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sdf wolfram documentation wolfram products wolfram one the definitive wolfram language and notebook experience mathematica the original technical computing environment system modeler multidomain modeling and simulation of complex systems compute services use with mathematica and wolfram one ai access use with mathematica and wolfram one finance platform wolfram alpha notebook edition application server enterprise private cloud wolfram engine wolfram player wolfram cloud app wolfram player app more mobile apps wolfram alpha wolfram alpha website wolfram alpha apis ai products wolfram ai ecosystem wolfram foundation tool wolfram cloud mcp wolfram local mcp agent one api cag component apis core technologies of wolfram products wolfram language computable data wolfram notebooks linguistic understanding additional deployment options wolfram cloud wolfram web engine wolframscript wstpserver group organizational licensing all products consulting solutions we deliver solutions for the ai era combining symbolic computation data driven insights and deep technical expertise wolfram consulting data science finance business artificial intelligence data science healthcare real estate engineering civil engineering automotive engineering sustainable energy science technology agtech biosciences environmental science food science quantum computation social and behavioral sciences more wolfram solutions technology for education research universities colleges teaching universities high schools resources for students education initiatives next gen edtech computer based math more solutions for education contact us learning support get started wolfram language introduction fast intro for programmers fast intro for math students wolfram language documentation more learning highlighted core areas demonstrations youtube daily study groups wolfram schools and programs books grow your skills wolfram u courses in computing science life and more community learn solve problems and share ideas blog news views and insights from wolfram resources for software developers tech support contact us support faqs support faqs contact us company about wolfram career center all sites resources connect follow contact us work with us student ambassador initiative wolfram for startups student opportunities jobs using wolfram language educational programs for adults summer school winter school educational programs for youth middle school camp high school research program computational adventures read stephen wolfram s writings wolfram blog wolfram tech books wolfram media complex systems educational resources wolfram mathworld wolfram in stem wolfram challenges wolfram problem generator wolfram initiatives wolfram science wolfram foundation history of mathematics project events stephen wolfram livestreams online in person events contact us connect follow for ais wolfram cloud your account your account user portal wolfram cloud search close navigation menu products wolfram one mathematica system modeler compute services use with mathematica and wolfram one ai access use with mathematica and wolfram one finance platform wolfram alpha notebook edition application server enterprise private cloud wolfram engine wolfram player wolfram cloud app wolfram player app more mobile apps wolfram alpha wolfram alpha website wolfram alpha apis ai products wolfram ai ecosystem wolfram foundation tool wolfram cloud mcp wolfram local mcp agent one api cag component apis core technologies wolfram language computable data wolfram notebooks linguistic understanding additional deployment options wolfram cloud wolfram web engine wolframscript wstpserver group organizational licensing all products consulting solutions wolfram consulting data science finance business artificial intelligence data science healthcare real estate engineering civil engineering automotive engineering sustainable energy science technology agtech biosciences environmental science food science quantum computation social and behavioral sciences more wolfram solutions technology for education research universities colleges teaching universities high schools resources for students education initiatives next gen edtech computer based math more solutions for education contact us learning support get started wolfram language introduction fast intro for programmers fast intro for math students wolfram language documentation grow your skills wolfram u courses in computing science life and more community learn solve problems and share ideas blog news views and insights from wolfram resources for software developers tech support contact us support faqs more learning highlighted core areas demonstrations youtube daily study groups wolfram schools and programs books support faqs contact us company about wolfram career center all sites resources connect follow contact us work with us student ambassador initiative wolfram for startups student opportunities jobs using wolfram language educational programs for adults summer school winter school educational programs for youth middle school camp high school research program computational adventures read stephen wolfram s writings wolfram blog wolfram tech books wolfram media complex systems educational resources wolfram mathworld wolfram in stem wolfram challenges wolfram problem generator wolfram initiatives wolfram science wolfram foundation history of mathematics project events stephen wolfram livestreams online in person events contact us connect follow for ais wolfram cloud your account user portal enable javascript to interact with content and submit forms on wolfram websites learn how wolfram language system documentation center close sdf sdf sd see also import export cloudexport cloudimport molecule formats fasta mol pdf xyz hin related guides 3d geometry modeling formats importing exporting listing of all formats scientific medical data formats chemical biomolecular formats see also import export cloudexport cloudimport molecule formats fasta mol pdf xyz hin related guides 3d geometry modeling formats importing exporting listing of all formats scientific medical data formats chemical biomolecular formats import export format see also import export cloudexport cloudimport molecule formats fasta mol pdf xyz hin related guides 3d geometry modeling formats importing exporting listing of all formats scientific medical data formats chemical biomolecular formats see also import export cloudexport cloudimport molecule formats fasta