[Cdk-devel] [ cdk-Patches-3032840 ] Support for multi molecule mol2 files

[SourceForge.net <no...@so...>]

Patches item #3032840, was opened at 2010-07-21 19:02
Message generated for change (Comment added) made by rajarshi
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3032840&group_id=20024

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Revision
Status: Open
Resolution: None
Priority: 7
Private: No
Submitted By: Rajarshi Guha (rajarshi)
Assigned to: Rajarshi Guha (rajarshi)
Summary: Support for multi molecule mol2 files

Initial Comment:
Patch adds support for mulkti molecule mol2 files, so that all molecules can be read into a List of molecules. Added unit testa and test file

----------------------------------------------------------------------

>Comment By: Rajarshi Guha (rajarshi)
Date: 2010-07-22 08:51

Message:
Sorry about the whitespace, but it was getting difficult to debug with the
current formatting and I had rearranged a lot of the old code anyway

Updated note on OB type fixes

Regarding, SINGLE_OR_DOUBLE - yes, it would be nice to have that, but its
not in the API at this point right?

Added missing @Test annotation and updated unit tests to check atom
counts.

Replaced patches with the 2 new patches

----------------------------------------------------------------------

Comment By: Egon Willighagen (egonw)
Date: 2010-07-22 03:13

Message:
Rajarshi, some comments:

* please do not change whitespace, or as little as possible
* can you please add info on which OB version this is for,
  and preferably where to find the upstream bug report?

+                        // fix OpenBabel atom type codes to SYBYL
specification
+                        if ("S.o2".equals(atomTypeStr)) atomTypeStr =
"S.O2";
+                        if ("S.o".equals(atomTypeStr)) atomTypeStr =
"S.O";

* we really need that IBond.Order.SINGLE_OR_DOUBLE, not? :)


+                                } else if ("am".equals(orderStr) ||
"ar".equals(orderStr)) {
+                                   
bond.setOrder(CDKConstants.BONDORDER_SINGLE);
+                                    bond.setFlag(CDKConstants.ISAROMATIC,
true);
+                                   
bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true);
+                                   
bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true);

* why is this test not tested anymore? ->

-    @Test public void testNCIfeb03_2D() throws Exception {
+     public void testNCIfeb03_2D() throws Exception {

* I suggest to test that the first IAtomContainer has the correct number
of atoms and bonds too, to test that we do not loose the last or first atom
or so, or do not reset properly



----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3032840&group_id=20024