rows { options { physical_type: PHYSICAL_STREAM_TYPE_QUADS max_name_table_size: 128 max_prefix_table_size: 16 max_datatype_table_size: 16 logical_type: LOGICAL_STREAM_TYPE_DATASETS version: 2 } } rows { prefix { value: "https://w3id.org/np/" } } rows { name { value: "RA0OCAvzsQw99nJc2vYJgQtieeaFnSmkQbNyPV60yjd5k" } } rows { namespace { name: "this" value { prefix_id: 1 } } } rows { prefix { value: "https://w3id.org/np/RA0OCAvzsQw99nJc2vYJgQtieeaFnSmkQbNyPV60yjd5k/" } } rows { name { } } rows { namespace { name: "sub" value { prefix_id: 2 } } } rows { prefix { value: "http://www.nanopub.org/nschema#" } } rows { namespace { name: "np" value { prefix_id: 3 name_id: 2 } } } rows { prefix { value: "http://purl.org/dc/terms/" } } rows { namespace { name: "dct" value { prefix_id: 4 name_id: 2 } } } rows { prefix { value: "http://purl.org/pav/" } } rows { namespace { name: "pav" value { prefix_id: 5 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" } } rows { namespace { name: "rdf" value { prefix_id: 6 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/2002/07/owl#" } } rows { namespace { name: "owl" value { prefix_id: 7 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/2004/03/trix/rdfg-1/" } } rows { namespace { name: "rdfg" value { prefix_id: 8 name_id: 2 } } } rows { prefix { value: "http://purl.org/dc/elements/1.1/" } } rows { namespace { name: "dce" value { prefix_id: 9 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/2001/XMLSchema#" } } rows { namespace { name: "xsd" value { prefix_id: 10 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { namespace { name: "rdfs" value { prefix_id: 11 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/ns/prov#" } } rows { namespace { name: "prov" value { prefix_id: 12 name_id: 2 } } } rows { prefix { value: "http://purl.org/nanopub/x/" } } rows { namespace { name: "npx" value { prefix_id: 13 name_id: 2 } } } rows { name { value: "hasAssertion" } } rows { name { value: "assertion" } } rows { name { value: "Head" } } rows { quad { s_iri { prefix_id: 1 name_id: 1 } p_iri { prefix_id: 3 name_id: 3 } o_iri { prefix_id: 2 } g_iri { } } } rows { name { value: "hasProvenance" } } rows { name { value: "provenance" } } rows { quad { p_iri { prefix_id: 3 } o_iri { prefix_id: 2 } } } rows { name { value: "hasPublicationInfo" } } rows { name { value: "pubinfo" } } rows { quad { p_iri { prefix_id: 3 } o_iri { prefix_id: 2 } } } rows { name { value: "type" } } rows { name { value: "Nanopublication" } } rows { quad { p_iri { prefix_id: 6 } o_iri { prefix_id: 3 } } } rows { prefix { value: "http://eurovoc.europa.eu/" } } rows { name { value: "2919" } } rows { prefix { value: "http://schema.org/" } } rows { name { value: "description" } } rows { quad { s_iri { prefix_id: 14 } p_iri { prefix_id: 15 } o_literal { } g_iri { prefix_id: 2 name_id: 4 } } } rows { name { value: "name" } } rows { quad { p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Environmental research" } } } rows { name { value: "DefinedTerm" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 15 } } } rows { name { value: "3941" } } rows { quad { s_iri { prefix_id: 14 } p_iri { prefix_id: 15 name_id: 13 } o_literal { } } } rows { quad { p_iri { } o_literal { lex: "Life sciences" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 15 } } } rows { name { value: "3946" } } rows { quad { s_iri { prefix_id: 14 name_id: 17 } p_iri { prefix_id: 15 name_id: 13 } o_literal { } } } rows { quad { p_iri { } o_literal { lex: "Physical sciences" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 15 } } } rows { name { value: "5966" } } rows { quad { s_iri { prefix_id: 14 name_id: 18 } p_iri { prefix_id: 15 name_id: 13 } o_literal { } } } rows { quad { p_iri { } o_literal { lex: "Chemistry" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 15 } } } rows { prefix { value: "https://w3id.org/ro-id/" } } rows { name { value: "02142eed-e7ad-4ecf-b92c-17535047e45e" } } rows { quad { s_iri { prefix_id: 16 name_id: 19 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Physics" } } } rows { prefix { id: 4 value: "https://w3id.org/ro/terms/earth-science#" } } rows { name { value: "IPTC" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 20 } } } rows { name { value: "path" } } rows { quad { p_iri { } o_literal { lex: "Science and technology/Natural science/Physics" } } } rows { name { value: "08b34e3d-b475-4ece-a0e7-0a6e52e6453e" } } rows { quad { s_iri { prefix_id: 16 