSMVYMQLSSLTSEDSAVFYCARLG-ND------MDYWGQGTSVTVSS
3ESU_F      YNGKFKGKATLTADKSSSTAYMQLSSLTSVDSAVYFCARSG-LLRY---AMDYWGQGTSVTVSS
1KTR_L      YNQKFKGRATLTVDKSSSTAYMELRSLTSEDSSVYYCESQS-G--------AYWGQGTTVTVSA
3ESV_G      YNGKFEGKAILTADKSSSTAYMQLSSLTSVDSAVYFCARSG-LLRY---AMDYWGQGTSVTVSS
4F9L_C      FNEKFKSKATLTVDKSSRTTYIQLSSLTSEDSAVYYCSRED-DYDGTPDAMDYWGQGTAVTVS-

But when I change the FASTA sequence name to 15 character length:

>AAAAAAAAAAAAAAA
DIELTQSPTTLSVTPGDRVSLSCRASQSISDYLHWYQQQSHESPRLLIKYASQSISGIPSRFSGSGSGSDFTLSINSVEPEDVGVYYCQNGHSFPLTFGAGTKLELKGGGGSGGGGSGGGGSQVQLQQSGAELVQPGASVKLSCKASGYTFTNYDINWVRQRPEQGLEWIGWIFPGDGSTQYNEKFQGKATLTTDTSSSTAYMQLSRLTSEDSAVYFCARQTTATWFAYWGQGTTVTVSS

Run the same code, this time the cluster is empty and all templates identity is 0:

print("####read fasta file#####")
gen = hm.alignment.AlignmentGenerator_hhblits.from_fasta("fasta/B7-H3_8H9_10_kq.fa",template_location="templates/B7-H3_8H9_10_kq/")
print("#####search template######")
gen.get_suggestion(database_dir="hhsuite_dbs/", n_threads=3)
gen.select_templates(list(temp.template)[0:10])
gen.alignment.sequences["AAAAAAAAAAAAAAA"].sequence

'DIELTQSPTTLSVTPGDRVSLSCRASQSISDYLHWYQQQSHESPRLLIKYASQSISGIPSRFSGSGSGSDFTLSINSVEPEDVGVYYCQNGHSFPLTFGAGTKLELKGGGGSGGGGSGGGGSQVQLQQSGAELVQPGASVKLSCKASGYTFTNYDINWVRQRPEQGLEWIGWIFPGDGSTQYNEKFQGKATLTTDTSSSTAYMQLSRLTSEDSAVYFCARQTTATWFAYWGQGTTVTVS'

gen.alignment.print_clustal(70)

AAAAAAAAAA  DIELTQSPTTLSVTPGDRVSLSCRASQSISDYLHWYQQQSHESPRLLIKYASQSISGIPSRFSGSGSGSD
6EJG_C      ----------------------------------------------------------------------
3WBD_B      ----------------------------------------------------------------------
5F3J_C      ----------------------------------------------------------------------
1H8O_B      ----------------------------------------------------------------------
1H8N_A      ----------------------------------------------------------------------
5KVE_L      ----------------------------------------------------------------------
3ESU_F      ----------------------------------------------------------------------
1KTR_L      ----------------------------------------------------------------------
3ESV_G      ----------------------------------------------------------------------
4F9L_C      ----------------------------------------------------------------------


AAAAAAAAAA  FTLSINSVEPEDVGVYYCQNGHSFPLTFGAGTKLELKGGGGSGGGGSGGGGSQVQLQQSGAELVQPGASV
6EJG_C      ----------------------------------------------------------------------
3WBD_B      ----------------------------------------------------------------------
5F3J_C      ----------------------------------------------------------------------
1H8O_B      ----------------------------------------------------------------------
1H8N_A      ----------------------------------------------------------------------
5KVE_L      ----------------------------------------------------------------------
3ESU_F      ----------------------------------------------------------------------
1KTR_L      ----------------------------------------------------------------------
3ESV_G      ----------------------------------------------------------------------
4F9L_C      ----------------------------------------------------------------------


AAAAAAAAAA  KLSCKASGYTFTNYDINWVRQRPEQGLEWIGWIFPGDGSTQYNEKFQGKATLTTDTSSSTAYMQLSRLTS
6EJG_C      ----------------------------------------------------------------------
3WBD_B      ----------------------------------------------------------------------
5F3J_C      ----------------------------------------------------------------------
1H8O_B      ----------------------------------------------------------------------
1H8N_A      ----------------------------------------------------------------------
5KVE_L      ----------------------------------------------------------------------
3ESU_F      ----------------------------------------------------------------------
1KTR_L      ----------------------------------------------------------------------
3ESV_G      ----------------------------------------------------------------------
4F9L_C      ----------------------------------------------------------------------


AAAAAAAAAA  EDSAVYFCARQTTATWFAYWGQGTTVTVS
6EJG_C      -----------------------------
3WBD_B      -----------------------------
5F3J_C      -----------------------------
1H8O_B      -----------------------------
1H8N_A      -----------------------------
5KVE_L      -----------------------------
3ESU_F      -----------------------------
1KTR_L      -----------------------------
3ESV_G      -----------------------------
4F9L_C      -----------------------------

gen.show_suggestion()
template coverage identity
6EJG_C 0.0 0.0
3WBD_B 0.0 0.0
5F3J_C 0.0 0.0
1H8O_B 0.0 0.0
1H8N_A 0.0 0.0
5KVE_L 0.0 0.0
3ESU_F 0.0 0.0
1KTR_L 0.0 0.0
3ESV_G 0.0 0.0
4F9L_C 0.0 0.0

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