molecule-signature - Release 2.1.0

2.1.0 (2025-02-06)

Feat

• enable entrypoint for command line usage

Fix

• hack rm file for windows
• parsing entry

Refactor

• cmd: shorten arguments name
• notebooks: refactor imports

- Python
Published by github-actions[bot] about 1 year ago

molecule-signature - 2.0.2

2.0.2 (2025-01-31)

Refactor

• notebooks: refactor imports

2.0.1 (2025-01-29)

Refactor

• utils.py: trigger cicd

2.0.0 (2025-01-29)

Feat

• enumerate_utils: new function to compare ecfp with ecfp of a smiles
• enumerate_signature: new function to handle automatically enum ecfp to mols
• fillfromsignatures: possibility to fill the alphabet from precomputed atomic or molecular signatures
• generate_stereoisomers: limit number of stereoisomers
• enumeratemoleculefrom_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
• customsortwith_dependent: new function to sorted lists
• enumeratemoleculefrom_signature: chirality addition
• Signature: includes stereo in neighbors
• utils::mol_filter: additional filters based on dative bonds and radicals
• utils::molfromsmiles: change option from 'keepstereo' to 'clearstereo'
• Signature: add 'use_stereo' argument to switch on stereo in Signatures
• enumeratemoleculefrom_signature: possibility to save the molecule in SVG at each reconstruction step

Fix

• utils: put back missing import
• enumeratemoleculefrom_signature: default value of repeat
• enumeratesignaturefrom_morgan: single atom morgan
• SignatureAlphabet: try except on signature computation
• testsolECFP: use_stereo and test mol is none
• load_alphabet: use_stereo argument
• flatmoleculecopy: pass though SMILES to update implicit Hs count
• flatmoleculecopy: use RemoveHs to get rid of explicit Hs
• molfromsmiles: 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
• molfromsmiles: keep stereo by default
• Signature: stereo for FP but fragments remain flat
• enumeratesignaturefrom_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'
• enumeratesignaturefrom_morgan: sorting of the morgan bits
• enumeratesignaturefrom_morgan: single atom atomic signature
• enumeratemoleculefrom_signature: single atom atomic signature
• enumerate_signature: formal charge, explicit H, implicit H, degree, valency
• atomicnumcharge: new sig version

Refactor

• change the location of testsignaturesorted_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
• signaturesortedarray: 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
• enumeratesignaturefrom_morgan: total ct in function
• enumerate_signature: suppress useless maxnbrsolution argument
• utils: suppress useless vector-dict conversion functions
• signature_alphabet: suppress useless vector-dict conversion functions
• signature_alphabet: suppress map_root parameter
• enumeratesignaturefrom_morgan: alphabet dictionary structure changed to a set
• signature_alphabet: alphabet dictionary structure changed to a set
• enumeratesignaturefrom_morgan: change useless dictionary structures to lists
• enumerate_utils: suppress useless MIN set
• enumeratesignaturefrom_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

1.6.0 (2024-11-06)

Feat

• Signature: append cis/trans bonds
• Signature: append chiral tags

Fix

• Signature: debug messages
• solve_partitions: part_C zero length

1.5.0 (2024-10-01)

Feat

• 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
• solutionofone_group: new method to find a candidate min
• enumerate_signature: alphabet without neighbors and change of separators
• enumerate_utils: change of separators

Fix

• solve_partitions: part_C zero length
• getconstraintmatrices: using unique bond signatures is enough
• enumeratesignaturefrom_morgan: different eq diophantine solutions can give the same signature
• sol_max: smaller sol max when non constant partition
• solve_partitions: negative maxnbrpartition
• partitionsonnon_constant: bad local bound when small maxnbrpartition
• solve_partitions: stop when empty dictionary
• enumeratesignaturefrom_morgan: take account of the counted bits in fragments
• restrictsolby_C: verbose badly placed
• solve_partitions: bug on timeout flag

Refactor

• sol_max: simplify computation of shape
• solve_partitions: satisfied constraint lines save as set instead of list
• sanitize_molecule: suppress unuseful comment
• signaturesortedarray: 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
• solutionofone_group: ensure merged_parts is sorted
• partitionsonnon_constant: shorter way to compute final partitions

