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CcpNmr ChemBuild

About ChemBuild

CcpNmr ChemBuild is a graphical tool to construct chemical compound definitions for NMR. While there are many chemical structure drawing packages available ChemBuild was especially created to handle concepts like protonation variants and magnetic equivalence which are required for NMR resonance assignment. Several different chemical file formats are supported, including PDB, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files, which store NMR-aware information.

Download and installation:

Download ChemBuild as a beta-test version from the leading edge release.

 

Development

CcpNmr ChemBuild was initially written by Tim Stevens with recent contributions from Magnus Lundborg. The program was created using Python and PySide, the Python bindings to Qt. ChemBuild is the first of the ‘Next Generation’ of CCPN applications that use a Qt rather than Tk based graphical interface.

 

Relationship to Other CCPN Applications

CcpNmr ChemBuild does not require any of the other CCPN components to be installed for most of its operation. However, a proper CCPN installation (which includes the Python API) is required for importing and exporting CCPN ChemComp.xml files; the residue and compound templates used in CcpNmr Analysis and CcpNmr FormatConverter. For ChemBuild to use an existing CCPN installation the PYTHONPATH environment variable must be set appropriately. From the version 1.0 release there is a special CCPN API release that can be extracted on top of the separate ChemBuild installation.

A screenshot from CcpNmr ChemBuild version 1.0.

A screenshot from CcpNmr ChemBuild version 1.0.

Changes Since Early Releases

Version 0.6 introduced a slighly less cluttered graphical interface, including ‘toolbox’ sidepanels which may be shrunk and expanded by grabbing their edge. The panels on the left side deal with the addition of atoms and compounds. The panels on the right deal with the modification of atomic properties and the variant forms of a compound.

Version 1.0 saw the introduction of the 'skeleton' compound view, i.e. to render the molecule as a carbon backbone, mostly without hydrogens, on a regularised grid.

Stereocentres (tetrahedral, octahedral or pyramidal) may be added to compounds by specifying local stereochemistry, i.e. that bonds go ‘up’ or ‘down’. From version 1.0 the R/S labelling may be automatically deduced by the program.

Alpha/beta stereo labelling may now be added, i.e. for surgar rings, which automatically creates variants with alternative stereochemistries at the stated centre.

Dative bonds may now be specified; the type is set after bond addition.

A perodic table has been added so that the user can add any chemical element (without having to resort to SMILES strings).

A file browser tree has been added so that compounds may be loaded/imported via drag-and-drop.

Via the main menu, the user now has the ability to select a directory (containing ChemBuild compound files) which is added alongside the standard compound library. Thus the user can add compounds and fragments of their own specification.

 

Limitations and Future Features

In its present incarnation ChemBuild pretty much does what you instruct it to. There is a degree of automation, especially with regards to defining variant compound forms and magnetic equivalence. However, the system is not guaranteed to create only sane chemistry, e.g the are no proper aromaticity checks. As development continues this situation will improve, but for now it is up to the user to make sure that compounds make sense.

The atom naming, which is important for NMR assignment, is currently only basic. Automated naming is merely sequential and does not follow any IUPAC conventions. Nonetheless, the atom names can be set to whatever the user desires, as long as there is no repetition.

Stereochemical centres can be added to compounds by stating that bonds go ‘in’ or ‘out’, as is common chemical drawing packages. However, at present the system is only two-dimensional in the way that it stores coordinates, as such stereochemistry is stored with a chiral order rule (like the SMILES stereo system) and does not alter depth coordinates. Also, it should be noted that although stereochemistry will be saved in ChemBuild’s native file format there is currently no export of relative stereochemical information to CCPN XML files (except simple R/S/alpha/beta labels).

As time allows the system will be expanded to include chemical sub-graph searches to add classification keywords to any compound.

Import and export of further chemical file formats will be added, most probably InChI and CML, but there is no intention to cover a vast array of formats.

The ‘Auto-arrange’ feature uses a very simple 2D force field to assist the graphical display and is not designed represent real conformations of the compounds. Integration with proper 3D molecular dynamics may occur in the future.

At present ChemBuild will not export ChemCompCoord XML files; the atom coordinate records used by CCPN templates. This will only be introduced after the addition of better 3D molecular dynamics.

At some time in the future ChemBuild will be connected to CCPN’s ACPYPE service, which will allow the generation of topology and parameter files (including partial charges) for common molecular dynamics engines.

 

Bug Reporting

The currently available version is a beta test release and bug reports are welcome. Bug reports should be made via the CCPNMR mailing list at JISC.

As always, please be clear in your descriptions and give enough detail for the developers to be able to reproduce the problem from scratch. However, as ChemBuild is not yet part of the main CCPN release the bug fixing schedule will not necssarily be prompt and replies to small matters may not be issued. Once CcpNmr Analysis v3.0 is released ChemBuild will be incorporated into the main CCPN distribution and will share the same bug reporting mechanism.