Open Babel: An open chemical toolbox

Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendorneutral formats. Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license fro

Early Origin for Human-Like Precision Grasping: A Comparative Study of Pollical Distal Phalanges in Fossil Hominins

Altres ajuts: Generalitat de Catalunya 2006 FI 00065 i beca de viatge 2008 BE1 00370Background: The morphology of human pollical distal phalanges (PDP) closely reflects the adaptation of human hands for refined precision grip with pad-to-pad contact. The presence of these precision grip-related traits in the PDP of fossil hominins has been related to human-like hand proportions (i.e. short hands with a long thumb) enabling the thumb and finger pads to contact. Although this has been traditionally linked to the appearance of stone tool-making, the alternative hypothesis of an earlier origin-related to the freeing of the hands thanks to the advent of terrestrial bipedalism-is also possible given the human-like intrinsic hand proportion found in australopiths. - Methodology/Principal Findings: We perform morphofunctional and morphometric (bivariate and multivariate) analyses of most available hominin pollical distal phalanges, including Orrorin, Australopithecus, Paranthropous and fossil Homo, in order to investigate their morphological affinities. Our results indicate that the thumb morphology of the early biped Orrorin is more human-like than that of australopiths, in spite of its ancient chronology (ca. 6 Ma). Moreover, Orrorin already displays typical human-like features related to precision grasping. - Conclusions: These results reinforce previous hypotheses relating the origin of refined manipulation of natural objects-not stone tool-making-with the relaxation of locomotor selection pressures on the forelimbs. This suggests that human hand length proportions are largely plesiomorphic, in the sense that they more closely resemble the relatively short-handed Miocene apes than the elongated hand pattern of extant hominoids. With the advent of terrestrial bipedalism, these hand proportions may have been co-opted by early hominins for enhanced manipulative capabilities that, in turn, would have been later co-opted for stone tool-making in the genus Homo, more encephalized than the previous australopiths. This hypothesis remains may be further tested by the finding of more complete hands of unequivocally biped early hominins

Neandertal-Modern Human Contact in Western Eurasia: Issues of Dating, Taxonomy, and Cultural Associations

Supporting Assimilation views of Neandertal/modern human interaction, chronostratigraphic reasoning indicates that the “transitional” industries of Europe predate modern human immigration, in agreement with their association with Neandertals in the Châtelperronian at the Grotte du Renne and St.-Césaire. Supporting the Neandertals' species separateness and less developed cognition, those industries are alternatively claimed to relate to pioneer groups of modern humans; the latter would have been the true makers of the precocious instances of symbolic material culture that, under Assimilation, are assigned to the Neandertals. However, the taxonomy of the Kent's Cavern and Grotta del Cavallo dental remains is uncertain, and their poor stratigraphic context precludes dating by association. The opposite happens at the Grotte du Renne, whose stratigraphic integrity is corroborated by both taphonomy and dating. Not questioning that the Early Ahmarian is a cultural proxy for modern humans and a source for the Protoaurignacian of Europe, its claimed emergence ~46–49 ka ago at Kebara refl ects the dating of Middle Paleolithic charcoal—to be expected, because the Early Ahmarian units at the back of the cave are made up of reworked Middle Paleolithic sediments derived from the entrance. The dating of inherited material also explains the old results for the Aurignacian of Willendorf II and Geissenklösterle. At the latter, the dates on anthropically modified samples of the hunted taxa (reindeer and horse) place its Aurignacian occupations in the same time range as elsewhere in Europe, after ~40 ka ago. The hypothesis that Neandertal/modern human contact in Europe resulted in a process of assimilation in connection with the spread of the Protoaurignacian ~41.5 ka ago remains unfalsified.info:eu-repo/semantics/publishedVersio

Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins

The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans) share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups.JAPC, JMJA and PP received fundings from Ministerio de Ciencia e Innovación, Gobierno de España (http://www.idi.mineco.gob.es), project CGL2011-30334, and Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía, España (http://www.juntadeandalucia.es/organismo​s/economiainnovacioncienciayempleo.html), project P11-HUM-7248 and Research Groups RNM-146 and HUM-607