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Topic: Simplified molecular input line entry specification

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	Simplified Molecular Input Line Entry Specification : SMILES (Site not responding. Last check: 2007-10-13)
		The Simplified Molecular Input Line Entry Specification, or SMILES for short, is a specification for unambiguously describing the structureof chemicals using ASCII character strings.
		The Simplified Molecular Input Line Entry Specification, or SMILES for short, is a specification for unambiguously describing the structure of chemicals using ASCII character strings.
		The SMILES specification was developed by David Weininger in the late 1980s.
	www.explainthat.info /sm/smiles.html (494 words)

	Simplified molecular input line entry specification - Wikipedia, the free encyclopedia
		The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings.
		The original SMILES specification was developed by Arthur Weininger and David Weininger in the late 1980s.
		In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph.
	en.wikipedia.org /wiki/Simplified_molecular_input_line_entry_specification (751 words)

	Simplified molecular input line entry specification - TheBestLinks.com - SMILES, ASCII, Atom, Chemistry, ...
		The simplified molecular input line entry specification (SMILES) is a specification for unambiguously describing the structure of chemicals using ASCII alpha-numeric strings.
		They were originally invented as a means for allowing the input and output of chemical information on early character based computer terminals.
		SMARTS is a modifications of SMILES that allows, in addition to the SMILES elements, the specification of wildcard atoms and bonds specifications.
	www.thebestlinks.com /SMILES.html (518 words)

	BioByte - CQSAR Packages
		It's method of entry and verification of structures and parameters is very user-friendly, and it produces a variety of 2-D graphs as output.
		From structural input via SMILES (or connection table via CCT), this delivers a calculated logP octanol/water and molar refractivity value with error estimate and calculation details.
		Simplified Molecular Input Line Entry Specification, a simple, easy to learn, yet comprehensive chemical nomenclature, used in all of BioByte's programs.
	www.biobyte.com /bb/prod/cqsar.html (315 words)

	Smile - Biocrawler (Site not responding. Last check: 2007-10-13)
		Smile was also the name of the band later known as Queen.
		The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules.
		In physiology, a smile is a facial expression formed by flexing muscles most notably near both ends of the mouth, but also around the eyes.
	www.biocrawler.com /encyclopedia/Smile (445 words)

	Simplified molecular input line entry specification: Facts and details from Encyclopedia Topic (Site not responding. Last check: 2007-10-13)
		The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical Produced by or used in a reaction involving changes in atoms or molecules
		SMARTS is a modification of SMILES that allows, in addition to the SMILES elements, the specification of wildcard In playing card terms, a wild card is a card that can be assigned any value its holder desires....
		This is used in specifying search structures and is widely used in chemical database A chemical database is a database specifically designed to store chemical information....
	www.absoluteastronomy.com /s/simplified_molecular_input_line_entry_specification (1423 words)

	Online Validation and Comparison of Molfile and CML Molecule Atom Connection Descriptors
		Molecular descriptors can take many (but often incompatible) forms one of which is a list of atom-coordinates and bond-connections, expressed in a variety of syntactic forms.
		Essentials such as the presence of precisely one line of text per declared atom can be checked (and is actually non trivial given that any of three combinations of character defining the end of a line might be present) but tests for e.g.
		We have described a molecular resource for partial validation of a molecular atom-connection descriptor and for comparison of two such descriptors which may have been sourced from unconnected locations on the Web.
	www.ch.ic.ac.uk /gkoutos/steve (3062 words)

	CERMN (Site not responding. Last check: 2007-10-13)
		The answer to the most commonly asked question about SMILES is: yes, it is an acronym, meaning Simplified Molecular Input Line Entry Specification.
		SMILES specifically represents a valence model of a molecule, not a computer data structure, a mathematical abstraction, or an "actual substance".
		The valence model of molecular structure has proved to be an incredibly useful model for chemistry, a "universal hook" upon which we hang our chemical information and chemical intelligence.
	www.cermn.unicaen.fr /services/smile/smiles-intro.php (575 words)

	Smiles (JOELib2-alpha API Documentation)
		Line structure of the SMILES in the file/inputstream.
		The input delimiter in the file/inputstream between line entries.
		The output delimiter in the file/outputstream between line entries.
	www-ra.informatik.uni-tuebingen.de /software/joelib/api2/joelib2/io/types/Smiles.html (255 words)

