- notebooks: refactor imports
- utils.py: trigger cicd
- enumerate_utils: new function to compare ecfp with ecfp of a smiles
- enumerate_signature: new function to handle automatically enum ecfp to mols
- fill_from_signatures: possibility to fill the alphabet from precomputed atomic or molecular signatures
- generate_stereoisomers: limit number of stereoisomers
- enumerate_molecule_from_signature: limit number of stereoisomers
- enumerate_signature: implicit Hs count in SMARTS
- MoleculeSignature: use stereo by default
- Signature: implicit Hs count in SMARTS
- signature_alphabet: add stereochemistry
- enumerate_utils: add utilities about stereochemistry and isotopic information
- custom_sort_with_dependent: new function to sorted lists
- enumerate_molecule_from_signature: chirality addition
- Signature: includes stereo in neighbors
- utils::mol_filter: additional filters based on dative bonds and radicals
- utils::mol_from_smiles: change option from 'keep_stereo' to 'clear_stereo'
- Signature: add 'use_stereo' argument to switch on stereo in Signatures
- enumerate_molecule_from_signature: possibility to save the molecule in SVG at each reconstruction step
- utils: put back missing import
- enumerate_molecule_from_signature: default value of repeat
- enumerate_signature_from_morgan: single atom morgan
- SignatureAlphabet: try except on signature computation
- test_sol_ECFP: use_stereo and test mol is none
- load_alphabet: use_stereo argument
- flat_molecule_copy: pass though SMILES to update implicit Hs count
- flat_molecule_copy: use RemoveHs to get rid of explicit Hs
- mol_from_smiles: remove superfluous Hs
- MoleculeSignature: update morgan bits index when flattening molecules
- AtomSignature: morgans bit always considered as a tuple
- generate_stereoisomers: high number of possible stereoisomers
- mol_from_smiles: keep stereo by default
- Signature: stereo for FP but fragments remain flat
- enumerate_signature_from_morgan: sort fragments by morgan bits
- MolecularGraph: simplification of the smiles computation
- MolecularGraph: better atom initialization
- Signature: only cis/trans stereo when the environment is big enough
- Signature: fix old attribute name 'morgan'
- enumerate_signature_from_morgan: sorting of the morgan bits
- enumerate_signature_from_morgan: single atom atomic signature
- enumerate_molecule_from_signature: single atom atomic signature
- enumerate_signature: formal charge, explicit H, implicit H, degree, valency
- atomic_num_charge: new sig version
- change the location of test_signature_sorted_array
- enumerate_utils: move a function + docstrings
- signature to molsig and metanetx alphabet as bonus only
- molsig to signature and signature_alphabet to SignatureAlphabet
- enumerate_utils: signature to molsig and signature_alphabet to SignatureAlphabet
- enumerate_signature: from signature to from molsig
- SignatureAlphabet: from signature to from molsig
- test_SignatureAlphabet: change script name
- SignatureAlphabet: change script name
- tests: rename module name
- rename module as molsig
- Signature: change 'rooted_smiles' arts to 'rooted‘
- Signature: remove deprecated signature str
- Signature: remove use_smarts arg
- notebooks: sweep
- Signature: remove deprecated function
- signature: sweep old code
- signature_alphabet: suppress useless functions
- signature_sorted_array: suppress useless parameter
- enumerate_signature: rename functions
- enumerate_utils: rename functions
- Signature: sweep unused method
- Signature: clean unused code
- datasets: remove old data
- enumerate_utils: black the code and sort packages
- enumerate_signature: black the code and sort packages
- solve_partitions: change timeout vocabulary to threshold
- enumerate_signature: change timeout vocabulary to threshold
- enumerate_signature_from_morgan: total ct in function
- enumerate_signature: suppress useless max_nbr_solution argument
- utils: suppress useless vector-dict conversion functions
- signature_alphabet: suppress useless vector-dict conversion functions
- signature_alphabet: suppress map_root parameter
- enumerate_signature_from_morgan: alphabet dictionary structure changed to a set
- signature_alphabet: alphabet dictionary structure changed to a set
- enumerate_signature_from_morgan: change useless dictionary structures to lists
- enumerate_utils: suppress useless MIN set
- enumerate_signature_from_morgan: suppress useless MIN set
- signature_alphabet: remove unnecessary or outdated functions