1.4.0 (2024-08-02)

Feat

• 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

Fix

• AtomSignature: Ensure canonic SMARTS whatever the input
• AtomSignature: stop trying to fix MolFromSmarts
• atomtosmarts: when possible direct extraction from SMARTS of query features
• MoleculeSignature: vector of morgan bits

Refactor

• Signature: sweep unused code
• atom_signature: better handle radius cuts
• atomtosmarts: SMARTS feature separator as a variable

1.3.2 (2024-07-29)

Feat

• 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

Fix

• AtomSignature: wrong radius for generation of neighbors
• enumerate_signature: import correction

1.3.1 (2024-07-16)

Fix

• AtomSignature: always use tuple for morgans
• MoleculeSignature: wrong attribute name

1.3.0 (2024-07-16)

Feat

• MoleculeSignature: allow generation of molecule signature with multiple morgan bit per atom
• AtomSignature: enable multiple morgan bits

1.2.0 (2024-07-15)

Feat

• AtomSignature: stop computing the with neighbors signature on init

Fix

• AtomSignature: force no implicit Hs
• AtomSignature: correctly handle negative charges

1.1.0 (2024-07-15)

Feat

• Signature: retrieve the signature with neighbors from the without one
• AtomSignature: export an AtomSignature as a RDKit Mol

Fix

• AtomSignature: use hashtag syntax for hydrogens
• enumeratemoleculefrom_signature: smiles cleaning before timeout condition
• signature_alphabet: suppress outdated arguments
• enumerate_signature: suppress outdated arguments
• MoleculeSignature: wrong attribute in test equality

Refactor

• 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
• enumeratesignaturefrom_morgan: simplification of some loops

1.0.0 (2024-07-11)

Feat

• MoleculeSignature: enable MoleculeSignature init from list and from string
• MoleculeSignature: complete rewrite of asstr now named tostring
• 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

Fix

• AtomSignature: fix attribute error
• enumeratesignaturefrom_morgan: bug when not enough fragments have been found
• enumerate_signature: second correction of the [nH] pb in the enum sig to mol
• atomicnumcharge: correction of formal charge extraction bug from smarts
• signature_alphabet: add missing parameters in print_out and load functions
• solve_partitions: bug when cleanlocalsolutions gives a zero solution
• updateconstraintmatrices: bug correction when AS is zero length v2
• updateconstraintmatrices: bug correction when AS is zero length
• enumeratemoleculefrom_signature: add boundary_bonds argument
• signature_alphabet: add boundarybounds and usesmarts in save method

Refactor

• 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

0.9.0 (2024-06-27)

Feat

• enumeration with smiles radius 2 and boundaries

Fix

• 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

0.8.0 (2024-06-26)

Feat

• Signature: revisit how to build SMARTS to be sure it will be canonic

Fix

• 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 enumeratemoleculefrom_signature
• Signature: fix map_root=False
• Signature: remove duplicated arg

0.7.0 (2024-06-21)

Feat

• MoleculeSignature: use multi-key sorting for the output

Fix

• Signature: homogenize MolToSmiles options
• MoleculeSignature: fix sorting
• asdeprecatedstring: fix args order

0.6.0 (2024-06-21)

Feat

• asdeprecatedstring: add on/off switch for root-style asdeprecatedstring output
• MoleculeSignature: add MoleculeSignature equality comparison
• integration of the new SMILES & SMARTS sig to the enum algo

Fix

• AtomSignature: AtomSignature equality comparison was always false
• Signature: disable SMARTS canonization
• Signature: fix canon_smarts unexpected argument

Refactor

• Signature: log status of SMARTS canonization at loading

0.4.0 (2024-06-19)

Feat

• 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 asdeprecatedstr methods
• Signature: new interface for interacting with signatures

Fix

• 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

Refactor

• Signature: update examples
• Signature: sweep code
• update imports
• signature: rename deprecated file
• signature: use available rdkit objects for BondType
• .gitignore: ignore .coverage file

0.3.0 (2024-04-25)

Feat

• signature_alphabet: enable fill from signature
• signature_alphabet: enable fill for existing alphabet

