ASMC 1.1.1

Tutorial

• The tutorial is now complete and corresponding inputs are available at docs/tutorial directory.

ASMC 1.1.0

Major Changes

• An asmc command can be created using pip install ./ within the ASMC directory. This allow to use asmc anywhere without using python script path
• The main workflow and the useful scripts have been reorganised, each purpose is now a subcommand:
  • run - the subcommand corresponding to the main workflow
  • identity - the subcommand corresponding to ASMC/asmc/compute_perc_id.py
  • extract - the subcommand corresponding to ASMC/asmc/extract_aa.py
  • compare - the subcommand corresponding to ASMC/asmc/compare_active_site.py
  • unique - the subcommand corresponding to ASMC/asmc/stats.py
  • pymol - this subcommand returns the path of the ASMC/asmc/zoom_active_site.py in order to load it in PyMol

New features

• The to_xlsx subcommand has been added in order to convert the groups_x_min_y.tsv to xlsx file

Bug fixes

• The alignment file to be specified in the input file for the -M/--msa option is now detected if it contains '.fasta', '.faa' or '.fa', even if another extension is added after it.
• Adds missing program exits after error detection while the -M/--msa option is used.

ASMC 1.0.3

Features

• User can now choose the unit of the sequence logos among (--units option):
  • bits
  • nats
  • probability
  • kT
  • kJ/mol
  • kcal/mol
• User can now choose the number of target models generated by MODELLER (-n, --nb-models option)

ASMC 1.0.2

Features

• User can now choose the resolution for the merged logos (only available for png format)

Breaking change

• For the --format option, if eps is selected, the logos are no longer merged into a single file but are available individually.

Docs

• README update
• Adds a worflow diagram

ASMC 1.0.1

Bug fix

• fix the path finding in ASMC/asmc/zoom_active_site.py

Docs

• README update
• Docstrings update
• CLI message update

ASMC 1.0.0

Features

• Detection of ligand-binding pockets based on reference structures (P2RANK software)
• Homology modelling (Modeller software). Several references can be given as inputs.
• Pairwise structural alignments (USalign software)
• Reads multiple sequence alignment
• Extracts active sites from pairwise structural alignements or multiple sequence alignement
• Calculates distance between sequences using an amino acid distance matrix based on physicochemical properties.
• Active site density-based clustering (DBSCAN algorithm)
• Create active site sequence logos for each group obtained