mol pdf xyz hin related guides 3d geometry modeling formats importing exporting listing of all formats scientific medical data formats chemical biomolecular formats sdf sdf sd import and export support version 2 of the sdf format background context mime type chemical x mdl sdf mdl molecule model files used in cheminformatics applications and on the web for storing and exchanging 3d molecule models plain text tabular format represents an arbitrary number of chemical compounds stores atomic coordinates chemical bond information and metadata maintained by elsevier molecular design limited mdl import export import file sdf imports a list of molecules from an sdf file export file sdf expr exports a molecule or list of molecules to an sdf file import file sdf elem imports the specified element from an sdf file import file sdf elem sub a sub b imports a subelement import file sdf elem 1 elem 2 imports multiple elements the import format can be specified with import file sdf or import file sdf elem export file sdf mol creates an sdf file from a molecule export file sdf mol 1 mol 2 creates an sdf file from a list of molecules export file sdf expr 1 expr 2 elem 1 elem 2 treats each expr i as specifying the corresponding elem i export file sdf expr opt 1 val 1 exports expr with the specified option elements taken to have the specified values export file sdf elem 1 expr 1 elem 2 expr 2 rules uses rules to specify the elements to be exported see the following reference pages for full general information import export import from or export to a file cloudimport cloudexport import from or export to a cloud object importstring exportstring import from or export to a string importbytearray exportbytearray import from or export to a byte array import elements general import elements elements list of elements and options available in this file summary summary of the file rules list of rules for all available elements data elements molecule a symbolic representation of the molecule model molecule n a symbolic representation of the n molecule metadata an association containing the metadata from the file metadata n the metadata for the n molecule graphics elements graphics3d 3d renderings of all molecule models stored in the file graphics3d n 3d rendering of the n molecule structurediagram 2d structure formulas of all molecules data representation elements edgerules connectivity data given as a list of lists of rules edgetypes bond types as a list of lists of strings formalcharges charges of the atoms given by vertextypes massnumbers isotope mass numbers vertexcoordinates 2d or 3d atomic coordinates typically in angstroms vertextypes all atoms or groups constituting the molecule typically given as a list of chemical element abbreviations import file sdf edgerules gives the connectivity data for all chemical compounds stored in the file as a list of lists of rules export file sdf vertlist coordlist vertextypes vertexcoordinates creates an sdf file from a specification of atom types and their 2d or 3d coordinates meta information element header header information for each molecule stored in the file given as a list of strings options general import options imagesize automatic specifies the overall size of the graphics to display background white specifies what background color to use viewpoint automatic point in space from which the 3d model is to be viewed with the default setting viewpoint automatic the wolfram language automatically calculates the optimal viewing angle for the imported molecule geometry selecting a 3d rendering style rendering ballandstick specifies the visualization method possible settings for rendering are ballandstick displays atoms and bonds as a ball and stick model spacefilling atoms shown as overlapping spheres wireframe bonds rendered as lines general export options include coordinatedimension automatic whether to include 2d or 3d coordinates header automatic a string to use on the first line includehydrogens automatic whether to include explicit hydrogen atoms with the setting of coordinatedimension automatic 3 will be chosen if the molecule expression contains explicit atomcoordinates and 2 will be chosen if the molecule contains atomdiagramcoordinates if neither is present coordinates will be generated automatically in this case three or two dimensional coordinates will be used depending on whether the molecule has explicit or implicit hydrogens respectively examples open all close all basic examples 2 show the import elements available in an sdf file wolfram language code import exampledata alkanes sdf elements import all molecules wolfram language code import exampledata alkanes sdf import the second molecule from the file wolfram language code import exampledata alkanes sdf molecule 2 import meta information for the second compound in this file wolfram language code import exampledata alkanes sdf metadata 2 this gives the atom types and their 2d coordinates for all structure diagrams stored in the file wolfram language code import exampledata alkanes sdf vertextypes vertexcoordinates export a list of molecules to an sdf file wolfram language code import exampledata alkanes sdf this creates an sdf file from the previous output wolfram language code export alk sdf export options 2 coordinatedimension 1 wolfram language code flatten import export test sdf molecule trinitrotoluene coordinatedimension 2 3 wolfram language code keys options header 1 use a list of pubchem compound ids to label the output wolfram language code exportstring molecule methane molecule propane sdf header cid297 cid6334 see also import export cloudexport cloudimport molecule formats fasta mol pdf xyz hin related guides 3d geometry modeling formats importing exporting listing of all formats scientific medical data formats chemical biomolecular formats history introduced in 2008 7 0 updated in 2019 12 0 give feedback top introduction for programmers introductory book wolfram function repository wolfram data repository wolfram data drop wolfram language products top products wolfram one mathematica ai access compute services system modeler wolfram alpha notebook edition wolfram alpha pro mobile apps wolfram engine wolfram player volume site licensing server deployment options consulting wolfram consulting repositories data repository function repository community paclet repository neural net repository prompt repository wolfram language example repository notebook archive wolfram github 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