Read Structure

Description

Read structural and volumetric chemical data. To specify a trajectory the file could contain a single structure (single frame); a sequence of structures (Multiframe from file); a sequence of files, each containing only one structure, sequentially numbered (Multifile); a list of file names, one per line, each containing only one structure (Frame list from file). Some format needs an additional file name before starting the reading.

Input Ports

None

Parameters

Select file format list Select the format of the file to be read. The available formats are listed on the STM4 web page.

File file browser The file name to be read or, for the Multifile trajectory, the first file in the sequence.
Additional file file browser Some file formats need an additional file. For example the DCD format needs a PDB file to specify the structure plus a DCD file to specify the trajectory. This file browser appears only if a format requiring an additional file has been selected.
Status line label Messages from the reader.
Read mode selection radio buttons Select how trajectories are read. Possible values are:
Single frame
The file contains a single structure.
Multiframe from file
The file contains a sequence of structures.
Multifile
The trajectory is specified by a sequence of files, each containing only one structure, sequentially numbered.
Frame list from file
The file contains a list of file names, one per line, each containing only one structure. Empty lines or lines starting with # are ignored.
Loop Loop module panel Cycle between the various steps. The first step is numbered 1 and the total number of steps is automatically computed from the input file.
Reader controls panel Controls for the specific format selected.
Read structure bonds mod_panel The panel for a Compute Bonds module that compute the bonds for the structure read.

Output Ports

structure_out MoleculeType Molecular structure data read.
volume_out Field_Unif The volumetric data, if present, with one or two components per node. Beware that the uniform field has been skewed, using xform, to match the unit cell.
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