core/indigo-core/molecule/src/molfile_loader.cpp (5 lines):
	- line 2148: // TODO: handle missing template case
	- line 2153: // TODO: handle modified monomer. Currently it leaves as is.
	- line 2243: // connect branch to base. which is incorrect!!! TODO: use substructure matcher to determine right monomer!!!
	- line 3175: // TODO: replace parent_group with parent_idx
	- line 3182: // TODO: check fix


core/indigo-core/molecule/src/molecule_arom.cpp (5 lines):
	- line 692: return PiValue(0, 2); // TODO: check different cases
	- line 705: return PiValue(0, 2); // TODO: check different cases
	- line 714: return PiValue(0, 2); // TODO: check different cases
	- line 722: return PiValue(0, 2); // TODO: check different cases
	- line 872: // DP TODO: implement smth. like Node::possibleOtherValueExcept() ...


core/indigo-core/layout/src/molecule_layout_graph_assign.cpp (4 lines):
	- line 242: // TODO: correct element marking (internal and non-planar)?
	- line 293: // TODO: repair exception with vec2f
	- line 438: // TODO: Start drawing from vertex with maximum code and continue to the right with one of two which has maximum code
	- line 1172: // TODO: check different attachment points


core/render2d/render_font_face_manager.h (3 lines):
	- line 114: // TODO: Hangul subset of Enclosed CJK Letters and Months
	- line 115: // TODO: Hangul subset of Halfwidth and Fullwidth Forms
	- line 138: // TODO: use wstring_convert instead of custom converter


bingo/bingo-core-c/src/mango_core_c.cpp (3 lines):
	- line 182: // TODO: pass this check inside MangoSubstructure
	- line 278: // TODO: pass this check inside MangoSubstructure
	- line 685: // TODO: remove copy/paste in mangoCML, mangoMolfile and etc.


core/indigo-core/molecule/src/base_molecule.cpp (3 lines):
	- line 3233: // TODO: special handling needed for LGRP
	- line 4568: Vec2f shift(len * symbol_size / 2.0f, symbol_size); // TODO: Add pseudoatom parsing
	- line 4919: // TODO: add check for query features defined for H, do not remove such hydrogens


core/indigo-core/molecule/src/molecule_allene_stereo.cpp (3 lines):
	- line 673: // TODO: this can be done without looping through all centers
	- line 728: // TODO: this can be done without looping through all centers
	- line 772: // TODO: this can be done without looping through all centers


utils/legio/src/com/epam/indigo/legio/MainFrame.java (3 lines):
	- line 520: // TODO add your handling code here:
	- line 524: // TODO add your handling code here:
	- line 528: // TODO add your handling code here:


core/indigo-core/molecule/src/sequence_saver.cpp (3 lines):
	- line 222: phosphate = "P"; // Assume that modified monomers always contains P and modified to sP with *. TODO: confirm it with BA
	- line 482: { // TODO: rewrite when connection will contain info about neighb ap_id
	- line 1093: phosphate = "P"; // Assume that modified monomers always contains P and modified to sP with *. TODO: confirm it with BA


core/indigo-core/molecule/src/molecule_substructure_matcher.cpp (3 lines):
	- line 441: // TODO: target.isPseudoAtom(super_idx) || target.isRSite(super_idx)
	- line 512: return target.stereocenters.getType(super_idx) == MoleculeStereocenters::ATOM_ABS; // TODO: Investigate right way to match
	- line 523: // MR TODO: match topology. Query bond in ring cannot match


api/c/bingo-nosql/src/bingo_matcher.cpp (2 lines):
	- line 461: // TODO: collect time infromation about the reading and matching measurements and
	- line 1413: // TODO: merge Indigo code into Bingo and stop this endless copy-paste


core/indigo-core/reaction/src/reaction_multistep_detector.cpp (2 lines):
	- line 323: // TODO: add upper limit
	- line 402: // TODO: add upper limit


core/indigo-core/layout/src/molecule_layout_graph_geom.cpp (2 lines):
	- line 483: // TODO: if vertex is internal - choose maximal free angle
	- line 785: // TODO: if vertex is internal - choose maximal free angle


core/render2d/render_internal.h (2 lines):
	- line 170: // TODO: remove dublicate with _placeBrackets(..)
	- line 207: // TODO: eliminate


bingo/bingo-core-c/src/ringo_core_c.cpp (2 lines):
	- line 127: // TODO: pass this check inside RingoSubstructure
	- line 333: // TODO: remove copy/paste in ringoRCML, ringoRxnfile and etc.


