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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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