Differences

This shows you the differences between two versions of the page.

--- structurelevels [2012/10/15 12:24] – created sanmark
+++ structurelevels [2013/02/07 09:59] (current) – spell fix sanmark
@@ Line 3: / Line 3: @@
 In the mcule database chemical structures can be described in three structure specification levels: conformers, structures and compounds.
-//**Conformers**// have a fully specified 3D structure including the position of all hydrogens. They are in a fixed tautomeric and protonation state, and they have a known absolute [[stereonotations|stereo configuration]] (as reflected in the geometry).
+//**Conformers**// have a fully specified 3D structure including the position of all hydrogens. They are in a fixed [[http://en.wikipedia.org/wiki/Tautomer|tautomeric]] and protonation state, and they have a known absolute [[stereonotations|stereo configuration]] (as reflected in the geometry).
 //**Structures**// refer to molecular structures representing a fixed tautomeric and protonation state as reflected by the 2D structural formula. They can have a fully defined or a partially or fully unknown/undefined [[stereonotations|stereo configuration]].
 //**Compounds**// refer to chemical compounds that can be represented by multiple molecular structures, i.e. with multiple tautomeric and protonation forms. Their [[stereonotations|stereo configuration]] can be well-defined as well as fully or partially unknown / undefined, similarly to the case of //structures//.
+^Structure specification level ^Identical                                           ^Different ^
+|Compound                      |Mesomers, tautomers, protonation states, conformers | Stereoisomers |
+|Structure                     |Mesomers, conformers                                | Stereoisomers, tautomers, protonation states |
+|Conformer                     |Mesomers                                            |Stereoisomers, tautomers, protonation states, conformers |
+Chemical structures with different stereo configurations are distinguished at all specification levels. Depending on the stereo configuration type, they represent a single isomer or a set of potential isomers and/or mixtures of isomers. Their stereo configurations are treated identical if and only if the represented isomers / set of isomers are identical. If the configuration differs, the chemical structures are treated as different database entries.
+//Compounds// can have more symmetries than //structures//. In //compounds// neither the number of hydrogens nor the position of some hydrogens are fixed. A //compound// can represent all realistic tautomeric and protonation states (//structures//). Therefore those asymmetry centers that are present only in one potential //structure// (tautomer and protonation state) are not treated as stereogenic at the //compound level//. Similarly, some cis-trans bonds found in a //structure// might be missing from the corresponding //compound//.
+{{ :speclevel2.png |}}
+====Relations====
+The three structure levels have the following relations: //compounds// can have (can be represented by) multiple //structures//, and //structures// with well-defined, known configurations can have multiple //conformers//. Inversely, //conformers// have exactly one //structure//, and //structures// have exactly one //compound//.
+===Relation to products===
+//Product// is a special entry type that can appear on the mcule.com’s interface. It is connected to the chemical structures stored in the mcule database. Suppliers’ //products// are real, physical substances. Since these products can contain molecules in different tautomer and protonation states, their structural content can be best described at the //compound level//. The chemical content of products might be undetermined and in exceptional cases it can be changed, for example when supplier notices that the molecular structure was misdrawn or incorrectly determined previously.
+In the mcule system only //products// with determined structures are registered. In the rare event of //product// structure correction, the corrected new structure is registered and will be associated with the //product//. Their structures are represented by //compounds// in the database: products with structures drawn in a different tautomeric form or protonation state are treated structurally equivalent.
+===Comparison to user structures/conformers===
+During the registration user structures/conformers (link) are kept intact. Structural equivalence is not detected, all entries are registered with an unique identifier in the user database. The only restriction is that user structures should have 2D coordinates whereas conformers should have 3D coordinates.
+During calculations they are treated similar to //structures// and //conformers// of the mcule database. User structures are considered as being in that specific tautomer and protomer form represented in the 2D structure.