Fix

• update import

Refactor

• tox.ini: add ignore case to flake8
• delete jupyter checkpoints
• sort imports, add docstrings and solve_partition tests
• src: add code
• hello world

- Python
Published by github-actions[bot] about 1 year ago

molecule-signature - 2.0.1

2.0.1 (2025-01-29)

Refactor

• utils.py: trigger cicd

2.0.0 (2025-01-29)

Feat

• enumerate_utils: new function to compare ecfp with ecfp of a smiles
• enumerate_signature: new function to handle automatically enum ecfp to mols
• fillfromsignatures: possibility to fill the alphabet from precomputed atomic or molecular signatures
• generate_stereoisomers: limit number of stereoisomers
• enumeratemoleculefrom_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
• customsortwith_dependent: new function to sorted lists
• enumeratemoleculefrom_signature: chirality addition
• Signature: includes stereo in neighbors
• utils::mol_filter: additional filters based on dative bonds and radicals
• utils::molfromsmiles: change option from 'keepstereo' to 'clearstereo'
• Signature: add 'use_stereo' argument to switch on stereo in Signatures
• enumeratemoleculefrom_signature: possibility to save the molecule in SVG at each reconstruction step

Fix

• utils: put back missing import
• enumeratemoleculefrom_signature: default value of repeat
• enumeratesignaturefrom_morgan: single atom morgan
• SignatureAlphabet: try except on signature computation
• testsolECFP: use_stereo and test mol is none
• load_alphabet: use_stereo argument
• flatmoleculecopy: pass though SMILES to update implicit Hs count
• flatmoleculecopy: use RemoveHs to get rid of explicit Hs
• molfromsmiles: 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
• molfromsmiles: keep stereo by default
• Signature: stereo for FP but fragments remain flat
• enumeratesignaturefrom_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'
• enumeratesignaturefrom_morgan: sorting of the morgan bits
• enumeratesignaturefrom_morgan: single atom atomic signature
• enumeratemoleculefrom_signature: single atom atomic signature
• enumerate_signature: formal charge, explicit H, implicit H, degree, valency
• atomicnumcharge: new sig version

Refactor

• change the location of testsignaturesorted_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
• signaturesortedarray: 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
• enumeratesignaturefrom_morgan: total ct in function
• enumerate_signature: suppress useless maxnbrsolution argument
• utils: suppress useless vector-dict conversion functions
• signature_alphabet: suppress useless vector-dict conversion functions
• signature_alphabet: suppress map_root parameter
• enumeratesignaturefrom_morgan: alphabet dictionary structure changed to a set
• signature_alphabet: alphabet dictionary structure changed to a set
• enumeratesignaturefrom_morgan: change useless dictionary structures to lists
• enumerate_utils: suppress useless MIN set
• enumeratesignaturefrom_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

1.6.0 (2024-11-06)

Feat

• Signature: append cis/trans bonds
• Signature: append chiral tags

Fix

• Signature: debug messages
• solve_partitions: part_C zero length

1.5.0 (2024-10-01)

Feat

• 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
• solutionofone_group: new method to find a candidate min
• enumerate_signature: alphabet without neighbors and change of separators
• enumerate_utils: change of separators

Fix

• solve_partitions: part_C zero length
• getconstraintmatrices: using unique bond signatures is enough
• enumeratesignaturefrom_morgan: different eq diophantine solutions can give the same signature
• sol_max: smaller sol max when non constant partition
• solve_partitions: negative maxnbrpartition
• partitionsonnon_constant: bad local bound when small maxnbrpartition
• solve_partitions: stop when empty dictionary
• enumeratesignaturefrom_morgan: take account of the counted bits in fragments
• restrictsolby_C: verbose badly placed
• solve_partitions: bug on timeout flag

Refactor

• sol_max: simplify computation of shape
• solve_partitions: satisfied constraint lines save as set instead of list
• sanitize_molecule: suppress unuseful comment
• signaturesortedarray: 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
• solutionofone_group: ensure merged_parts is sorted
• partitionsonnon_constant: shorter way to compute final partitions

1.4.0 (2024-08-02)

