core/indigo-core/molecule/ket

/**************************************************************************** * Copyright (C) from 2009 to Present EPAM Systems. * * This file is part of Indigo toolkit. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. ***************************************************************************/ #ifndef __ket_document__ #define __ket_document__ #include "molecule/ket_objects.h" #include "molecule/monomers_template_library.h" #include <rapidjson/document.h> // Temporary until direct conversion to molecule supported #include <deque> #include <set> #ifdef _WIN32 #pragma warning(push) #pragma warning(disable : 4251) #endif namespace indigo { class BaseMolecule; class DLLEXPORT KetDocument : public MonomerTemplateLibrary { public: DECL_ERROR; KetDocument() : _molecules(), original_format(0), _meta_objects(rapidjson::kArrayType), _r_groups(rapidjson::kArrayType), _json_molecules(rapidjson::kArrayType), _json_document(){}; KetDocument(const KetDocument& other) = delete; KetDocument& operator=(const KetDocument&) = delete; KetMolecule& addMolecule(const std::string& ref); std::unique_ptr<KetBaseMonomer>& addMonomer(const std::string& alias, const std::string& template_id); std::unique_ptr<KetBaseMonomer>& addMonomer(const std::string& id, const std::string& alias, const std::string& template_id); std::unique_ptr<KetBaseMonomer>& addMonomer(const std::string& id, const std::string& alias, const std::string& template_id, const std::string& ref); const std::unique_ptr<KetBaseMonomer>& getMonomerById(const std::string& ref) const; MonomerTemplate& addMonomerTemplate(const std::string& id, const std::string& monomer_class, IdtAlias idt_alias, bool unresolved = false); void addMonomerTemplate(const MonomerTemplate& monomer_template); KetAmbiguousMonomerTemplate& addAmbiguousMonomerTemplate(const std::string& subtype, const std::string& id, const std::string& name, IdtAlias idt_alias, std::vector<KetAmbiguousMonomerOption>& options); std::unique_ptr<KetBaseMonomer>& addAmbiguousMonomer(const std::string& alias, const std::string& template_id); std::unique_ptr<KetBaseMonomer>& addAmbiguousMonomer(const std::string& id, const std::string& alias, const std::string& template_id); std::unique_ptr<KetBaseMonomer>& addAmbiguousMonomer(const std::string& id, const std::string& alias, const std::string& template_id, const std::string& ref); using molecules_map = std::map<std::string, KetMolecule>; using templates_map = std::map<std::string, MonomerTemplate>; using monomers_map = std::map<std::string, std::unique_ptr<KetBaseMonomer>>; using ambiguous_templates_map = std::map<std::string, KetAmbiguousMonomerTemplate>; inline const molecules_map& molecules() const { return _molecules; }; inline const std::vector<std::string>& moleculesRefs() const { return _molecule_refs; }; inline const monomers_map& monomers() const { return _monomers; }; inline const std::vector<std::string>& monomersIds() const { return _monomers_ids; }; inline const templates_map& templates() const { return _templates; }; inline const std::vector<std::string>& templatesIds() const { return _templates_ids; }; KetConnection& addConnection(const std::string& conn_type, KetConnectionEndPoint ep1, KetConnectionEndPoint ep2); KetConnection& addConnection(KetConnectionEndPoint ep1, KetConnectionEndPoint ep2); KetConnection& addConnection(const std::string& mon1, const std::string& ap1, const std::string& mon2, const std::string& ap2); void connectMonomerTo(const std::string& mon1, const std::string& ap1, const std::string& mon2, const std::string& ap2); const std::vector<KetConnection> connections() const { return _connections; }; // Return list of connections between simple polimers // i.e. non-backbone and not sugar-base connections // connections that create a cycle place here too // parseSimplePolymers should be called to fill this list const std::vector<KetConnection> nonSequenceConnections() const { return _non_sequence_connections; }; int original_format; const ambiguous_templates_map& ambiguousTemplates() const { return _ambiguous_templates; }; const std::vector<std::string>& ambiguousTemplatesIds() const { return _ambiguous_templates_ids; }; BaseMolecule& getBaseMolecule(); bool hasAmbiguousMonomerTemplate(const std::string& id) const { return _ambiguous_templates.find(id) != _ambiguous_templates.end(); }; void processAmbiguousMonomerTemplates(); // Parse list of monomer and ist of connections stored in document and return list of simple polimers in term of HELM // Each simple polymer represented as list of monomer IDs. // Monomers connected from m[i] R2 to m[i+1] R1 for peptides // For RNA/DNA monomer placed in order Sugar-Base-Phosphate-Sugar... with standard connections // Each CHEM returned as separate simple polymer // Also store non-standard or creating cycle connections in nonSequenceConnections list void parseSimplePolymers(std::vector<std::deque<std::string>>& sequences, bool for_idt = false); MonomerClass getMonomerClass(const KetBaseMonomer& monomer) const; MonomerClass getMonomerClass(const std::string& monomer_id) const; const KetBaseMonomerTemplate& getMonomerTemplate(const std::string& template_id) const; void addMetaObject(const rapidjson::Value& node); void addRGroup(const rapidjson::Value& node); void addMolecule(const rapidjson::Value& node); const rapidjson::Value& metaObjects() const { return _meta_objects; }; const rapidjson::Value& rgroups() const { return _r_groups; }; const rapidjson::Value& jsonMolecules() const { return _json_molecules; }; void setFastaProps(std::vector<std::string> fasta_properties) { _fasta_properties = fasta_properties; }; const std::vector<std::string>& fastaProps() { return _fasta_properties; }; const std::string& monomerIdByRef(const std::string& ref); void addMonomerShape(const std::string& id, bool collapsed, const std::string& shape, Vec2f position, const std::vector<std::string>& monomers) { _monomer_shapes.emplace_back(id, collapsed, shape, position, monomers); } const std::vector<KetMonomerShape>& monomerShapes() const { return _monomer_shapes; } protected: void collect_sequence_side(const std::string& monomer_id, bool left_side, std::set<std::string>& monomers, std::set<std::string>& used_monomers, std::deque<std::string>& sequence, std::map<std::pair<std::string, std::string>, const KetConnection&>& ap_to_connection); private: molecules_map _molecules; std::vector<std::string> _molecule_refs; monomers_map _monomers; std::vector<std::string> _monomers_ids; std::map<std::string, std::string> _monomer_ref_to_id; templates_map _templates; std::vector<std::string> _templates_ids; ambiguous_templates_map _ambiguous_templates; std::vector<std::string> _ambiguous_templates_ids; std::vector<KetConnection> _connections; std::vector<KetConnection> _non_sequence_connections; std::map<std::string, KetBaseMonomerTemplate::TemplateType> _template_id_to_type; rapidjson::Value _meta_objects; rapidjson::Value _r_groups; rapidjson::Value _json_molecules; rapidjson::Document _json_document; std::vector<std::string> _fasta_properties; std::vector<KetMonomerShape> _monomer_shapes; }; } #ifdef _MSC_VER #pragma warning(pop) #endif #endif

core/indigo-core/molecule/ket_document.h (155 lines of code) (raw):