core/indigo-core/layout/src/molecule_layout_graph.cpp (2 lines):
	- line 325: // TODO: try to remove tree[];
	- line 424: if (respect_existing && preserve_existing_layout) // TODO:


core/indigo-core/molecule/src/molecule_cip_calculator.cpp (2 lines):
	- line 986: // FIXME: MK: This should also probably work with std::sort, but work incorrectly
	- line 991: // TODO: this is waaaaay too big, need to refactor


core/indigo-core/molecule/src/molecule_json_loader.cpp (2 lines):
	- line 785: // TODO:
	- line 1071: // TODO: placement = relative, display = display_units


bingo/bingo-elastic/java/src/main/java/com/epam/indigo/model/Helpers.java (2 lines):
	- line 84: // TODO: Generalize next two methods
	- line 85: // TODO: Move from helpers


core/indigo-core/molecule/src/molecule_cdxml_saver.cpp (2 lines):
	- line 21: #pragma warning(disable : 4315) // TODO: Fix CDXFont allign issue
	- line 1919: _output.writeBinaryWord(0); // TODO: change to kCDXObj_Document); // First object is document


utils/indigo-knime/com.epam.indigo.knime.plugin/src/com/epam/indigo/knime/common/splitter/IndigoSplitterNodeModel.java (2 lines):
	- line 44: // TODO Auto-generated method stub
	- line 51: // TODO Auto-generated method stub


core/render2d/src/render_internal.cpp (2 lines):
	- line 2227: d.isShort = d.length < (_settings.bondSpace + _settings.bondLineWidth) * 2; // TODO: check
	- line 2783: // TODO: replace remembering item ids and shifting each of them with single offset value for an atom


utils/indigo-knime/com.epam.indigo.knime.plugin/src/com/epam/indigo/knime/io/rxnreader/RXNReaderNodeModel.java (2 lines):
	- line 52: // TODO Auto-generated method stub
	- line 69: // TODO Auto-generated method stub


core/indigo-core/layout/src/pathway_layout.cpp (2 lines):
	- line 179: auto boldWidthLambda = [text_max_width](char ch) { return text_max_width / MAX_SYMBOLS; };   // TODO: implement bold font width
	- line 180: auto italicWidthLambda = [text_max_width](char ch) { return text_max_width / MAX_SYMBOLS; }; // TODO: implement italic font width


api/c/bingo-nosql/src/bingo-nosql.cpp (2 lines):
	- line 39: // TODO: warning C4273: 'indigo::BingoException::BingoException' : inconsistent dll linkage
	- line 254: // FIXME: MK: for some reason we need to aromatize input molecule. If we first clone and aromatize cloned, it won't work


bingo/sqlserver/Source/MangoFastIndexFetch.cs (1 line):
	- line 111: // TODO: add match with xyz test for binary molecules


core/indigo-core/molecule/src/molecule.cpp (1 line):
	- line 338: // TODO: take care of memory allocated here in _pseudo_atom_values


core/indigo-core/reaction/src/rsmiles_loader.cpp (1 line):
	- line 570: int idx = 0; // TODO: investigate right value for default idx


bingo/bingo-core-c/src/bingo_core_c.cpp (1 line):
	- line 895: // TODO: Name should be also extracted here...


bingo/bingo-elastic/java/src/main/java/com/epam/indigo/predicate/KeywordQuery.java (1 line):
	- line 7: // TODO proper name for


core/indigo-core/molecule/src/smiles_saver.cpp (1 line):
	- line 2110: // TODO: a more effective looping is possible


bingo/oracle/src/oracle/bingo_fingerprints.cpp (1 line):
	- line 606: // TODO: reload data if table was updated


bingo/bingo-core/src/core/ringo_exact.cpp (1 line):
	- line 106: // TODO: merge Indigo code into Bingo and stop this endless copy-paste


utils/indigo-service/frontend/ui/src/api/ApiService.js (1 line):
	- line 39: //TODO add possibility to upload library from S3 bucket


core/indigo-core/layout/src/molecule_layout_graph_border.cpp (1 line):
	- line 252: // TODO: check that point 'p' is equal to the one of cycle points (sometimes it happens)


core/indigo-core/molecule/src/canonical_smiles_saver.cpp (1 line):
	- line 70: // TODO: canonicalize allenes properly


core/indigo-core/molecule/molecule_sgroups.h (1 line):
	- line 116: // TODO: leave only parent_idx


core/indigo-core/layout/src/attachment_layout.cpp (1 line):
	- line 64: // TODO: what if negative?


core/indigo-core/molecule/src/molecule_dearom.cpp (1 line):
	- line 1577: // TODO QDEAROM


core/indigo-core/common/base_cpp/smart_output.cpp (1 line):
	- line 79: // TODO: MR: merge this with flushTable?


core/indigo-core/molecule/molecule_inchi_layers.h (1 line):
	- line 119: // TODO: Mobile hydrogens, fixed hydrogens


core/render2d/src/render_params.cpp (1 line):
	- line 194: rc.setDefaultScale((float)bondLength_px); // TODO: fix bondLength type


bingo/bingo-elastic/java/src/main/java/com/epam/indigo/elastic/ElasticRepository.java (1 line):
	- line 198: //        TODO do we need it?