Feat

• 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

Fix

• AtomSignature: Ensure canonic SMARTS whatever the input
• AtomSignature: stop trying to fix MolFromSmarts
• atomtosmarts: when possible direct extraction from SMARTS of query features
• MoleculeSignature: vector of morgan bits

Refactor

• Signature: sweep unused code
• atom_signature: better handle radius cuts
• atomtosmarts: SMARTS feature separator as a variable

1.3.2 (2024-07-29)

Feat

• 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

Fix

• AtomSignature: wrong radius for generation of neighbors
• enumerate_signature: import correction

1.3.1 (2024-07-16)

Fix

• AtomSignature: always use tuple for morgans
• MoleculeSignature: wrong attribute name

1.3.0 (2024-07-16)

Feat

• MoleculeSignature: allow generation of molecule signature with multiple morgan bit per atom
• AtomSignature: enable multiple morgan bits

1.2.0 (2024-07-15)

Feat

• AtomSignature: stop computing the with neighbors signature on init

Fix

• AtomSignature: force no implicit Hs
• AtomSignature: correctly handle negative charges

1.1.0 (2024-07-15)

Feat

• Signature: retrieve the signature with neighbors from the without one
• AtomSignature: export an AtomSignature as a RDKit Mol

Fix

• AtomSignature: use hashtag syntax for hydrogens
• enumeratemoleculefrom_signature: smiles cleaning before timeout condition
• signature_alphabet: suppress outdated arguments
• enumerate_signature: suppress outdated arguments
• MoleculeSignature: wrong attribute in test equality

Refactor

• 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
• enumeratesignaturefrom_morgan: simplification of some loops

1.0.0 (2024-07-11)

Feat

• MoleculeSignature: enable MoleculeSignature init from list and from string
• MoleculeSignature: complete rewrite of asstr now named tostring
• 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

Fix

• AtomSignature: fix attribute error
• enumeratesignaturefrom_morgan: bug when not enough fragments have been found
• enumerate_signature: second correction of the [nH] pb in the enum sig to mol
• atomicnumcharge: correction of formal charge extraction bug from smarts
• signature_alphabet: add missing parameters in print_out and load functions
• solve_partitions: bug when cleanlocalsolutions gives a zero solution
• updateconstraintmatrices: bug correction when AS is zero length v2
• updateconstraintmatrices: bug correction when AS is zero length
• enumeratemoleculefrom_signature: add boundary_bonds argument
• signature_alphabet: add boundarybounds and usesmarts in save method

Refactor

• 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

0.9.0 (2024-06-27)

Feat

• enumeration with smiles radius 2 and boundaries

Fix

• 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

0.8.0 (2024-06-26)

Feat

• Signature: revisit how to build SMARTS to be sure it will be canonic

Fix

• 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 enumeratemoleculefrom_signature
• Signature: fix map_root=False
• Signature: remove duplicated arg

0.7.0 (2024-06-21)

Feat

• MoleculeSignature: use multi-key sorting for the output

Fix

• Signature: homogenize MolToSmiles options
• MoleculeSignature: fix sorting
• asdeprecatedstring: fix args order

0.6.0 (2024-06-21)

Feat

• asdeprecatedstring: add on/off switch for root-style asdeprecatedstring output
• MoleculeSignature: add MoleculeSignature equality comparison
• integration of the new SMILES & SMARTS sig to the enum algo

Fix

• AtomSignature: AtomSignature equality comparison was always false
• Signature: disable SMARTS canonization
• Signature: fix canon_smarts unexpected argument

Refactor

• Signature: log status of SMARTS canonization at loading

0.4.0 (2024-06-19)

Feat

• 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 asdeprecatedstr methods
• Signature: new interface for interacting with signatures

Fix

• 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

Refactor

• Signature: update examples
• Signature: sweep code
• update imports
• signature: rename deprecated file
• signature: use available rdkit objects for BondType
• .gitignore: ignore .coverage file

0.3.0 (2024-04-25)

Feat

• signature_alphabet: enable fill from signature
• signature_alphabet: enable fill for existing alphabet

