Message Boards Message Boards

0
|
4682 Views
|
4 Replies
|
1 Total Likes
View groups...
Share
Share this post:

How do I create a list and/or table? Finding curated information.

I´m desperately trying my way to get list of things computed in wolfram. List of all organic compounds known for examples. List of neurotransmitters. List of x,y z and even better if I can compare them by structure. I tried 3d structure but I can't seem to get multiples...

I have tried to locate the syntax to these things... anybody?

POSTED BY: Henrik Martenzon
4 Replies

As Bruce Miller points out, the Documentation Center is the key place to go generally to drill down for information on what's in the Wolfram Language. It is a huge resource and works pretty well in finding content listings that are relevant. Once you are on any given page you can spider out from there from the contained links and resources. It's what I constantly do as I write code since I do not remember (nor am I at all up to date) with what's in the system. But I remind myself what things that I know that I know by just diving into the documentation center.

That said, you may have something else in mind. Perhaps you are wanting to create a targeted resource to a particular field--for example organic compounds. Though you could create a user interface to do this using Entities and ChemistryData and so on, similar to the Google Instant approach, it might be very slow since generally each query as you type needs to reach out to the cloud to gather relevant content. A solution to this might be to download the relevant namespace materials and build the application based on a local data set of these...

POSTED BY: David Reiss

To start looking for what Mathematica has on Chemistry, type "chemistry" into the documentation search field.

enter image description here

In the page for ChemicalData, for example, open the Details section for tables of the types of information available. enter image description here

POSTED BY: Bruce Miller

This will give you a list of all organic compound entities that Mathematica has available (warning: it is a long list!):

EntityList[EntityClass["Chemical", "Organic"]]

rather than execute that and fill up your screen, here are properties that you might access for these:

EntityValue[EntityClass["Chemical", "Organic"], "Properties"]

which gives

{EntityProperty["Chemical", "AcidityConstants"], 
 EntityProperty["Chemical", "AdjacencyMatrix"], 
 EntityProperty["Chemical", "AlternateNames"], 
 EntityProperty["Chemical", "AtomPositions"], 
 EntityProperty["Chemical", "AutoignitionPoint"], 
 EntityProperty["Chemical", "BeilsteinNumber"], 
 EntityProperty["Chemical", "BlackStructureDiagram"], 
 EntityProperty["Chemical", "BoilingPoint"], 
 EntityProperty["Chemical", "BondCounts"], 
 EntityProperty["Chemical", "BondEnergies"], 
 EntityProperty["Chemical", "BondLengths"], 
 EntityProperty["Chemical", "CASNumber"], 
 EntityProperty["Chemical", "CHBlackStructureDiagram"], 
 EntityProperty["Chemical", "CHColorStructureDiagram"], 
 EntityProperty["Chemical", "CIDNumber"], 
 EntityProperty["Chemical", "Codons"], 
 EntityProperty["Chemical", "ColorStructureDiagram"], 
 EntityProperty["Chemical", "CombustionHeat"], 
 EntityProperty["Chemical", "CriticalPressure"], 
 EntityProperty["Chemical", "CriticalTemperature"], 
 EntityProperty["Chemical", "Density"], 
 EntityProperty["Chemical", "DielectricConstant"], 
 EntityProperty["Chemical", "DipoleMoment"], 
 EntityProperty["Chemical", "DOTHazardClass"], 
 EntityProperty["Chemical", "DOTNumbers"], 
 EntityProperty["Chemical", "EdgeRules"], 
 EntityProperty["Chemical", "EdgeTypes"], 
 EntityProperty["Chemical", "EGECNumber"], 
 EntityProperty["Chemical", "ElectronAffinity"], 
 EntityProperty["Chemical", "ElementCounts"], 
 EntityProperty["Chemical", "ElementMassFraction"], 
 EntityProperty["Chemical", "ElementTypes"], 
 EntityProperty["Chemical", "EUNumber"], 
 EntityProperty["Chemical", "FlashPoint"], 
 EntityProperty["Chemical", "FormalCharges"], 
 EntityProperty["Chemical", "FormattedName"], 
 EntityProperty["Chemical", "Formula"], 
 EntityProperty["Chemical", "FormulaString"], 
 EntityProperty["Chemical", "FusionHeat"], 
 EntityProperty["Chemical", "GmelinNumber"], 
 EntityProperty["Chemical", "HBondAcceptorCount"], 
 EntityProperty["Chemical", "HBondDonorCount"], 
 EntityProperty["Chemical", "HenryLawConstant"], 
 EntityProperty["Chemical", "HildebrandSolubility"], 
 EntityProperty["Chemical", "HillFormula"], 
 EntityProperty["Chemical", "HillFormulaString"], 
 EntityProperty["Chemical", "InChI"], 
 EntityProperty["Chemical", "IonCounts"], 
 EntityProperty["Chemical", "IonEquivalents"], 
 EntityProperty["Chemical", "Ions"], 
 EntityProperty["Chemical", "IsoelectricPoint"], 
 EntityProperty["Chemical", "IsomericSMILES"], 
 EntityProperty["Chemical", "IUPACName"], 
 EntityProperty["Chemical", "LewisDotStructureDiagram"], 
 EntityProperty["Chemical", "LightSpeed"], 
 EntityProperty["Chemical", "LogAcidityConstants"], 
 EntityProperty["Chemical", "LowerExplosiveLimit"], 
 EntityProperty["Chemical", "MDLNumber"], 
 EntityProperty["Chemical", "MeanFreePath"], 
 EntityProperty["Chemical", "MeltingPoint"], 
 EntityProperty["Chemical", "Memberships"], 
 EntityProperty["Chemical", "MolarMass"], 
 EntityProperty["Chemical", "MolarVolume"], 
 EntityProperty["Chemical", "MolecularMass"], 
 EntityProperty["Chemical", "MoleculePlot"], 
 EntityProperty["Chemical", "Name"], 
 EntityProperty["Chemical", "NetCharge"], 
 EntityProperty["Chemical", "NFPAFireRating"], 
 EntityProperty["Chemical", "NFPAHazards"], 
 EntityProperty["Chemical", "NFPAHealthRating"], 
 EntityProperty["Chemical", "NFPALabel"], 
 EntityProperty["Chemical", "NFPAReactivityRating"], 
 EntityProperty["Chemical", "NonHydrogenCount"], 
 EntityProperty["Chemical", "NonStandardIsotopeCount"], 
 EntityProperty["Chemical", "NonStandardIsotopeCounts"], 
 EntityProperty["Chemical", "NonStandardIsotopeNumbers"], 
 EntityProperty["Chemical", "NSCNumber"], 
 EntityProperty["Chemical", "OdorThreshold"], 
 EntityProperty["Chemical", "OdorType"], 
 EntityProperty["Chemical", "PartitionCoefficient"], 
 EntityProperty["Chemical", "pH"], 
 EntityProperty["Chemical", "Phase"], 
 EntityProperty["Chemical", "ProtonAffinity"], 
 EntityProperty["Chemical", "RefractiveIndex"], 
 EntityProperty["Chemical", "RelativeMolecularMass"], 
 EntityProperty["Chemical", "Resistivity"], 
 EntityProperty["Chemical", "RotatableBondCount"], 
 EntityProperty["Chemical", "RTECSClasses"], 
 EntityProperty["Chemical", "RTECSNumber"], 
 EntityProperty["Chemical", "SideChainLogAcidityConstant"], 
 EntityProperty["Chemical", "SMILES"], 
 EntityProperty["Chemical", "Solubility"], 
 EntityProperty["Chemical", "SpaceFillingMoleculePlot"], 
 EntityProperty["Chemical", "StandardName"], 
 EntityProperty["Chemical", "SurfaceTension"], 
 EntityProperty["Chemical", "TautomerCount"], 
 EntityProperty["Chemical", "ThermalConductivity"], 
 EntityProperty["Chemical", "TopologicalPolarSurfaceArea"], 
 EntityProperty["Chemical", "UpperExplosiveLimit"], 
 EntityProperty["Chemical", "VanDerWaalsConstants"], 
 EntityProperty["Chemical", "VaporDensity"], 
 EntityProperty["Chemical", "VaporizationHeat"], 
 EntityProperty["Chemical", "VaporPressure"], 
 EntityProperty["Chemical", "VertexCoordinates"], 
 EntityProperty["Chemical", "VertexTypes"], 
 EntityProperty["Chemical", "Viscosity"]}

