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Import coordinates widget
Leif Laaksonen & Eero Häkkinen CSC 2002
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This is the main facility to import atom information (including coordinates)
into gOpenMol. This is almost always the first step because gOpenMol has to
know the molecular topology of the system before it can plot properties or
analyze trajectory information.
The supported file types can bee seen on the right side with the
radio buttons. There is also a button
to indicate that the next structure is added (appended) to the current
display. This new structure goes into e new data structure and it is not
possible to make bonds between atoms in different data structures.
With the file browser it is possible to change the directory and filter
the files with special file extensions. If the user has not done any
reconfiguration the default file extensions are applied. The file extensions
can be changed with the define command.
Supported file formats
gOpenMol support a variety of coordinate input files. Most are fully
readable formatted files. The supported file formats are:
- ADF
- Amsterdam Density Functional (ADF) output log file
- CHARMm/CHARMM
- CHARMM coordinate (crd) file. For the format please look into your
QUANTA/CHARMM documentation or the source code.
- CML
- Coordinate information in the Chemical Markup Language (CML, http://www.xml-cml.org/).
- Chem3D
- Binary Chem3D coordinate file (the plugin must be enabled)
- DL_Poly
- Coordinate information from the DL_Poly program.
- Frame
- The coordinates are taken from a trajectory file.
- GAMESS
- The GAMESS PUNCH file (dat) containing the MOLPLT infromation produced
with the MOLPLT=.TRUE. option.
- Gaussian
- The coordinates are imported from a GAUSSIANXX formatted checkpoint
file.
- GROMACS
- GROMACS coordinate data file.
- GROMOS96
- GROMOS96 coordinate data file.
- HYPERCHEM
- HyperChem input coordinate (hin) file.
- INSIGHT
- Insight coordinate (car) file.
- JAGUAR
- Coordinates from the Jaguar program.
- Mol2
- Mol2 coordinate file format.
- MOPAC
- Coordinates are imported from a MOPAC unformatted graphics output file.
- MUMOD
- Coordinate format used by the MUMOD program by Dr. Olle Teleman.
- OPENMOL
- Formatted coordinate input file to OpenMol.
- PDB
- The standard Brookhaven Protein Data Bank format.
- Spartan
- Spartan binary coordinate file (the plugin must be enabled)
- TINKER
- The Tinker coordinate input format.
- TURBOMOLE
- Coordinates from the TurboMole program.
- UHBD
- University of Houston Brownian Dynamics (UHBD) qcd coordinate reader.
- USER
- The user defined coordinate input reader.
- XMOL
- Xmol coordinate file format. The file can contain multiple entries
but gOpenMol reads only the first entry.
- XYZ
- Simple xyz coordinate input format.
- YASP
- Coordinate input file to the YASP program by Dr. Florian Muller-Plathe.
A file is selected to be processed by gOpenMol either by a
rapid double click on the file name or a single click on the
file name and a click at the Open button.
It is possible to "Peek" or look into a file before it is imported by
pressing the Peek button when a file name is defined.

The file browser is started by clicking on the Browse button.

If you are using a file extension that is not by default
known to gOpenMol you can unclick the "Select file format by extension"
and you get the list of supported gOpenMol input readers.

User defined input filter
The USER option for the input filters is a user defined Tcl script
that reads a user defined input format.
The called Tcl procedure is: lulReadUSERCoordinates FileName Action
Where the FileName is the name of the file and
the variable Action must be either 0 (=no append) or
1 (=append). Depending on if the structure will be appended to the
structure list of if it will be only one.
The code is in the /data/gopenmolrc.tcl file.
Line command: see import command
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LUL/2002/09
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