ChemProp Knowledge Base
Files not found for strange reasons
Large model collection crashes
Run-time popup warnings
Result export from ChemProp into Excel
Plain text editing, saving, exporting
Structure vs. substructure search
Normally, ChemProp should run on any version up from XP SP3. To run ChemProp smoothly in rare cases of serious problems, the XP SP3 compatiblity mode may be used . This can be achieved by right-clicking on the icons of the QSAR and database module in the start menu or on the desktop, and selecting properties, then opening the compatibility tab. The exact wording of these items depends on the language of the operating system. Further adaptations may be required for the database module. If you run into trouble, please contact us. With 64 bit versions (no matter whether XP, Vista, or 7), some particular models do not work. We are working on fixing this.
Occasionally, error messages may appear complaining on files not found, even though the files are there
definitely. There may be two reasons:
1. Some older modules written before 2000 rely on short path names. In particular, this affects the internal import from SMILES. The only workaround up to now is to completely install ChemProp in a folder tree with no individual part of the full path name exceeding 8 characters, and to avoid spaces in path/file names. This includes the program files,for that reason, ChemProp is not installed in the usual program folder.
2. User defined files treated in any parameter dialogue in the method selections should always be fully qualified, i.e., the full path name is required. Furthermore, as with 1., spaces in path and file names should be avoided.
Currently, the number of possible output values per run is limited due to system constraints. There is no fix limit, but depending on the system as well as on the selected models, about 30 to 40 output values are possible, otherwise the run will fail.
So, in case of an error message with a large model collection, please try to split into separate runs first.
The QSAR dialogue offers saving and loading of configurations as well as of job lists.
The General Options (button in the bottom right area) can be used to set up several pre-defined sets of general option, to define customized defaults, and to reset to the original ChemProp defaults.
In the Method area (bottom left quarter), several alternative opportunities to save and load method collections are provided. These are very powerful opportunities to define profiles. For details, please refer to the manual
The basic concept of ChemPop is to execute calculations in a batch-like mode, with user intervention at calculation start up only. However, some important warnings as e.g. chemical domain violation may be issued during the run in terms of popup messages. The user may disable this behaviour in the General Options dialogue (tab Miscellaneous) by checking off "Enable popup messages during calculations". In any case, all messages are being logged during the run, and can be accessed later from the overview page.
PreparationIn General Options, set the decimal delimiter to the character Excel expects, set the error / missing data string to any reasonable Excel function string (e.g., in the German Excel version, =nv() is a good choice), and leave the External HTML browser toggled off.
ExportIn the result window, with a proper Excel installation the right-click context menu should provide an Export to Excel opportunity. The triggered action depends on the position of the click: With clicking in the result table, the table will be exported solely and immediately. With clicking somewhere outside of the table, an export dialogue will appear. E.g., automatic date detection may be toggled off by means of the Options button in the right top corner of this dialogue in order to prevent data and CAS numbers from being miss-interpreted.
Use the Additional job results selector (middle right) to open plain text output in notepad.
In the Results section of the General Options dialogue, toggle Summaries in main and detail output provides access to column result and descriptor statistics. Once checked, the calculation detail output of fragment tables will be augmented by fragment statistics. Furthermore, the result output (both plain text and formatted) will contain a column statistics summary.
In the ChemProp main window, the Advanced queries and External substructure query items as well as the
Compounds menu provide means to lookup substructures in molecule lists or in the internal or external databases.
The search string will be modified automatically to obtain valid results, even for the typical case of more atoms in the molecule than looked for in the substructure string. For an exactly matching structure search, this needs to be toggled off, in order to obtain "not matching" in case of remaining atoms. It is very easy to extend the search string for that purpose:
- Preceed the string by "once\1 " (The space character is important!)
- Append "\A^|" at the end of the string
This directs the automated modification to a search for the opposite of any atom A^|, which never can match. Since the string is extended to a 2-lines search now, the additional 1 needs to be added according to the specification. Furthermore, once excludes multiple occurrences in larger structures.