utils/indigo-service/frontend/ui/src/components/search-properties/AppPropertiesSearch.jsx (1 line):
	- line 126: {/*TODO not working on python+elastic and not correct working on python+postgres*/}


utils/indigo-service/backend/service/v2/libraries_api.py (1 line):
	- line 352: # TODO: Improve incorrect file detection


core/indigo-core/molecule/src/molecule_json_saver.cpp (1 line):
	- line 1694: // TODO: the code below needs refactoring


core/indigo-core/reaction/src/reaction_enumerator_state.cpp (1 line):
	- line 1486: // TODO:


core/indigo-core/molecule/src/monomer_commons.cpp (1 line):
	- line 198: // TODO: return right value at this point


core/indigo-core/molecule/src/haworth_projection_finder.cpp (1 line):
	- line 119: /* TODO: Uncomment after validation


core/render2d/src/render_font_face_manager.cpp (1 line):
	- line 44: // TODO: fix faces realease


core/indigo-core/molecule/src/cmf_loader.cpp (1 line):
	- line 901: // TODO provide a readers map to avoid such "if"s


core/render2d/src/render_fonts.cpp (1 line):
	- line 196: { // TODO: remove


utils/indigo-service/backend/service/v2/validation.py (1 line):
	- line 43: # TODO: Move structure loading to validation phase


utils/chemdiff/src/com/epam/indigo/chemdiff/MultipleMoleculeItem.java (1 line):
	- line 81: // TODO: set name too...


core/indigo-core/molecule/src/query_molecule.cpp (1 line):
	- line 2611: // TODO: develop function to convert tree to CNF to simplify checks


core/indigo-core/molecule/src/molecule_inchi_component.cpp (1 line):
	- line 138: // TODO: Implement as in InChI


core/indigo-core/molecule/molecule_json_saver.h (1 line):
	- line 60: bool use_native_precision; // TODO: Remove option and use_native_precision allways - have to fix a lot of UTs


utils/indigo-service/backend/service/v2/indigo_api.py (1 line):
	- line 75: # TODO: Remove this when Indigo API supports smiles type option


api/c/indigo/src/indigo_molecule.cpp (1 line):
	- line 2138: // TODO: implement query.getAtomEdit(...) instead of getAtom(...) to update nei counters


core/indigo-core/common/base_cpp/tlscont.h (1 line):
	- line 94: // FIXME:MK: it's not thread safe, decide what to do


core/indigo-core/molecule/src/molecule_fingerprint.cpp (1 line):
	- line 241: /* TODO: implement FCFP fingerprints


api/cpp/src/IndigoSubstructureMatcher.h (1 line):
	- line 34: // TODO: return IndigoMatch instance instead of simple bool


api/c/indigo/src/indigo_deconvolution.cpp (1 line):
	- line 483: * TODO change to elem AP


core/indigo-core/molecule/src/molecule_tautomer_match.cpp (1 line):
	- line 328: // TODO: can check only for last chain


core/indigo-core/layout/metalayout.h (1 line):
	- line 259: // FIXME: The value is 1.6 instead of 1.0 due to backward compatibility, needs to be refactored


core/indigo-core/molecule/src/molecule_arom_match.cpp (1 line):
	- line 97: // MR: TODO: Handle this case in more details.


api/c/bingo-nosql/src/mmf/mmfile.cpp (1 line):
	- line 117: // TODO check result


bingo/sqlserver/Source/Bingo.cs (1 line):
	- line 1409: // TODO: cache settings


core/indigo-core/molecule/metadata_storage.h (1 line):
	- line 82: PtrPool<MetaObject> _meta_data; // TODO: should be replaced with list of unique_ptr


bingo/bingo-elastic/java/src/main/java/com/epam/indigo/model/IndigoRecord.java (1 line):
	- line 29: //    TODO add tau fingerprint, add support for other fingerprints


core/indigo-core/molecule/src/molecule_name_parser.cpp (1 line):
	- line 1245: // FIXME - process acids (acid names have whitespace)


core/indigo-core/molecule/src/molecule_inchi_layers.cpp (1 line):
	- line 628: // TODO: handle cumulene


core/indigo-core/molecule/src/molecule_morgan_fingerprint_builder.cpp (1 line):
	- line 224: throw Exception("FCFP is not implemented"); // TODO: implement ionizability


bingo/postgres/src/pg_core/bingo_pg_config.cpp (1 line):
	- line 73: // TODO use isset instead of -1 not set for variables


api/python/indigo/indigo/salts.py (1 line):
	- line 117: # TODO: add [Al(OH)4]-, [Sn(OH)6]2- ???


bingo/oracle/src/oracle/bingo_storage.cpp (1 line):
	- line 145: // TODO: implement a semaphore


bingo/oracle/src/oracle/bingo_oracle_context.cpp (1 line):
	- line 538: // TODO: implement a semaphore?


core/indigo-core/layout/src/molecule_layout_graph_assign_smart.cpp (1 line):
	- line 214: // TODO: repair exception with vec2f


core/indigo-core/molecule/src/molecule_cdxml_loader.cpp (1 line):
	- line 1462: // TODO: check if there are some fragments inside of group_frame_lambda and put them into r_fragments