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23 results for “RMG”
RMG-DB-11: Enumerating Reaction Space for Small Molecule Chemistry
<p>This repository presents approximately 750 million atom-mapped reaction SMILES. Reactions are generated by applying templates from the Reaction Mechanism Generator (RMG) database to a subset of the species from GDB11. Thus, we refer to this dataset as RMG-DB-11 i.e., the Reaction Mechanism Generator Database whose species contain up to 11 heavy atoms. All SMILES have been canonicalized by RDKit. All reactions are labeled with their corresponding RMG template.</p> <p>This data serves as a crucial starting point for quantitative predictive chemistry. Many methods that search for transition state structures require atom-mapped SMILES, which this repository provides. This data is also well-suited for unsupervised pre-training of various machine learning models.</p> <p>To parse the data with Python, start with <em>import pandas as pd</em>. Reactions with 1-8 heavy atoms can be parsed using the following code snippet: <em>pd.read_csv(<filepath>)</em>. Reactions with 9 heavy atoms can be parsed using <em>pd.read_pickle(<filepath>, compression='zip')</em>. The file names below include the word "zip" as a helpful hint to use the compression argument. Due to the large number of reactions with 10 and 11 heavy atoms, these are split into smaller chunks. First untar the file using <em>tar -xvf <tar_archive></em> to obtain several zipped pickle files that can each be parsed using the same method as with 9 heavy atoms.</p>
EMUE-RMG-3-CalibrationGasMixtures
<p>Preparation of calibration gas mixtures of ammonia (NH<sub>3</sub>) in nitrogen using permeation</p> <p>This example describes the uncertainty evaluation of the preparation of a calibration gas mixtures of ammonia in nitrogen by using permeation. The measurand is the amount fraction ammonia.</p> <p>Files contained in dataset are:</p> <ul> <li>EMUE-RMG-Preparation of calibration gas mixtures of ammonia (NH3) in nitrogen using permeation.pdf</li> <li>Permeation_example.tex: LaTeX file to be compiled in order to produce EMUE-RMG-Preparation of calibration gas mixtures of ammonia (NH3) in nitrogen using permeation.pdf</li> <li>Ammoniak-40a.pdf: figure file</li> <li>Ammoniak-62C.pdf: figure file</li> <li>EMPIR.jpg: figure file</li> <li>EMUELogo-03.jpg: figure file</li> <li>ExcelResiduals.png: figure file</li> <li>Mass Piece 20g plus 100mg.xls: data file containing weighing data of the linearity assessment</li> <li>Mass Piece 20g: data file containing weighing data of the linearity assessment</li> <li>MatrixResults.png: figure file</li> <li>MatrixA.png: figure file</li> <li>MatrixShow.png: figure file</li> <li>MMULT.png: figure file</li> <li>Model3.stan: model developed in R for computing the difference between two series of observations and modelling the effect of finite resolution for the uncertainty of weighing with the balance (RStan package was used)</li> <li>MyReferences.bib: bibliography file</li> <li>Permeation data Ammonia.xls: data file containing ammonia mixture data</li> <li>reference.bib: bibliography file</li> <li>Compendium.bib: bibliography file</li> <li>Weight_20g.pdf: figure file</li> <li>Weight_20g+100mg.pdf: figure file</li> <li>traceplot.pdf: figure file</li> <li>Two_weights_rev1.txt : Model developed in R for Evaluation of the mean and standard deviation of weighing a weight using the magnetic suspension balance of the permeation system. The input data are given in: Mass Piece 20g plus 100mg.xls, Mass Piece 20g and additionally Model3.stan.</li> </ul>
EMUE-RMG-1-GasFlowCalibration
<p>Flow meter calibration using the master meter method</p> <p>This example demonstrates the calibration of a gas flow measuring instrument by the so-called “master meter” method, i.e. by comparing the measured flow on a master meter (reference standard) and the measured flow on the device under test.</p> <p>Files contained in dataset are:</p> <ul> <li>Flow_meter_calibration_using_the_master_meter_method.pdf</li> <li>RMG11_ExampleSAGAS.tex: LaTeX file to be compiled in order to produce Flow_meter_calibration_using_the_master_meter_method.pdf,</li> <li>EMPIR.jpg: figure file,</li> <li>EMUELogo-03.jpg: figure file,</li> <li>SAGAS1.png: figure file,</li> <li>SAGASGUMandMCM.jpg: figure file,</li> <li>RMG11.bib: bibliography file,</li> <li>GUM_SAGAS.mat: MATLAB function that calculates measurement uncertainty by following the GUM principle,</li> <li>GUMSupp1_SAGAS.mat: MATLAB function that calculates measurement uncertainty by following GUM Supplement 1 principle (Monte Carlo method),</li> <li>InputData.mat: MATLAB function for input data,</li> <li>MainScript.mat: Model developed in MATLAB that calculates estimated gas flow error and the associated measurement uncertainty (GUM and Monte Carlo method). This file that uses MATLAB functions (developed for this example): SetFormattingSymbols, InputData, GUM_SAGAS, GUMSupp1_SAGAS, Results, PlotGUMAndMCM_SAGAS,</li> <li>PlotGUMAndMCM_SAGAS.mat: MATLAB function for plotting the results,</li> <li>Results.mat: MATLAB function for displaying the results,</li> <li>SetFormatingSymbols.mat: MATLAB function for setting formatting symbols.</li> </ul>
