TheComputational Crystallography Toolbox: crystallographic algorithms in a reusable software framework

2002 ◽  
Vol 35 (1) ◽  
pp. 126-136 ◽  
Author(s):  
Ralf W. Grosse-Kunstleve ◽  
Nicholas K. Sauter ◽  
Nigel W. Moriarty ◽  
Paul D. Adams
Keyword(s):  
Structural Genomics ◽  
Macromolecular Structure ◽  
Software Framework ◽  
Software Components ◽  
Software Developers ◽  
Space Groups ◽  
Reusable Software ◽  
New Methods ◽  
Structure Solution ◽  
Unit Cells

The advent of structural genomics initiatives has led to a pressing need for high-throughput macromolecular structure determination. To accomplish this, new methods and inevitably new software must be developed to accelerate the process of structure solution. To minimize duplication of effort and to generate maintainable code efficiently, a toolbox of basic crystallographic software components is required. The development of theComputational Crystallography Toolbox(cctbx) has been undertaken for this purpose. In this paper, the fundamental requirements for thecctbxare outlined and the decisions that have lead to its implementation are explained. Thecctbxcurrently contains algorithms for the handling of unit cells, space groups and atomic scatterers, and is released under an Open Source license to allow unrestricted use and continued development. It will be developed further to become a comprehensive library of crystallographic tools useful to the entire community of software developers.

Reusable software components

2002 ◽  
Vol XXII (3) ◽  
pp. 20-23
Author(s):  
Trudy Levine
Keyword(s):  
Software Components ◽  
Reusable Software

Reusable software components

1993 ◽  
Vol XIII (1) ◽  
pp. 60-62
Author(s):  
Trudy Levine
Keyword(s):  
Software Components ◽  
Reusable Software

Reusable software components

2004 ◽  
Vol XXIV (3) ◽  
pp. 47-48
Author(s):  
Trudy Levine
Keyword(s):  
Software Components ◽  
Reusable Software

Reusable software components

1994 ◽  
Vol XIV (6) ◽  
pp. 41-52 ◽  
Author(s):  
Trudy Levine
Keyword(s):  
Software Components ◽  
Reusable Software

Reusable software components

2000 ◽  
Vol XX (2) ◽  
pp. 27-37
Author(s):  
Trudy Levine
Keyword(s):  
Software Components ◽  
Reusable Software

Reusable software components

2005 ◽  
Vol XXV (2) ◽  
pp. 45-53
Author(s):  
Trudy Levine
Keyword(s):  
Software Components ◽  
Reusable Software

Crystal chemistry of transition metal diarsenates M 2As2O7 (M = Mn, Co, Ni, Zn): variants of the thortveitite structure

2010 ◽  
Vol 66 (6) ◽  
pp. 603-614 ◽  
Author(s):  
Matthias Weil ◽  
Berthold Stöger
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Transition Metal ◽  
Basic Structure ◽  
Structure Type ◽  
Ambient Conditions ◽  
Modulated Structure ◽  
Triclinic Crystal System ◽  
Space Groups ◽  
Unit Cells

The structures of the 3d divalent transition-metal diarsenates M 2As2O7 (M = Mn, Co, Ni, Zn) can be considered as variants of the monoclinic (C2/m) thortveitite [Sc2Si2O7] structure type with a ≃ 6.7, b ≃ 8.5, c ≃ 4.7 Å, α ≃ 90, β ≃ 102, γ ≃ 90° and Z = 2. Co2As2O7 and Ni2As2O7 are dimorphic. Their high-temperature (β) polymorphs adopt the thortveitite aristotype structure in C2/m, whereas their low-temperature (α) polymorphs are hettotypes and crystallize with larger unit cells in the triclinic crystal system in space groups P\bar 1 and P1, respectively. Mn2As2O7 undergoes no phase transition and likewise adopts the thortveitite structure type in C2/m. Zn2As2O7 has an incommensurately modulated crystal structure [C2/m(α,0,γ)0s] with q = [0.3190 (1), 0, 0.3717 (1)] at ambient conditions and transforms reversibly to a commensurately modulated structure with Z = 12 (I2/c) below 273 K. The Zn phase resembles the structures and phase transitions of Cr2P2O7. Besides descriptions of the low-temperature Co2As2O7, Ni2As2O7 and Zn2As2O7 structures as five-, three- and sixfold superstructures of the thortveitite-type basic structure, the superspace approach can also be applied to descriptions of all the commensurate structures. In addition to the ternary M 2As2O7 phases, the quaternary phase (Ni,Co)2As2O7 was prepared and structurally characterized. In contrast to the previously published crystal structure of the mineral petewilliamsite, which has the same idealized formula and has been described as a 15-fold superstructure of the thortveitite-type basic structure in space group C2, synthetic (Ni,Co)2As2O7 can be considered as a solid solution adopting the α-Ni2As2O7 structure type. Differences of the two structure models for (Ni,Co)2As2O7 are discussed.

NEURO-FUZZY BASED SEARCH ROBOT FOR SOFTWARE COMPONENTS

1999 ◽  
Vol 08 (02) ◽  
pp. 119-135
Author(s):  
YAU-HWANG KUO ◽  
JANG-PONG HSU ◽  
MONG-FONG HORNG
Keyword(s):  
Retrieval System ◽  
Software Component ◽  
Software Components ◽  
Personalized Search ◽  
Component Retrieval ◽  
Reusable Software ◽  
Major Mechanism ◽  
Fuzzy Models ◽  
Neuro Fuzzy

A personalized search robot is developed as one major mechanism of a personalized software component retrieval system. This search robot automatically finds out the Web servers providing reusable software components, extracts needed software components from servers, classifies the extracted components, and finally establishes their indexing information for local component retrieval in the future. For adaptively tuning the performance of software component extraction and classification, an adaptive thesaurus and an adaptive classifier, realized by neuro-fuzzy models, are embedded in this search robot, and their learning algorithms are also developed. A prototype of the personalized software component retrieval system including the search robot has been implemented to confirm its validity and evaluate the performance. Furthermore, the framework of proposed personalized search robot could be extended to the search and classification of other kinds of Internet documents.

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