[Chimera-users] classifying contact interactions

[M. Shahid]

Dear All,

I have a question regarding the contact interactions between a
protein-ligand complex.

I can retrieve the contacts by the findclash command in --nogui mode as
below:
chimera --nogui protligcomplex.pdb clash.com

and similarly I can find the hbonds.

The output I am getting is as below:
--------------------------------------------------------------------------------
32 contacts
atom1  atom2  overlap  distance
LIG 1 H    ALA 265.A O     1.045  1.435
LIG 1 O    ALA 265.A O     0.550  2.430
LIG 1 N   GLU 169.A OE2   0.439  2.666
LIG 1 H  GLU 169.A CD    0.116  2.584
LIG 1 O   ASN 253.A 1HD2  0.094  2.386
LIG 1 H    ALA 265.A C     0.090  2.610
LIG 1 C    ALA 265.A O     0.059  3.121
LIG 1 N   ASN 253.A OD1   -0.037  3.142
LIG 1 C    ALA 265.A O     -0.039  3.219
LIG 1 N   GLU 169.A HG3   -0.072  2.697
LIG 1 C   PHE 168.A HB2   -0.081  2.781
LIG 1 N   GLU 169.A CG    -0.113  3.438
LIG 1 N   GLU 169.A CD    -0.125  3.450
LIG 1 N   GLU 169.A CD    -0.128  3.453
LIG 1 C    MET 270.A HG2   -0.140  2.840
LIG 1 N   PHE 168.A CD2   -0.163  3.488
.......... .... ... .. .
--------------------------------------------------------------------------------

Now I want to further classify these contact interactions into more other
types:
Aromatic and Ionic (anion < - > cation).
Is there any way in Chimera to achieve this?
Or if I want to do it with some scripting, which atoms I would say are
involved in ionic
and aromatic interactions considering the distance value as well?
I would be very much grateful if someone suggest me a way to do this.

Thanks,

Best regards,

--
Shahid.
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