Brian Kelley 8609cd4883 Add StructChecker functionality ...

* StructChecker changes. Initial commit. First implementation. Added some tests.

* StructChecker: add  GoodAtoms and AcidicAtoms. new updates

* StructChecker: add new tests

* StructChecker: added TransformAugmentedAtoms()

* StructCheck: add structCheck to GraphMol. Fix compilation errors.

* StructChecker: add stereo verification and some utilities.

* StructChecker: function FixDubious3DMolecule was added

* StructChecker: checkStereo added. done with stereo.

* StructChecker: add StripSmallFragments()

* StructChecker: add AtomClash() function. Some cosmetic + tests

* StructChecker: checkAtoms() was started

* StructChecker: checkAtoms is ready

* StructChecker: user RingInfo from RDkit. Start regarge

* StructChecker: ReCharge molecule method prototype

* StructChecker: updates for ReCharge. Almost finished

* StructChecker: all ReCharge is done except external data tables loading

* StructChecker: add path tables into API. ReCharge completed

* Adds augmented atom data

Signed-off-by: Brian Kelley <brian.kelley@novartis.com>

* Removes extra files

Signed-off-by: Brian Kelley <brian.kelley@novartis.com>

* Adds path to test data via RDBASE environment

Signed-off-by: Brian Kelley <brian.kelley@novartis.com>

* Revert "Struct checker apr15"

* StructChecker: add missing tautomer tests

* Updates test to use RDBASE

* Adds initialization of data from data section

* Adds Python API and tests

* Fixes namespace for enum

* StructChecker: update/imporve strip small fragments

* StructChecker: fix acidic atoms (but logic does not work)

* StructChecker: fix match issue for CheckAtoms

* Adds macro guards

* Adds loading API and proper constructor

* Fixes tests, adds stereo test

* Fixes crash bug, matches[0] was being accessed from an empty match vector

* Reverts crash fix - conflicts with previous

* Adds the rest of the structure checker options

* StructChecker: fix atom matching for aromatic rings

* StructChecker: add tautomers checks. Update some tests

* StructChecker: stereo fixes. Add some tests

* StructChecker: fix check atoms. Start ligand symbol list

* StructChecker: fix some check atoms validation. Add Tranform to query lists. Start correct loading augmented atoms

* update

* another set of fixes

* StructChecker: fix loadDefaultAugmentedAtoms. Some changes in CheckAtom + tests + debug conditional breakpoints (TEMP operators)

* StructChecker: rewrited RecMatch() to sequential. Changed bond matching algorithm. small bug fixes

* Adds better logging of mismatched atoms

* Removes duplicated negative charge

* Fixes charges

* Adds nitro group test

* StructChecker: add better logging

* remove double logging

* Reformats code using RDKit's clang-format style

* StructChecker: Fix charge reformat using RDKit format.

* StructChecker: compilation restore after merge

* restore bond matching

* Removes the same fragments that strucheck does in case of ties

* Don't resanitize - this adds aromaticity which mucks things up

* Adds empty molecule checks

* Fixes atom clashes.

* Removes debug printing

* Removes debug logging info

* First pass at stereo fixes

* Fixes off by one error for dubious stereo fix

* Fixes more off by one errors

* Fixes more off by one errors

* More off by one fixes.

* Another off by one

* Fixes chiral flag set in molfile check

* Copies chiral flag over to largest fragment if necessary

* Poor man’s parity check.

* Find unspecified chiral centers ala Avalon.

* StructChecker: fix recursive match. Fix transformations

* StructChecker: fix transformation for atom list (using query atoms)

* Fixes checks && to &

* StructChecker: fix carboxylic acids tranform issue. Atom list is changed only if different

* StructChecker: documentation was updated

* Fixes snprintf and silences some warnings

* Adds Get/Set StructCheckerOptions

* Adds default AugmentedAtomTransforms

2016-10-24 08:00:07 +02:00

31 KiB

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