EMUE-RMG-2-Pressure drop measurement
<p>Pressure Drop Measurement</p> <p>This example demonstrates how correlations can sometimes be removed from an uncertainty evaluation by modifying the measurement equation so that strongly correlated quantity estimates do not appear together. This is demonstrated by an example considering the pressure drop in a pressurised vessel, in which the effect of correlation between temperature measurements is removed. In this example the uncertainty associated with an estimate of pressure drop is appreciably smaller when correlation is taken into consideration.</p> <p>Files contained in dataset are:</p> <ul> <li>EMUE-RMG- Pressure drop measurement – UKAS.pdf,</li> <li>EMPIR.jpg- figure file,</li> <li>EMUELogo-03.jpg- figure file,</li> <li>Example_A.tex: LaTeX file to be compiled in order to produce EMUE-RMG- Pressure drop measurement – UKAS.pdf,</li> <li>MCMandGUMnewWithCorr.jpg: figure file,</li> <li>MCMandGUMnewWithoutCor.jpg: figure file,</li> <li>reference.bib: bibliography file,</li> <li>Compendium.bib: bibliography file,</li> <li>GUM_WithCorrelations.mat /GUM_WithoutCorrelations.mat: MATLAB function that calculates measurement uncertainty by following the GUM principle (with or without correlations),</li> <li>GUMSupp1_WithCorrelations.mat /GUMSupp1_WithoutCorrelations.mat: MATLAB function that calculates measurement uncertainty by following GUM Supplement 1 principle (with or without correlations),</li> <li>InputData_WithCorrelations.mat /InputData_WithoutCorrelations.mat: MATLAB function for input data (with or without correlations),</li> <li>PlotGUM_WithCorrelations.mat /PlotGUM_WithoutCorrelations.mat: MATLAB function for plotting the results (with or without correlations),</li> <li>PlotGUMAndMCM_WithCorrelations.mat /PlotGUMAndMCM_WithoutCorrelations.mat: MATLAB function for plotting the results (with or without correlations),</li> <li>Results_WithCorrelations.mat /Results_WithoutCorrelations.mat: MATLAB function for displaying the results (with or without correlations),</li> <li>SetFormattingSymbols_WithCorrelations.mat /SetFormattingSymbols_WithoutCorrelations.mat: MATLAB function for setting formatting symbols,</li> <li>UKASPressureDropExample_WithCorrelations.mat /UKASPressureDropExample_WithoutCorrelations.mat: Model developed in MATLAB that calculates estimated pressure drop and the associated measurement uncertainty (GUM and Monte Carlo method). One file calculates the uncertainties with and the other without correlations. These files use MATLAB functions (developed for this example) that are listed above: SetFormattingSymbols, InputData, GUM, GUMSupp1, Results, PlotGUMAndMCM, PlotGUM.</li> </ul>
Figures 22-25 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 22-25 - Loxosceles amazonica, carapace, female. 22 Martins, state of Rio Grande do Norte, Brazil (MNRJ 7304) 23 Serra Negra do Norte, ESEC Seridó, state of Rio Grande do Norte, Brazil (MNRJ 6928, ref. Ser 8) 24 Santa Quitéria, state of Ceará, Brazil (MNRJ 6952) 25 São Raimundo Nonato, state of Piauí, Brazil (MNRJ 6927, ref. GSB11A-17). Scale bars: 1mm.
Figures 26-31 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 26-31 - Loxosceles amazonica, seminal receptacles. 26 Martins, state of Rio Grande do Norte, Brazil (MNRJ 6942) 27 São Raimundo Nonato, state of Piauí, Brazil (MNRJ 6927, ref. GSB11A-17) 28 Serra Negra do Norte, ESEC Seridó, state of Rio Grande do Norte, Brazil (MNRJ 6928, ref. Ser 8) 29 Açu, FLONA de Açu, state of Rio Grande do Norte, Brazil (MNRJ 6931) 30 Santa Quitéria, state of Ceará, Brazil (MNRJ 6952) 31 Macaíba, state of Rio Grande do Norte, Brazil (MNRJ 6949). Scale bars: 27–29 1 mm; 26, 30–31 0.5 mm.
Figures 32-35 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 32-35 - Loxosceles amazonica, habitus. 32–34 Female 32 Martins, state of Rio Grande do Norte, Brazil 33 Açu, FLONA de Açu, state of Rio Grande do Norte, Brazil 34 Macaíba, state of Rio Grande do Norte, Brazil 35 Male. Açu, FLONA de Açu, state of Rio Grande do Norte, Brazil (MNRJ 6936). Photos C. S. Fukushima.