Here are the first few of the (huge number of) organics that are returned by the

someOrganics={Entity["Chemical", "1,3Propanediol(2)13C1"], 
 Entity["Chemical", "1,4BisTrifluoromethylbenzene13C6"], 
 Entity["Chemical", 
  "1R,2RMinusPseudoephedrineNMethylHydrochlorideD3"], 
 Entity["Chemical", "2Butoxyethanol(O)D1"], 
 Entity["Chemical", "2Chlorodiphenyl(2,3,4,5,6)D5"], 
 Entity["Chemical", "4FluorobenzoylChloride(Carbonyl)13C1"], 
 Entity["Chemical", "4HydroxybenzoicAcid13C1"], 
 Entity["Chemical", "5Fluorouracil15N2"], 
 Entity["Chemical", "Acetamide(2)D3"], 
 Entity["Chemical", "Benzene(1,2,3,5)D4"]};

And from these and various properties (not all of which are available for each given Entity) you can get information like this

coords= EntityValue[Entity["Chemical", "Benzene(1,2,3,5)D4"], EntityProperty["Chemical", "VertexCoordinates"]]

Which gives

{{340.3, 100.}, {253.69, 50.}, {426.9, 
  50.}, {253.69, -50.}, {426.9, -50.}, {340.3, -100.}, {340.3, 
  162.}, {200., 81.}, {480.59, 
  81.}, {200., -81.}, {480.59, -81.}, {340.3, -162.}}

And you can visualize this like this, for example,

Graphics[{AbsolutePointSize[10], Point[coords]}]

I hope this helps to get you started...

POSTED BY: David Reiss

David Reiss, This was highly appreciated. I didn't have time to thank you before but thanks a lot!

I´m interested on building on that code the same way Google Instant works. If I'm interested in a specific topic but I don´t know exactly who to navigate to my query, what terminology is the most useful to search Wolfram for what is possible to search?

If I'm interested in chemistry for example, I would like to know what kind of information wolfram has access to and how I would build my query. The programming community is rather fond of every man try coding for themselves and then ask for help, as a sign of respect and effort put forth. This is not to be confused with such lack of effort.

Do you know whether its possible to search directly in wolfram to obtain a list of cheat sheets for specific area?

POSTED BY: Henrik Martenzon
Reply to this discussion
Community posts can be styled and formatted using the Markdown syntax.
Reply Preview
Attachments
Remove
or Discard

Group Abstract Group Abstract