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RELEASE_NOTES
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RELEASE_NOTES
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2019-10 Release 4.0
New scripts
===========
dbf - Computes topological and/or 3D distances between features
dicer - Structure fragmentation tool which can optionally use a query fle
hydrophobic_sections - Hydrophobic section descriptors
iwdescr - Calculate 200+ descriptors from a SMILES file
iwecfp - Extended Connectivity fingerprints for molecules
iwfp - Hashed path based fingerprints from SMILES file
jwsadb - Calculate charge surface area related descriptors for molecules
maccskeys - Generate MACCS keys
make_these_molecules - Structure enumeration using SMILES and specific reagents. Uses a rxn file, a reagents ID file and two reagent SMILES files.
molecular_abstraction - Performs molecular transformations associated with various molecular abstractions
molecular_transformations - Performs any number of molecular transformations on input molecules using reactions supplied
molecules_from_reagents - Synthesize molecules from isotopically labelled reactant sets; returns those identical to seeds in a given file
random_molecular_permutations - Chemistry aware molecular perturbation tool
remove_and_label - Removes atoms and isotopically labels the adjacent atoms
remove_matched_atoms - Strips fragments/matched atoms from molecules; can be used in place of a simple de-protection reaction
ring_fingerprint - Computes fingerprints based on ring properties, primarily aromatic rings
ring_replacement - Companion program to ring_extraction
ring_substitution - Computes ring substitution fingerprints
rule_of_five - Computes Pfizer/Lipinski rule-of-five on molecules in input file. Returns molecule id and the values of the properties calculated.
rxn_fingerprint - Takes a rxnsmi file, and generates reaction fingerprints
substitutions - Calculate rtable given a scaffold and a set of compounds
temperature - Computes 'temperature' descriptors
tnass - Does substructure searches with NEED/AVAILABLE flags
average - Compute the statistics on columns in a file.
dfilefilter - Filter a descriptor file with expressions of the descriptors
distribution - Calculate the distribution based on the input data set.
fetch_sdf_quick - Fetch records from one file based on the identifiers in another file
iwsplit - Splits a file into chunks based on regular expressions
normalise - Normalize the columns in a file
notenoughvariance - Filter out the data record without enough variance on columns
random_records - Randomly select records from the provided file
rearrange_columns - Rearrange the columns in one descriptor file to look like another descriptor file
tcount - Count number of lines, columns in a file
whatsmissing - Identifies missing descriptors from a descriptor file
gfp_distance_matrix_iwdm - Computes the distance matrix for a pool of gfp fingerprints; generates a binary file
gfp_leader_standard - Leader clustering implementation requiring MPR IW MK MK2
gfp_lnearneighbours_standard - Find the near neighbours between fingerprints
gfp_spread_standard - Do a spread design on fingerprint descriptors
gfp_to_descriptors_multiple - Converts multi component fingerprints to descriptors
iwstats - Computes Bsquared and other statistics for input file
nn_leader_and_jp - Performs Leader, Taylor-Butina, Jarvis-Patrick clustering starting from a tdt-formatted near-neighbour list
gfp_naive_bayesian - Naive Bayes predictive model training and prediction
Retired scripts
===============
Bug fixes
=========
Data
=========
Lib
=========
Updates
=======
Known issues
============
The generated fingerprints can not be shared across OS's
2019-04 Release 3.0
New scripts
===========
gfp_add_descriptors - Adds descriptors to the gfp file with matching ID
gfp_lnearneighbours - Selects near neighbour based on gfp descriptors, uses SMILES, can handle LARGE numbers of cpds
gfp_to_descriptors - Converts fingerprints to descriptors
gfp_profile_activity_by_bits - Scans a fingerprint file and computes average activity associated with each bit
gfp_pairwise_distances - Calculates the pairwise distance between molecule
gfp_distance_filter - Filters molecules according to how close they are to members of a comparison pool
gfp_sparse_to_fixed - Converts non-colliding fingerprints to fixed counted, or binary forms
gfp_spread_v2 - Calculates the distance spread of fingerprints against target fingerprint or group of fingerprints
gfp_single_linkage - Finds the single linkage in the gfp fingerpint set
gfp_spread_buckets_v2 - Calculates the distance spread of fingerprints against target fingerprint or group of fingerprints while considering a bucketized variable like activity or CLOGP
gfp_nearneighbours_single_file - Finds near neighbours within a set of fingerprints
gfp_nearneighbours - Finds near neighbours of a set of fingerprints
gfp_leader_v2 - Performs clustering with leader (sphere exclusion) algorithm on gfp descriptors