Figures 18-21 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 18-21 - Loxosceles amazonica, carapace. 18–19 Male 18 São Raimundo Nonato, state of Piauí, Brazil (MNRJ 6927, ref. GSB11A-17) 19 Santa Quitéria, state of Ceará, Brazil (MNRJ 6950) 20–21 Female 20 holotype, Santa Isabel, state of Mato Grosso, Brazil (AMNH) 21 Açu, FLONA de Açu, state of Rio Grande do Norte, Brazil (MNRJ 7305). Scale bars: 1mm.
Figures 14-17 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 14-17 - Loxosceles amazonica, male carapace. 14–15 Açu, FLONA de Açu, state of Rio Grande do Norte, Brazil 14 MNRJ 6935 15 MNRJ 6936 16 Serra Negra do Norte, ESEC Seridó, state of Rio Grande do Norte, Brazil (MNRJ 6928, ref. Ser 7) 17 Martins, state of Rio Grande do Norte, Brazil (MNRJ 6947). Scale bars: 1mm.
Figures 7-13 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 7-13 - Loxosceles amazonica, male palpal bulbs, left palp. 7–8 Santa Quitéria, state of Ceará, Brazil (MNRJ 6950) 7 retrolateral 8 prolateral 9–10 São Raimundo Nonato, state of Piauí, Brazil (MNRJ 6927, ref. GSB11A-17) 9 retrolateral 10 prolateral. 11–13 dorsal 11 Açu, FLONA de Açu, state of Rio Grande do Norte, Brazil (MNRJ 6936) 12 Serra Negra do Norte, ESEC Seridó, state of Rio Grande do Norte, Brazil (MNRJ 6928, ref. Ser 7) 13 Santa Quitéria, state of Ceará, Brazil (MNRJ 6950). Scale bars: 1mm.
Figures 78-79 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 78-79 - 78 Map showing records of L. amazonica, L. willianilsoni sp. n. and L. muriciensis sp. n. Area inside rectangle represented on Figure 79. Records of L. amazonica include also those from Azevedo et al. (2014), Gertsch (1967) and Silveira (2015). 79 Expanded map showing the records of the illustrated specimens of L. amazonica, L. willianilsoni sp. n. and L. muriciensis sp. n.
Figures 76-77 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 76-77 - Loxosceles muriciensis sp. n. male holotype, habitus. 76 overall aspect 77 carapace pattern. Photos R. Bertani.
Figures 70-73 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 70-73 - Loxosceles muriciensis sp. n., male holotype. 70 carapace 71–73 right palpal bulb 71 dorsal (mirrored) 72 prolateral (mirrored) 73 retrolateral (mirrored). Scale bars: 70, 72–73 1mm;71 0.5mm.
Figures 74-75 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 74-75 - Loxosceles muriciensis sp. n., female paratype. 74 carapace 75 seminal receptacles. Scale bars: 1 mm.
Figures 58-61 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 58-61 - Loxosceles willianilsoni sp. n., seminal receptacles variation. 58 MNRJ 6957 59 MNRJ 6956 60 MNRJ 6959 61 MNRJ 6951. Scale bars: 58–60 1 mm; 61 0.5 mm.
Figures 66-69 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 66-69 - Loxosceles willianilsoni sp. n. habitat in Martins, state of Rio Grande do Norte, Brazil 66 Casa de Pedra cave 67 entrance of the cave 68–69 caatinga vegetation surrounding the cave 68 dry season 69 rainy season. Photos C. S. Fukushima.
Figures 56-57 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 56-57 - Loxosceles willianilsoni sp. n., female paratype (MNRJ 6954). 56 carapace 57 seminal receptacles. Scale bar: 1 mm.
Figures 1-6 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 1-6 - Loxosceles amazonica, male palpal bulbs. 1–2 Serra Negra do Norte, ESEC Seridó, state of Rio Grande do Norte, Brazil (MNRJ 6928, ref. Ser 7), left palp. 1 retrolateral 2 prolateral 3–4 Açu, FLONA de Açu, state of Rio Grande do Norte, Brazil (MNRJ 6939), left palp 3 retrolateral 4 prolateral 5–6 Martins, state of Rio Grande do Norte, Brazil (MNRJ 7306), right palp (mirrored) 5 retrolateral 6 prolateral. Scale bars: 1mm.
Figures 52-55 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 52-55 - Loxosceles willianilsoni sp. n., male holotype (MNRJ 6953). 52 carapace 53–55 left palpal bulb 53 dorsal 54 prolateral 55 retrolateral. Scale bar 1mm.
Figures 62-65 from: Fukushima CS, Andrade RMG, Bertani R (2017) Two new Brazilian species of Loxosceles Heinecken & Lowe, 1832 with remarks on amazonica and rufescens groups (Araneae, Sicariidae). ZooKeys 667: 67-94. https://doi.org/10.3897/zookeys.667.11369
Figures 62-65 - Loxosceles willianilsoni sp. n., habitus. 62 specimen walking inside Casa de Pedra cave 63 female 64 male 65 carapace pattern, male. Photos 62, 64 C. S. Fukushima; 63, 65 R. Bertani.
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