[Cdk-devel] [ cdk-Patches-3075123 ] SMSD Chem filter updates plus few updates

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Patches item #3075123, was opened at 2010-09-24 23:08
Message generated for change (Settings changed) made by egonw
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Category: master
>Group: Needs Revision
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Asad (asadrahman)
Assigned to: Nobody/Anonymous (nobody)
Summary: SMSD Chem filter updates plus few updates

Initial Comment:
a) This patch deals with redesigning/refactoring of the chemfilters.
b) Changes in the bond energy calculation for "R" grp.
c) MCSPlus bug fix for size match.
d) VF lib improvised in terms of code layout and speed.


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>Comment By: Egon Willighagen (egonw)
Date: 2010-10-07 22:27

Message:
Asad,

some observations:

* the first patch removes a number of files, which cannot relate to the
commit message
* some patches have no content:

-rw-r--r-- 1 egonw egonw     0 2010-09-24 22:53
0006-Missed-few-changes-hence-I-have-to-copy-and-paste-th.patch
-rw-r--r-- 1 egonw egonw     0 2010-09-24 22:53
0009-removed-the-old-test-and-added-new-set-of-test-cases.patch

* patch 0001, MoleculeSanityCheck:

please use variables names of at least 3 characters, and provide some
information why it is OK to ignore an exception:

+            } catch (Exception e) {
+            }

* please do not sign-off your own patches
* patch 0003 seems to create files without license/copyright:


diff --git a/src/main/org/openscience/cdk/smsd/filters/BaseFilter.java
b/src/main/org/openscience/cdk/smsd/filters/BaseFilter.java
new file mode 100644
index 0000000..5b9c7b2
--- /dev/null
+++ b/src/main/org/openscience/cdk/smsd/filters/BaseFilter.java
@@ -0,0 +1,69 @@
+package org.openscience.cdk.smsd.filters;

* the constructor method of ChemicalFilters does not have JavaDoc
* the ChemicalFilters.sortResultsByEnergies() method should describe when
an exception is thrown:

+     * @throws CDKException

* the 0003 ChemicalFilter class contains this comment:

// actually, never thrown, but in the interface

Can you explain which API 'throws' a CDKException but never really does?
Can you please file a bug report for that?

* 0003 EnergyFilter has several methods without JavaDoc. For all @Override
methods, you can use:

/** {@inheritDoc} */

or so... search the existing source code for examples...

* the IChemicalFilter interface lacks JavaDoc
* about patch 0004... if you fix bugs, please provide a matching unit
test
* patch 0008 StereoFilterTest does not seem to have a copyright/license
header

Asad, I cleaned up the patches a bit, so that files do not get removed and
added, resulting in a new .zip file. Please consider using those as
starting point for patch revisions.


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