gfp_distance_matrix - Computes the distance matrix for a pool of gfp fingerprints; generates a human-readable ascii matrix
descriptor_file_to_01_fingerprints - Converts a integer descriptor file to fingerprints, either fixed 0/1 or non colliding counted
nplotnn - Processes the output of several gfp nearneighbour tools into SMILES
tdt_sort - Sorts fields of a TDT file or stream according to specific tag, properties, or the degree of each node
tdt_join - Joins two TDT streams, possible with different identifiers
descriptors_to_fingerprint - Converts a descriptors to a sparse fingerprint
Retired scripts
===============
Bug fixes
=========
iwdemerit - Fix the crash when smiles contain multiple hydrogen atoms
Data
=========
Lib
=========
libgfp.a
Updates
=======
Known issues
============
The output precision and format for the float point numbers might be different
on mac and linux os
The generated fingerprints can not be shared across OS's
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2019-01 Release 2.1
New scripts
===========
Retired scripts
===============
Bug fixes
=========
Data
=========
Lib
=========
Updates
=======
rxn_substructure_search - Reorganize and rationalize the interface of the scripts
- Add some missing functionality for example reaction smiles search
rxn_standardize - Reorganize and rationalize the interface of the scripts
- Add component cleaning option
Known issues
============
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2018-10 Release 2.0
New scripts
===========
random_smiles - Generate random smiles based on input smiles
preferred_smiles - Write either unique smiles (if interpretable) or non aromatic unique form
rotatable_bonds - Calculate the rotatable bonds in the modules
concat_files - Concatenates descriptor files by joining on identifiers
msort - Sorts a molecule file by various criteria
tp_first_pass - Runs molecules through the Lilly medchem rules, skip to next molecule upon crossing a threshold or instant kill rule
mol2qry - Converts a molecule to a query file
molecular_scaffold - Chemical structure fragmentation tool to recursively cuts molecules into fragments
molecule_subset - Extracts a subset of atoms from set of molecules based on a single substructure
rgroup - Identifies substituents from substructure matched molecule
ring_extraction - Extracts rings from molecules
ring_trimming - Exhaustively trim rings from ring systems, preserving aromaticiy
sp3_filter - Filter molecules according to sp3 content
tautomer_generation - Enumerate tautomeric forms for molecules
smiles_mutation - Generate new smiles from a set of input molecules by random strong operations
rxn_substructure_search - Search substructure over reactions
activity_consistency - Group identical molecules (including isomers) with varying activity values
Retired scripts
===============
Bug fixes
=========
Data
=========
Lib
=========
Updates
=======
Known issues
============
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2018-06 Release 1.0
New scripts
===========
common_names - Merge identical chemical structures to one common name in a SMILES file (also see unique_molecules tool). Useful for identifying unique chemical structures in a SMILES file.
fetch_smiles_quick - Fetches records from one file based on identifiers in another file
unique_molecules - Filters out duplicate chemical structures based on unique smiles
unique_rows - Identifies the unique rows in a file
iwcut - Extract columns from a text file
fileconv - Structure file utility to clean up SMILES files and filter on specific criteria. It can also be used to convert between chemical file formats including, e.g from SDF to SMILES
rxn_signature - Generates reaction signatures for input reactions
rxn_standardize - Checks and standardizes input chemical reactions; converts to a reaction smiles file format
tsubstructure - Perform 2D substructure searches with SMILES/SMARTS against SMILES files
retrosynthesis - Defines synthetic routes for input chemical structures by deconstructing input molecules into reactants using a set of known reactions templates. Conceptually, the inverse process of chemical reaction synthesis as implemented by tool trxn
trxn - Performs reactions between reactant molecules to enumerate product structures. Uses a control reaction file, a scaffold SMILES file and zero or more reactant SMILES files. Conceptually inverse of retrosynthesis process as implemented by tool retrosynthesis
iwdemerit - Computes demerit of a molecule. In this context demerits refers to non-desirable molecular structure characteristics/features
Retired scripts
===============
Bug fixes
=========
Data
=========
Lib
=========
libaccumulator.a
libiwbits.a
libiwmolecule.a
libiwstring.a
libiwtemplate.a
libcmdline.a
libiwcrex.a
libiwnormalisation.a
libiwstring_data_source.a
libsparsefp.a
libcmdline_v2.a
libiwhistogram.a
libiwqsort.a
libiwstring_string_data_source.a
libxmlParser.a
libiwaray.a
libiwmisc.a
libiwrandom.a
libiwtdt.a
Updates
=======
Known issues
============
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~