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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.

Development

CcpNmr ChemBuild was written by Tim Stevens with contributions from Magnus Lundborg.

The program was initially created using Python 2 and PySide, the Python bindings to Qt. ChemBuild was the first of the ‘Next Generation’ of CCPN applications that use a Qt rather than Tk based graphical interface.

The program has now been updated to use Python 3 and PyQt4 (another wrapper around Qt).

A screenshot from CcpNmr ChemBuild version 1.0.

A screenshot from CcpNmr ChemBuild version 1.0.

Limitations and Future Features

For now, import and export of CCPN ChemComps in ChemBuild uses the CCPN v2 API, not the CCPN v3 API.

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 may 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.