	Organic nomenclature - Biocrawler (Site not responding. Last check: 2007-10-13)
		There is also an older naming system for organic compounds known as common nomenclature, which is often used for simple, well-known compounds, and also for complex compounds whose IUPAC names are too complex for everyday use.
		Simplified molecular input line entry specification (SMILES) strings are commonly used to describe organic compounds, and as such are a form of 'naming' them.
		This page was last modified 20:33, 30 Apr 2005.
	www.biocrawler.com /encyclopedia/Organic_nomenclature (483 words)

	PerlMol - Chemistry::File::SMILES - SMILES linear notation parser/writer
		When used on input, assign single or double bond orders to "aromatic" or otherwise unspecified bonds (i.e., generate the Kekule structure).
		Stereochemical descriptors such as @, @@, /, and \ will be silently ignored on input, and will certainly not be produced on output.
		Reading branches that start before an atom, such as (OC)C, which should be equivalent to C(OC) and COC, according to some variants of the SMILES specification.
	www.perlmol.org /pod/Chemistry/File/SMILES.html (414 words)

	Trimethoxyamphetamine: Facts and details from Encyclopedia Topic (Site not responding. Last check: 2007-10-13)
		Molecular mass The molecular mass of a substance (less accurately called molecular weight and abbreviated as mw) is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal...
		SMILES The simplified molecular input line entry specification or smiles is a specification for unambiguously describing the structure of chemical molecules using short ascii alpha-numeric strings....
		TMAs, also known as trimethoxyamphetamines, are a family of isomer A compound that exists in forms having different arrangements of atoms but the same molecular weight
	www.absoluteastronomy.com /t/trimethoxyamphetamine (1221 words)

	ICM User's Guide: Constructing New Objects
		Remember to delete the previous entry if it is in the box.
		The first is to input the ICM script directly into the 'IcmCode' field.
		This arrow can be generated both as a solid object or as a simpler line representation.
	www.molsoft.com /gui/construct.html (1430 words)

	Simplified Molecular Input Line Entry Specification: Definition and Links by Encyclopedian.com (Site not responding. Last check: 2007-10-13)
		Simplified Molecular Input Line Entry Specification: Definition and Links by Encyclopedian.com
		Link to this page: The easy way of educating your website visitors.
		Post a link to definition / meaning of " Simplified Molecular Input Line Entry Specification " on your site.
	www.encyclopedian.com /sm/SMILES.html (241 words)

	Computers in Chemistry
		If one compares input to output formats in Babel with current literature, it might be preferable to batch-process files in Boogie, Conjure, Feature, or ShelX to output as standard file types used by popular programs such as MDLI's Isis/Draw or Cambridge Software's ChemDraw.
		The first PCs and Macintoshes were limited in speed and memory compared with scientific minicomputers, but their omnipresence persuaded developers and research groups to migrate older minicomputer formats to the new systems.
		Thus additional file formats that allow representation of molecular spectra (NMR, vibrational) and details of wavefunctions (orbital shape, charge separation) were developed.
	pubs.acs.org /subscribe/journals/tcaw/10/i04/html/TCAW04comp.html (1542 words)

	Simplified molecular input line entry specification - tScholars.com (Site not responding. Last check: 2007-10-13)
		Simplified molecular input line entry specification - tScholars.com
		Feed contents directly to your desktop or websites.
		The term Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation regardless.
	www.tscholars.com /encyclopedia/Simplified_molecular_input_line_entry_specification (857 words)

	Chemistry::Smiles - SMILES parser
		This object-oriented module parses a SMILES (Simplified Molecular Input Line Entry Specification) string.
		It can either return the molecule as a Chemistry::Mol object or be used via callback functions.
		The SMILES specification is not fully implemented yet.
	cpan.uwinnipeg.ca /htdocs/Chemistry-Smiles/Chemistry/Smiles.html (356 words)

	Neighbor_Search: General Usage & Hints (Site not responding. Last check: 2007-10-13)
		Neighbor_Search calculates the "neighborhood" for compound(s) which are input by the user.
		SMILES stands for Simplified Molecular Input Line Entry Specification and takes a bit of time to learn.
		Once the compound is input, one or more databases to search against may be selected.
	www.daylight.com /meetings/mug97/Odonnell/demo/neighbor_search_usage.html (427 words)

	C&EN: SCIENCE & TECHNOLOGY - CHEMICAL 'NAMING' METHOD UNVEILED
		The other key players included Stephen R. Heller, Stephen E. Stein, and Dmitrii Tchekhovskoi, who are all associated with the Physical and Chemical Properties Division of the National Institute of Standards and Technology (NIST).
		Searches for compounds identified by their registry numbers can be conducted in CAS databases for a fee or in databases such as the Environmental Protection Agency's Substance Registry System for free.
		Other identification methods for chemicals include the Simplified Molecular Input Line Entry Specification (SMILES) language.
	pubs.acs.org /email/cen/html082205061024.html (1465 words)

