Dear PyMOL users
I'm using MOPAC to do quantum chemical calculations of enzymes.
I'm wondering if PyMOL could be used to output a PDB file in MOPAC format.
An example of this format is here:
C( 1 LEU 24) 9.04500000 +0 4.94400000 +0 19.45600000 +0
0.4527
O( 2 LEU 24) 8.05600000 +1 5.59200000 +1 19.15100000 +1
-0.5188
H( 3 LEU 24) 10.04000000 +1 5.40500000 +1 19.57200000 +1
0.1090
N( 4 ASP 25) 9.08100000 +1 3.59500000 +1 19.71600000 +1
-0.4910
C( 5 ASP 25) 7.89300000 +1 2.76600000 +1 19.57800000 +1
-0.0307
C( 6 ASP 25) 7.70800000 +0 1.88300000 +0 20.81000000 +0
0.3465
O( 7 ASP 25) 8.44900000 +1 0.95600000 +1 21.12200000 +1
-0.4321
C( 8 ASP 25) 7.97500000 +1 1.90500000 +1 18.33900000 +1
-0.4663
C( 9 ASP 25) 6.66900000 +1 1.15400000 +1 18.28400000 +1
0.7179
O( 10 ASP 25) 5.64600000 +1 1.70700000 +1 18.79700000 +1
-0.7657
O( 11 ASP 25) 6.69700000 +1 0.02300000 +1 17.72800000 +1
-0.6565
H( 12 ASP 25) 7.03100000 +1 3.43800000 +1 19.54700000 +1
0.1841
H( 13 ASP 25) 8.81500000 +1 1.20200000 +1 18.39200000 +1
0.1979
H( 14 ASP 25) 8.10000000 +1 2.50700000 +1 17.43400000 +1
0.1919
H( 15 ASP 25) 9.95700000 +1 3.14300000 +1 19.95300000 +1
0.2791
H( 16 ASP 25) 6.98200000 +1 2.29500000 +1 21.52500000 +1
0.1043
What I'm especially interested in is the "+0" and "+1" flags, which
sometimes are required but are quite inconvenient to find for single
atoms in a large file, it's also very error prone. The parenthesis after
the atom type can be omitted, also the very last column (0.4527, ...)
Would it be possible to write a PyMOL plugin, where single atoms could
be added to a selection (using point-and-click) and when saving to the
MOPAC file, the selected atoms would be written with the "+0" flags?
Any hints on what part of the API to look at are very appreciated.
Best regards
Martin
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