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "tryptophan-choline force field improvement" } } } rows { name { value: "Phrase" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 23 } } } rows { name { value: "normScore" } } rows { quad { p_iri { } o_literal { lex: "30.441898527004913" } } } rows { name { value: "score" } } rows { quad { p_iri { } o_literal { lex: "18.6" } } } rows { name { value: "1a33ec44-1314-4e9b-b0f4-9476e11d0c7b" } } rows { quad { s_iri { prefix_id: 16 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "manuscripts file" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 23 } } } rows { quad { p_iri { } o_literal { lex: "8.67430441898527" } } } rows { quad { p_iri { } o_literal { lex: "5.3" } } } rows { name { value: "1b8dc5b9-3af9-4db4-91b7-47e4762481cf" } } rows { quad { s_iri { prefix_id: 16 name_id: 27 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "subdirectory" } } } rows { name { value: "Concept" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "5.389221556886228" } } } rows { quad { p_iri { } o_literal { lex: "4.5" } } } rows { name { value: "1e7f2235-59f3-486d-9c05-8208bc9b6650" } } rows { quad { s_iri { prefix_id: 16 name_id: 29 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "quartermaster" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "8.622754491017965" } } } rows { quad { p_iri { } o_literal { lex: "7.2" } } } rows { name { value: "1eb8b1da-9a9a-4f3d-85dd-f7806d7716ac" } } rows { quad { s_iri { prefix_id: 16 name_id: 30 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "biochemistry" } } } rows { prefix { value: "https://w3id.org/contentdesc#" } } rows { name { value: "Domain" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 5 name_id: 31 } } } rows { quad { p_iri { prefix_id: 4 name_id: 24 } o_literal { lex: "58.82352941176471" } } } rows { quad { p_iri { } o_literal { lex: "6.0" } } } rows { name { value: "1fd4a1b7-7f08-4932-81b9-e3e8219a45bd" } } rows { quad { s_iri { prefix_id: 16 name_id: 32 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "improvement" } } } rows { name { value: "Lemma" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 33 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "16.083916083916083" } } } rows { quad { p_iri { } o_literal { lex: "6.9" } } } rows { name { value: "2497f9a5-a789-4c12-87f7-36adaafe0b2f" } } rows { quad { s_iri { prefix_id: 16 name_id: 34 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "betterment" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "11.616766467065867" } } } rows { quad { p_iri { } o_literal { lex: "9.7" } } } rows { name { value: "2a817a60-bda4-4de6-811b-8b464c6f4fbe" } } rows { quad { s_iri { prefix_id: 16 name_id: 35 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Organic chemical" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 20 } } } rows { quad { p_iri { } o_literal { lex: "Economy, business and finance/Economic sector/Chemicals/Organic chemical" } } } rows { name { value: "38d6400b-ef9c-491a-87db-aa0e19241052" } } rows { quad { s_iri { prefix_id: 16 name_id: 36 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "comparison" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "4.6706586826347305" } } } rows { quad { p_iri { } o_literal { lex: "3.9" } } } rows { name { value: "3b59da1c-05ba-4240-9d9c-5fb7b28ad53c" } } rows { quad { s_iri { prefix_id: 16 name_id: 37 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "earth sciences" } } } rows { name { value: "FieldOfResearch" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 38 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.620610237121582" } } } rows { name { value: "42c9b12d-dec9-4e1d-bfa3-e6b20ca574ed" } } rows { quad { s_iri { prefix_id: 16 name_id: 39 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "force field" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 33 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "23.076923076923077" } } } rows { quad { p_iri { } o_literal { lex: "9.9" } } } rows { name { value: "42da6fae-3c5d-402f-a475-e3de433fb9c5" } } rows { quad { s_iri { prefix_id: 16 name_id: 40 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "validation" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "7.664670658682635" } } } rows { quad { p_iri { } o_literal { lex: "6.4" } } } rows { name { value: "43eecec7-f276-4fa6-a009-b6d74bee5ac4" } } rows { quad { s_iri { prefix_id: 16 name_id: 41 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Diseases