- SignatureAlphabet: remove unuseful parameters
- signature_alphabet: remove unnecessary or outdated functions
- enumerate_utils: remove unnecessary or outdated functions
- enumerate_utils: unification of smiles notation
- enumerate_utils: remove unnecessary or outdated functions
- Signature: morgan_bit renamed to morgan bits and does not accept interger anymore
- Signature: remove unused import
- Signature: remove 'all_bits' option as we always use all bits
- Signature: append cis/trans bonds
- Signature: append chiral tags
- Signature: debug messages
- solve_partitions: part_C zero length
- Signature: add morgans argument for to_string methods
- solve_partitions: clean solutions early by max values
- 1.create_alphabets: update with new sig form
- 2.reverse_engineer: update enum pipeline for sig without neigh and full ecfp
- enumerate_signature: signature without neighbors and change of separators
- signature_alphabet: change of separators
- solution_of_one_group: new method to find a candidate min
- enumerate_signature: alphabet without neighbors and change of separators
- enumerate_utils: change of separators
- solve_partitions: part_C zero length
- get_constraint_matrices: using unique bond signatures is enough
- enumerate_signature_from_morgan: different eq diophantine solutions can give the same signature
- sol_max: smaller sol max when non constant partition
- solve_partitions: negative max_nbr_partition
- partitions_on_non_constant: bad local bound when small max_nbr_partition
- solve_partitions: stop when empty dictionary
- enumerate_signature_from_morgan: take account of the counted bits in fragments
- restrict_sol_by_C: verbose badly placed
- solve_partitions: bug on timeout flag
- sol_max: simplify computation of shape
- solve_partitions: satisfied constraint lines save as set instead of list
- sanitize_molecule: suppress unuseful comment
- signature_sorted_array: change sig in string to list
- enumerate_signature: change sig in string to list
- solve_partitions: add a function to refactor the restriction on C
- solve_partitions: restriction on C only when necessary
- solution_of_one_group: ensure merged_parts is sorted
- partitions_on_non_constant: shorter way to compute final partitions
- Signature: function to set canonic aam for fragment
- Signature: add function to extract features from a SMARTS
- Signature: add function to extract features from a SMARTS
- AtomSignature: Ensure canonic SMARTS whatever the input
- AtomSignature: stop trying to fix MolFromSmarts
- atom_to_smarts: when possible direct extraction from SMARTS of query features
- MoleculeSignature: vector of morgan bits
- Signature: sweep unused code
- atom_signature: better handle radius cuts
- atom_to_smarts: SMARTS feature separator as a variable
- signature_alphabet: alphabet without neighbors
- solve_partitions: new solving method for diophantine systems coming from full ecfp
- enumerate_signature: reduced ecfp changed to full ecfp
- AtomSignature: wrong radius for generation of neighbors
- enumerate_signature: import correction
- AtomSignature: always use tuple for morgans
- MoleculeSignature: wrong attribute name
- MoleculeSignature: allow generation of molecule signature with multiple morgan bit per atom
- AtomSignature: enable multiple morgan bits
- AtomSignature: stop computing the with neighbors signature on init
- AtomSignature: force no implicit Hs
- AtomSignature: correctly handle negative charges
- Signature: retrieve the signature with neighbors from the without one
- AtomSignature: export an AtomSignature as a RDKit Mol
- AtomSignature: use hashtag syntax for hydrogens
- enumerate_molecule_from_signature: smiles cleaning before timeout condition
- signature_alphabet: suppress outdated arguments
- enumerate_signature: suppress outdated arguments
- MoleculeSignature: wrong attribute in test equality
- AtomSignature: atom_signature as a class function
- Signature: sweep deprecated functions
- Signature: update default value for atom_signature
- reduced_fingerprint: int type of morgan vectors
- enumerate_signature_from_morgan: simplification of some loops
- MoleculeSignature: enable MoleculeSignature init from list and from string
- MoleculeSignature: complete rewrite of as_str now named to_string
- AtomSignature: add from_string constructor
- AtomSignature: improve to_string export
- utils: add functions to sanitize and filter molecular structures
- signature_alphabet: add merge and compatibility functions