Fix

• update import

Refactor

• tox.ini: add ignore case to flake8
• delete jupyter checkpoints
• sort imports, add docstrings and solve_partition tests
• src: add code
• hello world

- Python
Published by github-actions[bot] about 1 year ago

molecule-signature - 2.0.0

2.0.0 (2025-01-29)

Feat

• enumerate_utils: new function to compare ecfp with ecfp of a smiles
• enumerate_signature: new function to handle automatically enum ecfp to mols
• fillfromsignatures: possibility to fill the alphabet from precomputed atomic or molecular signatures
• generate_stereoisomers: limit number of stereoisomers
• enumeratemoleculefrom_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
• customsortwith_dependent: new function to sorted lists
• enumeratemoleculefrom_signature: chirality addition
• Signature: includes stereo in neighbors
• utils::mol_filter: additional filters based on dative bonds and radicals
• utils::molfromsmiles: change option from 'keepstereo' to 'clearstereo'
• Signature: add 'use_stereo' argument to switch on stereo in Signatures
• enumeratemoleculefrom_signature: possibility to save the molecule in SVG at each reconstruction step

Fix

• utils: put back missing import
• enumeratemoleculefrom_signature: default value of repeat
• enumeratesignaturefrom_morgan: single atom morgan
• SignatureAlphabet: try except on signature computation
• testsolECFP: use_stereo and test mol is none
• load_alphabet: use_stereo argument
• flatmoleculecopy: pass though SMILES to update implicit Hs count
• flatmoleculecopy: use RemoveHs to get rid of explicit Hs
• molfromsmiles: 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
• molfromsmiles: keep stereo by default
• Signature: stereo for FP but fragments remain flat
• enumeratesignaturefrom_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'
• enumeratesignaturefrom_morgan: sorting of the morgan bits
• enumeratesignaturefrom_morgan: single atom atomic signature
• enumeratemoleculefrom_signature: single atom atomic signature
• enumerate_signature: formal charge, explicit H, implicit H, degree, valency
• atomicnumcharge: new sig version

Refactor

• change the location of testsignaturesorted_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
• signaturesortedarray: 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
• enumeratesignaturefrom_morgan: total ct in function
• enumerate_signature: suppress useless maxnbrsolution argument
• utils: suppress useless vector-dict conversion functions
• signature_alphabet: suppress useless vector-dict conversion functions
• signature_alphabet: suppress map_root parameter
• enumeratesignaturefrom_morgan: alphabet dictionary structure changed to a set
• signature_alphabet: alphabet dictionary structure changed to a set
• enumeratesignaturefrom_morgan: change useless dictionary structures to lists
• enumerate_utils: suppress useless MIN set
• enumeratesignaturefrom_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

1.6.0 (2024-11-06)

Feat

• Signature: append cis/trans bonds
• Signature: append chiral tags

Fix

• Signature: debug messages
• solve_partitions: part_C zero length

1.5.0 (2024-10-01)

Feat

• 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
• solutionofone_group: new method to find a candidate min
• enumerate_signature: alphabet without neighbors and change of separators
• enumerate_utils: change of separators

Fix

• solve_partitions: part_C zero length
• getconstraintmatrices: using unique bond signatures is enough
• enumeratesignaturefrom_morgan: different eq diophantine solutions can give the same signature
• sol_max: smaller sol max when non constant partition
• solve_partitions: negative maxnbrpartition
• partitionsonnon_constant: bad local bound when small maxnbrpartition
• solve_partitions: stop when empty dictionary
• enumeratesignaturefrom_morgan: take account of the counted bits in fragments
• restrictsolby_C: verbose badly placed
• solve_partitions: bug on timeout flag

Refactor

• sol_max: simplify computation of shape
• solve_partitions: satisfied constraint lines save as set instead of list
• sanitize_molecule: suppress unuseful comment
• signaturesortedarray: 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
• solutionofone_group: ensure merged_parts is sorted
• partitionsonnon_constant: shorter way to compute final partitions

1.4.0 (2024-08-02)

Feat

• 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

Fix

• AtomSignature: Ensure canonic SMARTS whatever the input
• AtomSignature: stop trying to fix MolFromSmarts
• atomtosmarts: when possible direct extraction from SMARTS of query features
• MoleculeSignature: vector of morgan bits

