trisyoungs / aten Goto Github PK

Intensive routines are not threaded, so responsiveness of GUI (most
importantly the Canvas display) is poor to non-existent.

Original issue reported on code.google.com by [email protected] on 29 Apr 2008 at 8:51

aten: 2.1, windows: 7
I saved the default configuration as a prefs.dat file without changing any of the defaults. Aten creates the file C:\users\username\aten\prefs.dat with contents:

// Element Data // Program Preferences
When I restart aten I get the following in the console:

Error occurred here (line 2 in file 'C:\Users\sturgmancohen\aten\prefs.dat'):

^

And reports that preference file not found.

Processes requiring a valid forcefield expression will stop dead if all the
necessary terms are not found. Similarly, some processes do not require
intramolecular terms but will fail anyway if some of these terms are missing.

User should be able to choose between:
1. Stop and re-think.
2. Ignore missing FF terms.
3. Add missing FF terms to forcefield with default values. These may then
be adjusted in the FF editor.

Original issue reported on code.google.com by [email protected] on 29 Apr 2008 at 8:56

A method is required whereby filters can be reloaded while the code is
running (instead of having to restart).

Original issue reported on code.google.com by [email protected] on 29 Apr 2008 at 8:58

I am working with Windows 7 and version 2.1. I have reproduced this with the my own force field files and with force field files that come standard with aten. When I select a file to open, nothing happens in aten. No error message. No force field loaded.

Spacegroup definitions only include standard setting information -
alternative settings need to be implemented.

Original issue reported on code.google.com by [email protected] on 29 Apr 2008 at 8:49

• Develop a tool plugin with that users can select QM atoms and generate a template Py-ChemShell input script to edit

Simple:
1. Load any MSI file.
2. Observe lots of debug output and incorrect elements / coordinates in
loaded model.

Original issue reported on code.google.com by [email protected] on 29 Apr 2008 at 8:57

On Ubuntu Xenial (16.4) compiled with Qt 5.5.1, at least .xyz, .pdb and .mol2 output uses "," instead of "." as decimal separator, e.g.:

mol2:
@MOLECULE
PDB Model
3 0

SMALL
NO_CHARGES
Coordinates churned out by Aten

@ATOM
1 O 5,00000 9,20600 14,08800 O

 2      H     5,43000     9,96700    13,49700      H

 3      H     5,31900     9,36200    14,99300      H

PDB:

REMARK Aten-created PDB
TITLE PDB Model
CRYST1 1,000 1,000 1,000 90,00 90,00 90,00 P 1 1

ATOM 1 O0 MOL 0 5,000 9,206 14,088 1,00 1,00 O
ATOM 2 H0 MOL 1 5,430 9,967 13,497 1,00 1,00 H
ATOM 3 H0 MOL 1 5,319 9,362 14,993 1,00 1,00 H
TER
END

XYZ:

3
PDB Model
O 5,000000 9,206000 14,088000 0,000000
H 5,430000 9,967000 13,497000 0,000000
H 5,319000 9,362000 14,993000 0,000000

The problem seems to be caused by Qt localization settings.

A patch to fix missing include directories:
cubemodel.txt

How to reproduce:

1. Launch the program using 4K monitor (2x scaling)
2. Draw an atom or use selection tool