and conditions" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 20 } } } rows { quad { p_iri { } o_literal { lex: "Health/Diseases and conditions" } } } rows { name { value: "45c97f98-4cfc-4aec-a86d-972e5ee7c719" } } rows { quad { s_iri { prefix_id: 16 name_id: 42 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "armed forces" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 5 name_id: 31 } } } rows { quad { p_iri { prefix_id: 4 name_id: 24 } o_literal { lex: "22.549019607843135" } } } rows { quad { p_iri { } o_literal { lex: "2.3" } } } rows { name { value: "51678519-ffd4-4990-a2ef-45e8cebea870" } } rows { quad { s_iri { prefix_id: 16 name_id: 43 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "force field" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "16.047904191616766" } } } rows { quad { p_iri { } o_literal { lex: "13.4" } } } rows { name { value: "5a3f3091-042f-4b19-9448-202c9bc06e4a" } } rows { quad { s_iri { prefix_id: 16 name_id: 44 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "geology" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 38 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.620610237121582" } } } rows { name { value: "6510d15b-80ba-43f6-bd4e-bd8cb28ff442" } } rows { quad { s_iri { prefix_id: 16 name_id: 45 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "force field parameter validation" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 23 } } } rows { quad { p_iri { } o_literal { lex: "14.238952536824875" } } } rows { quad { p_iri { } o_literal { lex: "8.7" } } } rows { name { value: "6d49e53b-ee7d-487c-8005-f3d33075c010" } } rows { quad { s_iri { prefix_id: 16 name_id: 46 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "calculation" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "5.9880239520958085" } } } rows { quad { p_iri { } o_literal { lex: "5.0" } } } rows { prefix { id: 7 value: "https://w3id.org/ro-id/6d7f7856-f2c8-4172-9a35-ef22b6cc4561/#" } } rows { name { value: "enrichment_service-account-enrichment" } } rows { quad { s_iri { prefix_id: 7 name_id: 47 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "service-account-enrichment" } } } rows { prefix { value: "http://xmlns.com/foaf/0.1/" } } rows { name { value: "Agent" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 8 name_id: 48 } } } rows { prefix { value: "https://w3id.org/ro-id/6d7f7856-f2c8-4172-9a35-ef22b6cc4561/" } } rows { name { value: "about" } } rows { quad { s_iri { prefix_id: 9 name_id: 2 } p_iri { prefix_id: 15 name_id: 49 } o_iri { prefix_id: 14 name_id: 12 } } } rows { quad { o_iri { name_id: 16 } } } rows { quad { o_iri { } } } rows { quad { o_iri { } } } rows { name { value: "author" } } rows { prefix { } } rows { name { value: "mailto:nathalie.reuter@rohub.com" } } rows { quad { p_iri { prefix_id: 15 name_id: 50 } o_iri { prefix_id: 10 } } } rows { name { value: "contentSize" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#integer" } } rows { quad { p_iri { prefix_id: 15 } o_literal { lex: "9458" datatype: 1 } } } rows { name { value: "contentUrl" } } rows { quad { p_iri { } o_literal { lex: "https://api.rohub.org/api/ros/6d7f7856-f2c8-4172-9a35-ef22b6cc4561/crate/download/" } } } rows { name { value: "creator" } } rows { name { value: "mailto:georgehadib@gmail.com" } } rows { quad { p_iri { } o_iri { prefix_id: 10 } } } rows { name { value: "dateCreated" } } rows { quad { p_iri { prefix_id: 15 } o_literal { lex: "2022-03-22 02:18:57.862656+00:00" } } } rows { name { value: "dateModified" } } rows { quad { p_iri { } o_literal { lex: "2025-03-05 00:45:31.255755+00:00" } } } rows { name { value: "datePublished" } } rows { quad { p_iri { } o_literal { lex: "2022-03-22 02:18:57.862656+00:00" } } } rows { quad { p_iri { name_id: 13 } o_literal { lex: "Results for Tyrosine-choline, Phenylalanine-choline and Tryptophan-choline force field improvements. For ease of processing, results from both works are kept together. Results are divided in QM calculations+force field comparison and improvements, and force field parameter validations.\n\nIf you have trouble navigating, please send email to LINK: mailto:reza.611@gmail.com.\n\n\n### Please see the file \"file_organisations\" for the directories and subdirectories.