MolDB6
a free software package for creating a web-based, searchable molecular
structure/reaction database
Norbert Haider, University of
Vienna, 2014-2018
norbert.haider@univie.ac.at
These instructions explain how to set up MolDB6 as a web-based, fully
searchable
molecular structure database. Structures and data can be added via a
web interface or by import from an MDL SD file (at the server
command-line). This import option
is shown by an example (see below), using the SD files which are freely
available from the PubChem FTP site at ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF/.
Analogously, reactions and data can be imported from an MDL RD file.
For some information about the original ideas, please visit
moldb.html
The previous version, MolDB5R, is documented at
moldb5rdoc.html
MolDB6 is a collection of fully functional PHP scripts for running a
structure/reaction database with search options for text, functional
groups, and
structure/substructure. Included are also some Perl scripts for
database setup and data import/export
from/to an SD or RD file.
Download: ../download/chemistry/moldb/moldb6.tar.gz
Some screenshots: moldb6screenshots.html
Features
- Structure+data import from SD files, export to SD files
- Reaction+data import from RD files, export to RD files
- Text search
- Browse functioanlity
- Functional group search
- Extended functional group search in reaction data
collections (creation or loss of groups)
- Structure/substructure/similarity search in structure data
collections
- Structure/substructure search in reaction data collections
- Support for multiple data collections within one MySQL
database
- All search operations (text, functional groups,
substructure) can span multiple data collections
- Web-based administration tool for data collection
management, structure and data input/editing
- Runs on different operating systems: Linux, Mac OS X,
Windows
New features in MolDB6 as
compared to MolDB5R:
- Support for different graphical structure editors (JME,
JSME, GGA Ketcher, FlaME), user-selectable
- When used with JSME, mobile devices (iOS and Android
smartphones and tablets) are fully supported as clients
- Structure and reaction structure search are combined in one
search form
- Automatically generated data fields for molecular formula
and molecular weight
- Optional: automaticallly generated data field for InChIKey
strings
- Short-cut links for copying and erasing (in addition to
editing) an entry from the "details" page
- Easy cloning of the data structure of existing data
collections
Documentation
Features
Technical background
Installation
Using MolDB6
Administration of MolDB6
Appendix A
(permissions and privileges)
Appendix B
(configuration file settings)
Appendix C
(performance tuning)
NH, 2014-08-20; last update: 2018-01-12