- 3.drug_application.ipynb: draft of a notebook to enumerate drug molecules and create drug databases
- enumerate_signature: add new timeouts
- 2.reverse_engineer: add outputs of timeout with enumeration
- AtomSignature: fix attribute error
- enumerate_signature_from_morgan: bug when not enough fragments have been found
- enumerate_signature: second correction of the [nH] pb in the enum sig to mol
- atomic_num_charge: correction of formal charge extraction bug from smarts
- signature_alphabet: add missing parameters in print_out and load functions
- solve_partitions: bug when clean_local_solutions gives a zero solution
- update_constraint_matrices: bug correction when AS is zero length v2
- update_constraint_matrices: bug correction when AS is zero length
- enumerate_molecule_from_signature: add boundary_bonds argument
- signature_alphabet: add boundary_bounds and use_smarts in save method
- MoleculeSignature: constructor accept None mol
- MoleculeSignature: rewrite to_list to stick with AtomSignature behaviour
- MoleculeSignature: update repr
- MoleculeSignature: clean code
- MoleculeSignature: rename attributes
- MoleculeSignature: remove unused neighbor argument
- AtomSignature: change repr method to keep on track with attribute names
- AtomSignature: edit class attribute names
- MoleculeSignature: remove dispensable attributes
- AtomSignature: rename variables
- AtomSignature: remove dispensable attributes
- AtomSignature: update atom signature comparison methods
- Signature: remvove legacy implementation for computing signature
- Signature: use smarts syntex as default
- enumerate_signature: suppress useless arguments
- signature_old: move the last usefull functions from signature_old to other scripts
- enumerate_utils: suppress useless signature_neighbor
- enumerate_utils: move test functions from notebooks to scripts
- enumeration with smiles radius 2 and boundaries
- Signature: remove rdcanon calls
- correction of the [nH] pb in the enum sig to mol
- suppress src. from local imports
- Signature: double check neighbor output is required
- Signature: revisit how to build SMARTS to be sure it will be canonic
- Signature: put back boundary_bonds on / off option
- .gitignore: **/.ipynb_checkpoints/
- signature_alphabet: integration of the SMARTS and SMILES sig in the computation of the alphabet
- add of root=False when signature is used in the enumeration
- enumerate_signature: mol None bug in enumerate_molecule_from_signature
- Signature: fix map_root=False
- Signature: remove duplicated arg
- MoleculeSignature: use multi-key sorting for the output
- Signature: homogenize MolToSmiles options
- MoleculeSignature: fix sorting
- as_deprecated_string: fix args order
- as_deprecated_string: add on/off switch for root-style as_deprecated_string output
- MoleculeSignature: add MoleculeSignature equality comparison
- integration of the new SMILES & SMARTS sig to the enum algo
- AtomSignature: AtomSignature equality comparison was always false
- Signature: disable SMARTS canonization
- Signature: fix canon_smarts unexpected argument
- Signature: log status of SMARTS canonization at loading
- Signature: enable new signature computation from MoleculeSignature objects
- Signature: enable new signature generation from AtomSignature objects
- Signature: improve atom to smarts conversion
- Signature: additional options for AtomSignature
- Signature: sort atom signatures
- Signature: add few tests of combinations
- Signature: add few examples
- Signature: add as_deprecated_str methods
- Signature: new interface for interacting with signatures
- canon_smarts: add file of primitives
- canon_smarts: work around for unknown primitives
- Signature: stop crashing for H and HH molecules
- Signature: stop complaining about molecule having a max radius of 1
- Signature: additional args could be passed to MolToSmiles
- Signature: fix exception on molecule made of a single atom
- Signature: fix deprecated fingerprint generation
- Signature: update examples
- Signature: sweep code
- update imports
- signature: rename deprecated file
- signature: use available rdkit objects for BondType
- .gitignore: ignore .coverage file
- signature_alphabet: enable fill from signature
- signature_alphabet: enable fill for existing alphabet
- update import
- tox.ini: add ignore case to flake8
- delete jupyter checkpoints
- sort imports, add docstrings and solve_partition tests
- src: add code
- hello world