Stereo Analysis - calculating stereo descriptors

This manual gives you a walk-through on how to use the Stereo Analysis module:

Introduction

Stereochemistry involves the study of the relative spatial arrangement of atoms and their transformations. Stereochemistry defines different isomerisms that describe the molecule's behaviour in the space. These isomer groups cover the entire space of organic molecules. We do not give further details on stereochemistry here, instead we refer to Marvin's stereochemistry summary.

It can be important to determine a molecule's stereochemical behaviour. This can be achieved by calculating stereochemical descriptors for the molecule.

ChemAxon's Stereo Analysis module is able to calculate stereochemical descriptors for a molecule, giving an analysis of the stereochemical properties present in the input.

Usage

The stereo analysis functionality is built in different ChemAxon products.

Stereo analysis with cxcalc

Stereo Analysis module is integrated into the cxcalc command line tool. The general command syntax is

cxcalc [general options] [input files/strings] stereoanalysis [stereoanalysis options] [input files/strings]

where the stereoanalysis options are the following:

stereoanalysis options: -h --help this help message -T --type stereo descriptor type [tetrahedral | cistrans | axial | atrop] (default: not set)

Examples

Here are some examples of how to use the stereo analysis module via cxcalc :

  • Calculating tetrahedral stereo descriptors for the following molecule:

    images/download/thumbnails/1806669/sa1.png

    cxcalc stereoanalysis "[H][[email protected]](Cl)(Br)I"

    The output shows the recognized tetrahedral stereo descriptors:

    TETRAHEDRAL [1] - [4, 3, 2, 0] : S

  • Calculating cis-trans stereo descriptors:

    images/download/thumbnails/1806669/sa2.png

    cxcalc stereoanalysis "Cl/C=C\C=C\Cl"

    The output shows the recognized cis-trans stereo descriptors:

    CISTRANS [1, 2] - [0, 3] : Z  CISTRANS [3, 4] - [2, 5] : E
  • Calculating axial stereo descriptors for a molecule:

    images/download/thumbnails/1806669/sa3.png

    cxcalc stereoanalysis CC=C=CC

    The output shows the recognized axial stereo descriptors:

    AXIAL [1, 3] - [0, 4] : WIGGLY

  • Calculating atrop stereo descriptor for a molecule:

    images/download/thumbnails/1806669/sa4.png

    cxcalc stereoanalysis "CCC1=C(C(C)=CC=C1)C1=CC=CC=C1C"

    The output shows the recognized atrop stereo descriptors:

    ATROP [3, 9] - [4, 2, 14, 10] : UNKNOWN
  • Calculating all stereo descriptors for a molecule with different stereo features:

    images/download/thumbnails/1806669/sa5.png

    cxcalc stereoanalysis "ClC(Br)C1CCCC(C1)/C=C/Cl"

    The output shows the recognized stereo descriptors:

    TETRAHEDRAL [7] - [9, 8, 6] : UNKNOWN TETRAHEDRAL [3] - [1, 8, 4] : UNKNOWN TETRAHEDRAL [1] - [2, 0, 3] : UNKNOWN CISTRANS [9, 10] - [7, 11] : E
  • Listing just the cis-trans stereo descriptors for the previous molecule:

    cxcalc stereoanalysis -T cistrans "ClC(Br)C1CCCC(C1)/C=C/Cl"

    The output is:

    CISTRANS [9, 10] - [7, 11] : E

Stereo analysis with Chemical Terms

The stereo analysis module is also integrated into ChemAxon's Chemical Terms language. The stereo descriptors can be calculated by two different functions in Chemical Terms:

  • stereoanalysis(): calculates and returns stereo descriptors of all types for the input molecule.

  • stereoanalysis(T): calculates and returns stereo centers of type T. T can be any stereo function defined in the API.

Examples

The following examples show how the functions above can be used with the Chemical Terms evaluator command line tool:

  • Calculating all stereo descriptors for geldanamycin:

    evaluate -e "stereoanalysis()" geldanamycin

    The output is:

    TETRAHEDRAL [26] - [27, 23, 31] : S CISTRANS [18, 20] - [16, 19, 21] : E TETRAHEDRAL [36] - [37, 2, 34] : R TETRAHEDRAL [4] - [3, 6, 5] : R CISTRANS [21, 22] - [20, 23] : Z TETRAHEDRAL [34] - [36, 33, 35] : S TETRAHEDRAL [23] - [24, 26, 22] : S TETRAHEDRAL [2] - [1, 36, 3] : S CISTRANS [31, 33] - [26, 32, 34] : E
  • Calculating only tetrahedral stereo centers for the same molecule:

    evaluate -e "stereoanalysis('tetrahedralStereoCenters')" geldanamycin

    The output is:

    2;4;23;26;34;36
  • Calculating the number of unknown, resolved, tetrahedral stereocenters for the following molecule with the count() function:

    images/download/thumbnails/1806669/stereo_CT.png

    evaluate -e "count(stereoanalysis('unknownResolvedStereoCenters'))" "C[[email protected]@H]1OP(O)(=O)O[[email protected]@H](C)C1C |o1:7,r|"
  • Finding only the carbon tetrahedral stereocenters can be done using the filter() function for the same molecule:

    evaluate -e "filter(stereoanalysis('tetrahedralStereoCenters'), \"match('C')\")" "C[[email protected]@H]1OP(O)(=O)O[[email protected]@H](C)C1C |o1:7,r|"