	HTML paper International Journal of Molecular Sciences
		A first step is to determine initial reasonnable geometries that are going to be included in the GAMESS input file, before starting energy computation and geometry optimization.
		We have used the geometry database server CORINA (COoRdINAtes) that generates a set of atomic coordinates.
		In order to use CORINA one should enter the description of the molecule using a SMILES (Simplified Molecular Input Line Entry Specification) string.
	www.mdpi.org /ijms/papers/i5040110-html/geometry.htm (77 words)

	Ken Stauffer's Resume
		Developed a parser in C++/Yacc for the SMILES language (Simplified Molecular Input Line Entry Specification).
		The input is a smiles string and the output was a connected graph of atoms (then nodes of the graph) and bonds connecting the atoms.
		The final project consisted of 15,000 lines of code.
	www.stauffercom.com /resume.html (990 words)

	Molecular Modeling and Visualization (Site not responding. Last check: 2007-10-13)
		Molecular Dynamics of Membrane Protein and Receptor Protein Binding
		Molecular Modeling in Organic Chemistry Courses (Alan J. Shusterman) [en]
		SMILES (Simplified Molecular Input Line Entry Specification) [en]
	www.chemie.fu-berlin.de /chemistry/index/molmod (64 words)

	Gliding down from graphs to trees
		We note that by pasting the line segment P1 on −P2 we obtain the two dimensional sphere.
		P1 and P2 are directed paths, so the orientation of the path is important, as can be seen from the next example.
		We note that by pasting the line segment P1 on P2 we obtain the projective 2-sphere.
	www.idealliance.org /papers/extreme03/xml/2003/Venkatesan01/EML2003Venkatesan01.xml (2484 words)

	e3 Information Overload, E-Resources for Engineering Education: What is SMILES? (Site not responding. Last check: 2007-10-13)
		SMILES (Simplified Molecular Input Line Entry Specification) is a simple yet comprehensive chemical nomenclature.
		SMILES is widely used as a general-purpose chemical nomenclature and data exchange format.
		If you have entered an email address in the box, clicking this checkbox will subscribe your email address to this entry so that you are notified if any updates or additional comments occur on the entry.
	blog.case.edu /bcg8/2006/03/01/what_is_smiles (250 words)

	[No title] (Site not responding. Last check: 2007-10-13)
		Chemistry/File::SMILES version 0.32 =================================== This object-oriented module parses and produces SMILES (Simplified Molecular Input Line Entry Specification) strings.
		It is a File I/O driver for the PerMol Toolkit.
		For more information about SMILES, see The SMILES Home Page at http://www.daylight.com/dayhtml/smiles/ This module is under development and doesn't implement the full SMILES syntax yet.
	www.ualberta.ca /~neitsch/sunsite.ualberta.ca/CPAN/modules/by-module/Pod/ITUB/Chemistry-File-SMILES-0.32.readme (162 words)

	[No title] (Site not responding. Last check: 2007-10-13)
		Chemistry/File::SMILES version 0.40 =================================== This object-oriented module parses and produces SMILES (Simplified Molecular Input Line Entry Specification) strings.
		For more information about SMILES, see The SMILES Home Page at http://www.daylight.com/dayhtml/smiles/ Missing features: * Branches that start before an atom, such as (OC)C, which should be equivalent to C(CO) and COC, according to some variants of the SMILES specification.
		INSTALLATION To install this module type the following: perl Makefile.PL make make test make install DEPENDENCIES Chemistry::Mol 0.24 Chemistry::Canonicalize 0.10 Chemistry::Bond::Find 0.21 Chemistry::Ring::Find 0.10 List::Util 0 COPYRIGHT AND LICENSE Copyright (C) 2004 Ivan Tubert This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
	www.ualberta.ca /~neitsch/sunsite.ualberta.ca/CPAN/modules/by-module/Chemistry/Chemistry-File-SMILES-0.40.readme (141 words)

	ACD/ChemFolder \| Input/Output Formats
		Input/Output formats supported through the ACD/ChemSketch, when coupled with the ACD/ChemBasic set of tools, greatly augments ChemFolder's ability to accept data from different sources.
		Even if your favorite format (such as GIF) is not supported as direct input, you CAN place these images in ACD/ChemSketch by opening the file with another program (such as Windows Paint) and pasting it into ChemSketch.
		Some of the supported formats require installation of ChemBasic Goodies.
	www.acdlabs.com /products/chem_dsn_lab/chemfolder/formats.html (386 words)

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