#1319 SmilesGenerator and Implicit -> Explicit Hydrogens

[Duece99]

Hello,

I noticed this in the SmilesGenerator source code after finding that despite using the AtomContainerManipulator to remove hydrogen atoms from molecules, I still got explicit hydrogens in SMILES Strings:

 if (symbol.equals("*") && a.getImplicitHydrogenCount() != null && a.getImplicitHydrogenCount() > 0)
                    buffer.append("H").append(a.getImplicitHydrogenCount());

Is it intentional that the getImplicitHydrogenCount() method is used? I'm guessing this' a remnant of something that's otherwise been changed in a later version.

Ed.

[John May]

Hi Ed,

That generator doesn’t existing any more :-) - 1.5.4 was released yesterday https://github.com/cdk/cdk/wiki/1.5.4-Release-Notes

J

On 20 Dec 2013, at 15:43, Duece99 duece99@users.sf.net wrote:

[bugs:#1319] SmilesGenerator and Implicit -> Explicit Hydrogens

Status: open
Created: Fri Dec 20, 2013 03:43 PM UTC by Duece99
Last Updated: Fri Dec 20, 2013 03:43 PM UTC
Owner: nobody

Hello,

I noticed this in the SmilesGenerator source code after finding that despite using the AtomContainerManipulator to remove hydrogen atoms from molecules, I still got explicit hydrogens in SMILES Strings:

if (symbol.equals("*") && a.getImplicitHydrogenCount() != null && a.getImplicitHydrogenCount() > 0)
buffer.append("H").append(a.getImplicitHydrogenCount());
Is it intentional that the getImplicitHydrogenCount() method is used? I'm guessing this' a remnant of something that's otherwise been changed in a later version.

Ed.

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[Duece99]

Ah, my bad - thanks for the update :)

On 20 December 2013 16:34, John May jwmay@users.sf.net wrote:

Hi Ed,

That generator doesn’t existing any more :-) - 1.5.4 was released
yesterday https://github.com/cdk/cdk/wiki/1.5.4-Release-Notes

J

On 20 Dec 2013, at 15:43, Duece99 duece99@users.sf.net wrote:

[bugs:#1319] http://sourceforge.net/p/cdk/bugs/1319/ SmilesGenerator
and Implicit -> Explicit Hydrogens

Status: open
Created: Fri Dec 20, 2013 03:43 PM UTC by Duece99
Last Updated: Fri Dec 20, 2013 03:43 PM UTC
Owner: nobody

Hello,

I noticed this in the SmilesGenerator source code after finding that
despite using the AtomContainerManipulator to remove hydrogen atoms from
molecules, I still got explicit hydrogens in SMILES Strings:

if (symbol.equals("*") && a.getImplicitHydrogenCount() != null &&
a.getImplicitHydrogenCount() > 0)
buffer.append("H").append(a.getImplicitHydrogenCount());
Is it intentional that the getImplicitHydrogenCount() method is used? I'm
guessing this' a remnant of something that's otherwise been changed in a
later version.

Ed.

Sent from sourceforge.net because cdk-bugs@lists.sf.net is subscribed to
https://sourceforge.net/p/cdk/bugs/

To unsubscribe from further messages, a project admin can change settings
at https://sourceforge.net/p/cdk/admin/bugs/options. Or, if this is a
mailing list, you can unsubscribe from the mailing list.

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organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
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• [bugs:#1319] http://sourceforge.net/p/cdk/bugs/1319/ SmilesGenerator
  and Implicit -> Explicit Hydrogens*

Status: open
Created: Fri Dec 20, 2013 03:43 PM UTC by Duece99
Last Updated: Fri Dec 20, 2013 03:43 PM UTC
Owner: nobody

Hello,

I noticed this in the SmilesGenerator source code after finding that
despite using the AtomContainerManipulator to remove hydrogen atoms
from molecules, I still got explicit hydrogens in SMILES Strings:

if (symbol.equals("*") && a.getImplicitHydrogenCount() != null && a.getImplicitHydrogenCount() > 0)
buffer.append("H").append(a.getImplicitHydrogenCount());

Is it intentional that the getImplicitHydrogenCount() method is used?
I'm guessing this' a remnant of something that's otherwise been changed in
a later version.

Ed.

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/cdk/bugs/1319/

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[John May]

Fixed in 1.5.x

[Duece99]

Can't wait to see the next CDK release for KNIME :-)
On Jan 5, 2014 3:45 PM, "John May" jwmay@users.sf.net wrote:

Fixed in 1.5.x

• [bugs:#1319] http://sourceforge.net/p/cdk/bugs/1319/ SmilesGenerator
  and Implicit -> Explicit Hydrogens*

Status: closed
Created: Fri Dec 20, 2013 03:43 PM UTC by Duece99
Last Updated: Fri Dec 20, 2013 03:43 PM UTC
Owner: nobody

Hello,

I noticed this in the SmilesGenerator source code after finding that
despite using the AtomContainerManipulator to remove hydrogen atoms
from molecules, I still got explicit hydrogens in SMILES Strings:

if (symbol.equals("*") && a.getImplicitHydrogenCount() != null && a.getImplicitHydrogenCount() > 0)
buffer.append("H").append(a.getImplicitHydrogenCount());

Is it intentional that the getImplicitHydrogenCount() method is used?
I'm guessing this' a remnant of something that's otherwise been changed in
a later version.

Ed.

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/cdk/bugs/1319/

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