1,720,971 research outputs found
Computing stoichiometric molecular composition from crystal structures
No full textAlgoritmų stechiometriškai teisingiems molekulių kompleksams atstatyti iš kristalografinės informacijos failų (CIF) kūrimasCrystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases
Development of the Deposition Software for Small Molecule Open Crystallographic Database COD
No full textŠiame dokumente aprašomas atviros mažų molekulių kristalografinės duomenų bazės COD
automatinės duomenų įkėlimo programinės įrangos, leidžiančios užtikrinti spartų duomenų bazės
augimą, poreikis, kūrimas, kūrimo metu priimti sprendimai bei spręsti uždaviniai.This document presents the description of demand, solutions and development of the deposition software for small molecule open crystallographic database COD
A posteriori metadata from automated provenance tracking: Integration of AiiDA and TCOD
No full textSiekdami geresnio duomenų atsekamumo teoretinės medžiagotyros srityje įgyvendinome skaičiavimų platformos AiiDA ir teoretinės atviros mažų molekulių kristalografinės duomenų bazės TCOD integravimą.In order to make results of computational scientific research findable, accessible, interoperable and
re-usable, it is necessary to decorate them with standardised metadata. However, there are a number
of technical and practical challenges that make this process difficult to achieve in practice. Here the
implementation of a protocol is presented to tag crystal structures with their computed properties,
without the need of human intervention to curate the data. This protocol leverages the capabilities
of AiiDA, an open-source platform to manage and automate scientific computational workflows, and
the TCOD, an open-access database storing computed materials properties using a well-defined and
exhaustive ontology. Based on these, the complete procedure to deposit computed data in the TCOD
database is automated. All relevant metadata are extracted from the full provenance information
that AiiDA tracks and stores automatically while managing the calculations. Such a protocol also
enables reproducibility of scientific data in the field of computational materials science. As a proof
of concept, the AiiDA–TCOD interface is used to deposit 170 theoretical structures together with
their computed properties and their full provenance graphs, consisting in over 4600 AiiDA nodes
Fitting of univariate mixture distributions to data using various approaches
No full textStatistinių skirstinių mišinių parinkimas vienmačiams duomenimsFitting of univariate mixture distributions to data using various approache
Use of Prior Small Molecule Crystallographic Knowledge for Refinement of Macromolecular Structures: Application of the Crystallography Open Database
No full textMažų molekulių stereocheminės informacijos rinkiniai, skirti molekulių patikslinimui ir tikrinimui, susiduria su dviem apribojimais: licencijomis bei
galimu atsilikimu nuo sparčiai besivystančių tyrimų rezultatų. Naujas mažų molekulių stereocheminės informacijos rinkinys išvedamas iš atviros prieigos mažų molekulių duomenų bazės COD naudojantis nauja mažų molekulių cheminės įvairovės aprašymo metodika bei Bajeso (Bayesian) karkasu, sukuriamos priemonės automatiniam rinkinio atnaujinimui realiame laike. Automatiniais metodais išvestas stereocheminės informacijos rinkinys yra palyginamas su ankstesniais darbais šioje srityje bei panaudojamas neįprastiems mažų molekulių geometriniams bruožams aptikti, bet galėtų būti pagerintas ištaisius COD duomenų klaidas bei pagerinus naudojamo tikėtinumo maksimizavimo algoritmo inicializaciją bei konvergavimo greitį.Libraries of small molecule stereochemical information, used for
refinement and validation of small molecules and macromolecule-ligand complexes,
are subjected to two limitations: licensing and possibility to become outdated. A
novel library of small molecule stereochemical information is constructed from the
Crystallography Open Database (COD), harnessing a new method for description
of the variety of small molecule chemical environments and Bayesian framework.
Means for automatic renewal of the library in the real time are devised. The result
of the research is comparable to the previous works and proves to be useful in the
detection of unusual geometric features in small molecules. The library can be
improved by devising better means of initialisation of the expectation maximisation
algorithm and speeding up the convergence
COD::CIF::Parser: an error-correcting CIF parser for the Perl language
No full textA syntax-correcting CIF parser, COD::CIF::Parser, is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser, the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.A syntax-correcting CIF parser, COD::CIF::Parser, is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser, the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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