Refactor

• Signature: sweep unused code
• atom_signature: better handle radius cuts
• atomtosmarts: SMARTS feature separator as a variable

1.3.2 (2024-07-29)

Feat

• 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

Fix

• AtomSignature: wrong radius for generation of neighbors
• enumerate_signature: import correction

1.3.1 (2024-07-16)

Fix

• AtomSignature: always use tuple for morgans
• MoleculeSignature: wrong attribute name

1.3.0 (2024-07-16)

Feat

• MoleculeSignature: allow generation of molecule signature with multiple morgan bit per atom
• AtomSignature: enable multiple morgan bits

1.2.0 (2024-07-15)

Feat

• AtomSignature: stop computing the with neighbors signature on init

Fix

• AtomSignature: force no implicit Hs
• AtomSignature: correctly handle negative charges

1.1.0 (2024-07-15)

Feat

• Signature: retrieve the signature with neighbors from the without one
• AtomSignature: export an AtomSignature as a RDKit Mol

Fix

• AtomSignature: use hashtag syntax for hydrogens
• enumeratemoleculefrom_signature: smiles cleaning before timeout condition
• signature_alphabet: suppress outdated arguments
• enumerate_signature: suppress outdated arguments
• MoleculeSignature: wrong attribute in test equality

Refactor

• 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
• enumeratesignaturefrom_morgan: simplification of some loops

1.0.0 (2024-07-11)

Feat

• MoleculeSignature: enable MoleculeSignature init from list and from string
• MoleculeSignature: complete rewrite of asstr now named tostring
• 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

Fix

• AtomSignature: fix attribute error
• enumeratesignaturefrom_morgan: bug when not enough fragments have been found
• enumerate_signature: second correction of the [nH] pb in the enum sig to mol
• atomicnumcharge: correction of formal charge extraction bug from smarts
• signature_alphabet: add missing parameters in print_out and load functions
• solve_partitions: bug when cleanlocalsolutions gives a zero solution
• updateconstraintmatrices: bug correction when AS is zero length v2
• updateconstraintmatrices: bug correction when AS is zero length
• enumeratemoleculefrom_signature: add boundary_bonds argument
• signature_alphabet: add boundarybounds and usesmarts in save method

Refactor

• 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

0.9.0 (2024-06-27)

Feat

• enumeration with smiles radius 2 and boundaries

Fix

• 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

0.8.0 (2024-06-26)

Feat

• Signature: revisit how to build SMARTS to be sure it will be canonic

Fix

• 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 enumeratemoleculefrom_signature
• Signature: fix map_root=False
• Signature: remove duplicated arg

0.7.0 (2024-06-21)

Feat

• MoleculeSignature: use multi-key sorting for the output

Fix

• Signature: homogenize MolToSmiles options
• MoleculeSignature: fix sorting
• asdeprecatedstring: fix args order

0.6.0 (2024-06-21)

Feat

• asdeprecatedstring: add on/off switch for root-style asdeprecatedstring output
• MoleculeSignature: add MoleculeSignature equality comparison
• integration of the new SMILES & SMARTS sig to the enum algo

Fix

• AtomSignature: AtomSignature equality comparison was always false
• Signature: disable SMARTS canonization
• Signature: fix canon_smarts unexpected argument

Refactor

• Signature: log status of SMARTS canonization at loading

0.4.0 (2024-06-19)

Feat

• 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 asdeprecatedstr methods
• Signature: new interface for interacting with signatures

Fix

• 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

Refactor

• Signature: update examples
• Signature: sweep code
• update imports
• signature: rename deprecated file
• signature: use available rdkit objects for BondType
• .gitignore: ignore .coverage file

0.3.0 (2024-04-25)

Feat

• signature_alphabet: enable fill from signature
• signature_alphabet: enable fill for existing alphabet

Fix

• update import

Refactor

• tox.ini: add ignore case to flake8
• delete jupyter checkpoints
• sort imports, add docstrings and solve_partition tests
• src: add code
• hello world

- Python
Published by github-actions[bot] about 1 year ago