\n\n# Results files are organised based on QM calculations and force field comparisons (also improvements), and Parameters validations where you have the test cases. For the QM calculations, they are based on the softwares and methods used. PSI4 directories for energy decompositions and SAPT methods, further divided in subdiectories. NWCHEM is for all other QM methods, and those can be differentiated by the dircetoty names which contains the method (DFT, MP2, CCSD(T)) and basis sets. CHARMM* directories contains the force field comparison vs the improvements test.\n\nThe Khan_etal_JCTC_2016 paper contains phenol-TMA and benzene-TMA cases. The Khan_etal_JCTC_2019 contains the indole-TMA case.\n\nFor the QM part, benzene-tma and indole-tma directories have naming explicitly (i.e. NWCHEM_cat_pi_benzene_tma/, PSI4_calc_benzene_tma/, CHARMM_pes_cat_pi_benzene_tma/). For phenol-TMA, look at the *_RESTART directories; these are the production ones for CHARMM and NWCHEM cases. For PSI4, it is PSI4_calc/). Other directories are old tests with different PES conditions (relaxation etc.). I did not remove them for my personal reference.\n\n# For the Parameters validations, reboot_piplc-dmpc/ is the test case for Khan_etal_JCTC_2016; all others are for Khan_etal_JCTC_2019.\n\n### Manuscripts files are seperated for both these works in the main directories with submission files and figures. The raw data are also there. You will also find the raw data in the different results subdirectories.\n\n*** I am writing this very quickly, so some explanations might not be obvious. If you have doubt, please send email to LINK: mailto:reza.611@gmail.com." } } } rows { name { value: "encodingFormat" } } rows { quad { p_iri { name_id: 59 } o_literal { lex: "application/ld+json" } } } rows { name { value: "hasPart" } } rows { prefix { value: "https://w3id.org/ro-id/6d7f7856-f2c8-4172-9a35-ef22b6cc4561/folders/" } } rows { name { value: "1bf7ee26-d3bb-4cc3-a7e4-830ccc3308db" } } rows { quad { p_iri { } o_iri { prefix_id: 11 } } } rows { name { value: "24bfb8db-86a7-4643-a7f7-fd82ac93af38" } } rows { quad { o_iri { } } } rows { name { value: "9697f106-4d50-471c-acb9-de5359dfa56e" } } rows { quad { o_iri { } } } rows { name { value: "9d0344fb-3af9-4551-8b59-c6ae2e47250e" } } rows { quad { o_iri { } } } rows { name { value: "identifier" } } rows { quad { p_iri { prefix_id: 15 } o_literal { lex: "https://w3id.org/ro-id/6d7f7856-f2c8-4172-9a35-ef22b6cc4561" } } } rows { name { value: "license" } } rows { prefix { value: "https://choosealicense.com/no-permission/" } } rows { quad { p_iri { } o_iri { prefix_id: 12 name_id: 2 } } } rows { quad { p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "2019_Khan_etal_JCTC" } } } rows { prefix { value: "http://w3id.org/ro-id/rohub/model#" } } rows { name { value: "creation_mode" } } rows { quad { p_iri { prefix_id: 13 name_id: 67 } o_literal { lex: "MANUAL" } } } rows { prefix { id: 1 value: "http://purl.org/wf4ever/ro#" } } rows { name { value: "ResearchObject" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 1 name_id: 68 } } } rows { prefix { id: 3 value: "http://purl.org/wf4ever/roevo#" } } rows { name { value: "LiveRO" } } rows { quad { o_iri { prefix_id: 3 } } } rows { name { value: "Dataset" } } rows { quad { o_iri { prefix_id: 15 } } } rows { prefix { id: 2 value: "http://w3id.org/ro/earth-science#" } } rows { name { value: "DataResearchObject" } } rows { quad { o_iri { prefix_id: 2 } } } rows { quad { o_iri { prefix_id: 4 name_id: 71 } } } rows { quad { p_iri { prefix_id: 5 name_id: 31 } o_literal { lex: "https://w3id.org/ro-id/1eb8b1da-9a9a-4f3d-85dd-f7806d7716ac" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/45c97f98-4cfc-4aec-a86d-972e5ee7c719" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/f94049ca-f965-407c-bbd6-9dec6d0b4f36" } } } rows { quad { p_iri { prefix_id: 4 name_id: 28 } o_literal { lex: "https://w3id.org/ro-id/1b8dc5b9-3af9-4db4-91b7-47e4762481cf" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/1e7f2235-59f3-486d-9c05-8208bc9b6650" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/2497f9a5-a789-4c12-87f7-36adaafe0b2f" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/38d6400b-ef9c-491a-87db-aa0e19241052" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/42da6fae-3c5d-402f-a475-e3de433fb9c5" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/51678519-ffd4-4990-a2ef-45e8cebea870" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/6d49e53b-ee7d-487c-8005-f3d33075c010" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/9d724b70-f51e-4801-a33c-0ddacb9f6380" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/a373b5e2-9377-4ea5-ac77-3000d7e4ea1d" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/b4696554-3ad0-482c-a812-64ad881bf2df" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/bd4b37ee-9510-4d1b-a866-d5ac716d7d6d" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/f1de38ae-6531-4b97-b7cb-871e09afdb6c" } } } rows { quad { p_iri { name_id: 38 } o_literal { lex: "https://w3id.org/ro-id/3b59da1c-05ba-4240-9d9c-5fb7b28ad53c" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/5a3f3091-042f-4b19-9448-202c9bc06e4a" } } } rows { quad { p_iri { name_id: 20 } o_literal { lex: "https://w3id.org/ro-id/02142eed-e7ad-4ecf-b92c-17535047e45e" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/2a817a60-bda4-4de6-811b-8b464c6f4fbe" } } 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name_id: 73 } o_literal { lex: "https://w3id.org/ro-id/b2bb9f47-e1bf-472d-b70d-b04bbbb8cdd1" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/c15316b5-7fc7-4545-a8bb-f8d31e4060d6" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/fe8868e4-2180-433d-b349-a8b9f0a2692c" } } } rows { prefix { id: 16 value: "https://www.w3.org/ns/iana/link-relations/relation#" } } rows { name { value: "cite-as" } } rows { quad { p_iri { prefix_id: 16 } o_literal { lex: "Nathalie Reuter. \"2019_Khan_etal_JCTC.\" ROHub. Mar 22 ,2022. https://w3id.org/ro-id/6d7f7856-f2c8-4172-9a35-ef22b6cc4561." } } } rows { quad { s_iri { prefix_id: 11 name_id: 61 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "metadata" } } } rows { prefix { id: 7 value: "http://purl.org/wf4ever/wf4ever#" } } rows { name { value: "Folder" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 7 name_id: 75 } } } rows { quad { o_iri { prefix_id: 15 name_id: 70 } } } rows { quad { s_iri { prefix_id: 11 name_id: 62 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "raw data" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 7 name_id: 75 } } } rows { quad { o_iri { prefix_id: 15 name_id: 70 } } } rows { prefix { value: "https://w3id.org/ro-id/6d7f7856-f2c8-4172-9a35-ef22b6cc4561/resources/" } } rows { name { value: "d429730d-0d92-45e0-8dec-7729b90a2ab9" } } rows { quad { s_iri { prefix_id: 11 name_id: 63 } p_iri { prefix_id: 15 name_id: 60 } o_iri { prefix_id: 8 name_id: 76 } } } rows { quad { p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "data" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 7 name_id: 75 } } } rows { quad { o_iri { prefix_id: 15 name_id: 70 } } } rows { name { value: "9faa8baa-e43c-459d-a5bf-d4dcf265d187" } } rows { quad { s_iri { prefix_id: 11 name_id: 64 } p_iri { prefix_id: 15 name_id: 60 } o_iri { prefix_id: 8 name_id: 77 } } } rows { quad { p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "biblio" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 7 name_id: 75 } } } rows { quad { o_iri { prefix_id: 15 name_id: 70 } } } rows { quad { s_iri { prefix_id: 8 name_id: 77 } p_iri { prefix_id: 15 name_id: 50 } o_iri { prefix_id: 10 name_id: 55 } } } rows { quad { p_iri { prefix_id: 15 name_id: 53 } o_literal { lex: "https://doi.org/10.1021/acs.jctc.8b00839" } } } rows { quad { p_iri { } o_iri { prefix_id: 10 } } } rows { quad { p_iri { prefix_id: 15 } o_literal { lex: "2022-03-22 02:19:11.787124+00:00" } } } rows { quad { p_iri { } o_literal { lex: "2022-03-22 02:19:12.026713+00:00" } } } rows { quad { p_iri { name_id: 66 } o_iri { prefix_id: 12 name_id: 2 } } } rows { quad { p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "https://doi.org/10.1021/acs.jctc.8b00839" } } } rows { name { value: "sdDatePublished" } } rows { quad { p_iri { name_id: 78 } o_literal { lex: "2022-03-22 02:19:11.787124+00:00" } } } rows { prefix { value: "http://purl.org/dc/terms/" } } rows { name { value: "BibliographicResource" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 9 name_id: 79 } } } rows { name { value: "Resource" } } rows { quad { o_iri { prefix_id: 7 } } } rows { name { value: "MediaObject" } } rows { quad { o_iri { prefix_id: 15 } } } rows { name { value: "bibliographicCitation" } } rows { quad { s_iri { prefix_id: 8 name_id: 76 } p_iri { prefix_id: 9 name_id: 82 } o_literal { lex: "Reuter, N. (2021).2019_Khan_etal_JCTC [Data set]. Norstore. https://doi.org/10.11582/2021.00104" } } } rows { name { value: "rightsHolder" } } rows { quad { p_iri { } o_literal { lex: "Nathalie Reuter" } } } rows { quad { p_iri { name_id: 10 } o_literal { lex: "Simulation" } } } rows { quad { p_iri { prefix_id: 15 name_id: 50 } o_iri { prefix_id: 10 name_id: 55 } } } rows { quad { p_iri { prefix_id: 15 name_id: 53 } o_literal { lex: "https://archive.sigma2.no/pages/public/datasetDetail.jsf?id=10.11582/2021.00104" } } } rows { quad { p_iri { } o_iri { prefix_id: 10 } } } rows { quad { p_iri { prefix_id: 15 } o_literal { lex: "2021-11-22 00:00:00" } } } rows { quad { p_iri { } o_literal { lex: "2022-03-22 02:19:16.071315+00:00" } } } rows { quad { p_iri { name_id: 13 } o_literal { lex: "Results for Tyrosine-choline, Phenylalanine-choline and Tryptophan-choline force field improvements. For ease of processing, results from both works are kept together. Results are divided in QM calculations+force field comparison and improvements, and force field parameter validations.\n\nIf you have trouble navigating, please send email to LINK.\n\n\n### Please see the file \"file_organisations\" for the directories and subdirectories.\n\n# Results files are organised based on QM calculations and force field comparisons (also improvements), and Parameters validations where you have the test cases. For the QM calculations, they are based on the softwares and methods used. PSI4 directories for energy decompositions and SAPT methods, further divided in subdiectories. NWCHEM is for all other QM methods, and those can be differentiated by the dircetoty names which contains the method (DFT, MP2, CCSD(T)) and basis sets. CHARMM* directories contains the force field comparison vs the improvements test.\n\nThe Khan_etal_JCTC_2016 paper contains phenol-TMA and benzene-TMA cases. The Khan_etal_JCTC_2019 contains the indole-TMA case.\n\nFor the QM part, benzene-tma and indole-tma directories have naming explicitly (i.e. NWCHEM_cat_pi_benzene_tma/, PSI4_calc_benzene_tma/, CHARMM_pes_cat_pi_benzene_tma/). For phenol-TMA, look at the *_RESTART directories; these are the production ones for CHARMM and NWCHEM cases. For PSI4, it is PSI4_calc/). Other directories are old tests with different PES conditions (relaxation etc.). I did not remove them for my personal reference.\n\n# For the Parameters validations, reboot_piplc-dmpc/ is the test case for Khan_etal_JCTC_2016; all others are for Khan_etal_JCTC_2019.\n\n### Manuscripts files are seperated for both these works in the main directories with submission files and figures. The raw data are also there. You will also find the raw data in the different results subdirectories.\n\n*** I am writing this very quickly, so some explanations might not be obvious. If you have doubt, please send email to LINK." } } } rows { quad { p_iri { name_id: 66 } o_iri { prefix_id: 12 name_id: 2 } } } rows { quad { p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "2019_Khan_etal_JCTC" } } } rows { quad { p_iri { name_id: 78 } o_literal { lex: "2021-11-22 00:00:00" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 7 name_id: 70 } } } rows { quad { o_iri { name_id: 80 } } } rows { quad { o_iri { prefix_id: 15 } } } rows { prefix { id: 14 value: "https://schema.org/" } } rows { name { value: "maintainer" } } rows { quad { p_iri { prefix_id: 14 name_id: 84 } o_literal { lex: "Nathalie Reuter" } } } rows { prefix { id: 13 value: "https://w3id.org/ro-id/6d7f7856-f2c8-4172-9a35-ef22b6cc4561/" } } rows { name { value: "ro-crate-metadata.json" } } rows { name { value: "conformsTo" } } rows { prefix { id: 1 value: "https://w3id.org/ro/crate/" } } rows { name { value: "1.1" } } rows { quad { s_iri { prefix_id: 13 } p_iri { prefix_id: 9 } o_iri { prefix_id: 1 } } } rows { quad { p_iri { prefix_id: 15 name_id: 49 } o_iri { prefix_id: 13 name_id: 2 } } } rows { name { value: "CreativeWork" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 88 } } } rows { prefix { id: 3 value: "https://w3id.org/ro-id/" } } rows { name { value: "77b8f708-1da5-4937-88c1-bf913536e396" } } rows { quad { s_iri { prefix_id: 3 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "directory" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 33 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "12.121212121212121" } } } rows { quad { p_iri { } o_literal { lex: "5.2" } } } rows { name { value: "780df816-5a29-4a1e-ada6-975c80157441" } } rows { quad { s_iri { prefix_id: 3 name_id: 90 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "QM" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 33 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "12.121212121212121" } } } rows { quad { p_iri { } o_literal { lex: "5.2" } } } rows { name { value: "822a91de-8ad6-49aa-821a-fed4a5f225a0" } } rows { quad { s_iri { prefix_id: 3 name_id: 91 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "force field comparison" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 23 } } } rows { quad { p_iri { } o_literal { lex: "20.29459901800327" } } } rows { quad { p_iri { } o_literal { lex: "12.4" } } } rows { name { value: "8fe39cdd-2592-442a-ab2f-75bce594e8bc" } } rows { quad { s_iri { prefix_id: 3 name_id: 92 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "IT-computer sciences" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 20 } } } rows { quad { p_iri { } o_literal { lex: "Science and technology/Technology and engineering/IT-computer sciences" } } } rows { name { value: "91a19a15-66ea-4795-b53f-18d843c39303" } } rows { quad { s_iri { prefix_id: 3 name_id: 93 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "choline" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 33 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "12.121212121212121" } } } rows { quad { p_iri { } o_literal { lex: "5.2" } } } rows { name { value: "931b0404-6d29-470f-bb13-ac082723d322" } } rows { quad { s_iri { prefix_id: 3 name_id: 94 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "chemistry and materials (general)" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 72 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.38146594166755676" } } } rows { name { value: "9d724b70-f51e-4801-a33c-0ddacb9f6380" } } rows { quad { s_iri { prefix_id: 3 name_id: 95 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "result" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "6.107784431137724" } } } rows { quad { p_iri { } o_literal { lex: "5.1" } } } rows { name { value: "a373b5e2-9377-4ea5-ac77-3000d7e4ea1d" } } rows { quad { s_iri { prefix_id: 3 name_id: 96 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "raw data" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "7.18562874251497" } } } rows { quad { p_iri { } o_literal { lex: "6.0" } } } rows { name { value: "b2bb9f47-e1bf-472d-b70d-b04bbbb8cdd1" } } rows { quad { s_iri { prefix_id: 3 name_id: 97 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Results are divided in QM calculations+force field comparison and improvements, and force field parameter validations." } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 73 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: 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o_literal { lex: "chemistry and materials" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 72 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.38146594166755676" } } } rows { name { value: "dfcc6de7-f307-4a3d-b80f-1ea59b685cea" } } rows { quad { s_iri { prefix_id: 3 name_id: 103 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "validation" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 33 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "10.955710955710956" } } } rows { quad { p_iri { } o_literal { lex: "4.7" } } } rows { name { value: "e13cc288-ae77-4cc5-9a27-2223c47c4bd9" } } rows { quad { s_iri { prefix_id: 3 name_id: 104 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "results file" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 23 } } } rows { quad { p_iri { } o_literal { lex: "13.58428805237316" } } } rows { quad { p_iri { } o_literal { lex: "8.3" } } } rows { name { value: "e68dd0da-25b0-4f21-83a8-2090c91f2290" } } rows { quad { s_iri { prefix_id: 3 name_id: 105 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "file" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 33 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "13.51981351981352" } } } rows { quad { p_iri { } o_literal { lex: "5.8" } } } rows { name { value: "ebb04bc3-1b64-4723-abb1-2bb1e9fb5c41" } } rows { quad { s_iri { prefix_id: 3 name_id: 106 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Newspaper" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 20 } } } rows { quad { p_iri { } o_literal { lex: "Arts, culture and entertainment/Mass media/Newspaper" } } } rows { name { value: "f1de38ae-6531-4b97-b7cb-871e09afdb6c" } } rows { quad { s_iri { prefix_id: 3 name_id: 107 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "file" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 28 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "9.461077844311378" } } } rows { quad { p_iri { } o_literal { lex: "7.9" } } } rows { name { value: "f94049ca-f965-407c-bbd6-9dec6d0b4f36" } } rows { quad { s_iri { prefix_id: 3 name_id: 108 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "computer science" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 5 name_id: 31 } } } rows { quad { p_iri { prefix_id: 4 name_id: 24 } o_literal { lex: "18.627450980392158" } } } rows { quad { p_iri { } o_literal { lex: "1.9" } } } rows { name { value: "fe8868e4-2180-433d-b349-a8b9f0a2692c" } } rows { quad { s_iri { prefix_id: 3 name_id: 109 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Results for Tyrosine-choline, Phenylalanine-choline and Tryptophan-choline force field improvements." } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 4 name_id: 73 } } } rows { quad { p_iri { name_id: 24 } o_literal { lex: "28.061224489795915" } } } rows { quad { p_iri { } o_literal { lex: "11.0" } } } rows { quad { s_iri { prefix_id: 10 name_id: 55 } p_iri { prefix_id: 15 name_id: 14 } o_literal { lex: "Geo H." } } } rows { prefix { id: 2 value: "http://xmlns.com/foaf/0.1/" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 2 name_id: 48 } } } rows { name { value: "email" } } rows { quad { s_iri { prefix_id: 10 name_id: 51 } p_iri { prefix_id: 15 name_id: 110 } o_literal { lex: "nathalie.reuter@rohub.com" } } } rows { quad { p_iri { name_id: 14 } o_literal { lex: "Nathalie Reuter" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 2 name_id: 48 } } } rows { prefix { id: 16 value: "https://w3id.org/np/RA0OCAvzsQw99nJc2vYJgQtieeaFnSmkQbNyPV60yjd5k/" } } rows { prefix { id: 11 value: "http://www.w3.org/ns/prov#" } } rows { name { value: "wasDerivedFrom" } } rows { prefix { id: 8 value: "https://api.rohub.org/api/ros/6d7f7856-f2c8-4172-9a35-ef22b6cc4561/crate/download/" } } rows { quad { s_iri { prefix_id: 16 name_id: 4 } p_iri { prefix_id: 11 name_id: 111 } o_iri { prefix_id: 8 name_id: 85 } g_iri { prefix_id: 16 name_id: 7 } } } rows { prefix { id: 12 value: "https://w3id.org/np/" } } rows { name { value: "created" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#dateTime" } } rows { quad { s_iri { prefix_id: 12 name_id: 1 } p_iri { prefix_id: 9 name_id: 112 } o_literal { lex: "2026-05-19T13:47:45.024+02:00" datatype: 2 } g_iri { prefix_id: 16 name_id: 9 } } } rows { prefix { id: 7 value: "https://w3id.org/kpxl/gen/terms/" } } rows { name { value: "RoCrateBot" } } rows { quad { p_iri { prefix_id: 9 name_id: 54 } o_iri { prefix_id: 7 name_id: 113 } } } rows { prefix { id: 14 value: "http://purl.org/nanopub/x/" } } rows { name { value: "introduces" } } rows { quad { p_iri { prefix_id: 14 } o_iri { prefix_id: 13 name_id: 2 } } } rows { prefix { id: 1 value: "https://w3id.org/fdof/ontology#" } } rows { name { value: "FAIRDigitalObject" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 1 name_id: 115 } } } rows { name { value: "RoCrateNanopub" } } rows { quad { o_iri { prefix_id: 7 } } } rows { prefix { id: 5 value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { name { value: "label" } } rows { quad { p_iri { prefix_id: 5 } o_literal { lex: "2019_Khan_etal_JCTC" } } } rows { name { value: "sig" } } rows { name { value: "hasAlgorithm" } } rows { quad { s_iri { prefix_id: 16 } p_iri { prefix_id: 14 } o_literal { lex: "RSA" } } } rows { name { value: "hasPublicKey" } } rows { quad { p_iri { } o_literal { lex: "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAxszSDYX5tuCSkP7UiCtftYPFNQVTjgNu0I5fwdML2DLRDlp0xzmsQXRk8oHuvwGvG1aMjj6cpUqO+0rz2Sg/wvHOgUpkRH8VJXvmlkhafMLCMtUtk5JIx7e+fkzCby+fnmD7kMkGLrT+OaExWwEDmNlCAt0TPKcHSdwsjso2isXjtAsGevyCMke8ufnFYpjs746JES1eNzVnHnn2Kp/lqcm60GM+J8dLgRZp7fX0anW098xhKym6+xXFzqeju0vYRIHBPerv+r7skWxwk+a7Sd8msqVeYEv6NTqnyWvyWb6Yh8cvj04N6qm/T6C5FUPLQhzSaQgMVMU6yLqjPuu9DwIDAQAB" } } } rows { name { value: "hasSignature" } } rows { quad { p_iri { } o_literal { lex: "Z6P993gm/edEypI9FcqZLjwI0dxF/kl3uUdPg+s1Sy8BpC3AXchK23uTlU7IbXhfhbI6mgPn+lLoUvo4Uk/tkPjts3l6gH6EoEJIgHXNEyo4mbT2J9Oxpb5LmU+3WQ///lxlTR5v3a97wyZR9LZAY5SRupFY0fIVe/ji4b8bOs4mCR11XOORYym+vQTrSD420fo+S0ZBCP6o3+d8aQVzneVGn/nyMg9GuJ+OzEppXkq/KkbBAVCWVxfpEFhUyCJABYB0FjRnypIC9snXzyNzgZdr8poJtwVUa7LqcwQDAyqQiD6iEJ6Kf0lolT8nLB7PgaBHQ8aZq5RFdjpgT9/8dg==" } } } rows { name { value: "hasSignatureTarget" } } rows { quad { p_iri { } o_iri { prefix_id: 12 name_id: 1 } } } rows { name { value: "signedBy" } } rows { quad { p_iri { prefix_id: 14 name_id: 123 } o_iri { prefix_id: 7 name_id: 113 } } }