#1372 AtomContainer properties are returned as unmodifiable collection in 1.5.11

[Nina Jeliazkova]

Since 1.5.11 the atomcontainer properties collection returns unmodifiable map.

@Override
public Map<Object, Object> getProperties() {
    return properties == null ? Collections.emptyMap()
                              : Collections.unmodifiableMap(properties);
}

I've probably missed when this change was discussed.
I can see the reason (and the inefficient workaround through cloning), but this change is likely to break a lot of code, e.g. in the simple scenario of reading the structure and properties form SDF file, calculating something and putting back into properties.

[Nina Jeliazkova]

OK, there is setProperty() which should be used instead, still existing code needs to be modified.

[John May]

For encapsulation the caller shouldn't have direct access to the underlying
array/collection. I understand existing code that makes than assumption
will break but the benefit is we can show an empty map without allocating
the maps. If we looped over an molecule with 20 atoms and called
getProperties() on each atom just to see if there were any this silently
allocates 1KB of arrays let alone the object overhead.

Regards,
John W May
john.wilkinsonmay@gmail.com

On 9 September 2015 at 07:39, Nina Jeliazkova vedina@users.sf.net wrote:

OK, there is setProperty() which should be used instead, still existing
code needs to be modified.

---

• [bugs:#1372] http://sourceforge.net/p/cdk/bugs/1372/ AtomContainer
  properties are returned as unmodifiable collection in 1.5.11*

Status: open
Group: cdk-1.6.x
Created: Wed Sep 09, 2015 06:35 AM UTC by Nina Jeliazkova
Last Updated: Wed Sep 09, 2015 06:35 AM UTC
Owner: John May

Since 1.5.11 the atomcontainer properties collection returns unmodifiable
map.

@Override
public Map<Object, Object=""> getProperties() {
return properties == null ? Collections.emptyMap()
: Collections.unmodifiableMap(properties);
}

I've probably missed when this change was discussed.
I can see the reason (and the inefficient workaround through cloning), but
this change is likely to break a lot of code, e.g. in the simple scenario
of reading the structure and properties form SDF file, calculating
something and putting back into properties.

---

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[Nina Jeliazkova]

Thanks, this is fine, consider this closed.

[John May]

Would you consider moving AMBIT to github Nina? I'd be more than happy to test and patch changes like this if it was easy.

[Nina Jeliazkova]

Not impossible :)

On 9 September 2015 at 12:26, John May jwmay@users.sf.net wrote:

Would you consider moving AMBIT to github Nina? I'd be more than happy to
test and patch changes like this if it was easy.

---

• [bugs:#1372] http://sourceforge.net/p/cdk/bugs/1372/ AtomContainer
  properties are returned as unmodifiable collection in 1.5.11*

Status: open
Group: cdk-1.6.x
Created: Wed Sep 09, 2015 06:35 AM UTC by Nina Jeliazkova
Last Updated: Wed Sep 09, 2015 07:55 AM UTC
Owner: John May

Since 1.5.11 the atomcontainer properties collection returns unmodifiable
map.

@Override
public Map<Object, Object=""> getProperties() {
return properties == null ? Collections.emptyMap()
: Collections.unmodifiableMap(properties);
}

I've probably missed when this change was discussed.
I can see the reason (and the inefficient workaround through cloning), but
this change is likely to break a lot of code, e.g. in the simple scenario
of reading the structure and properties form SDF file, calculating
something and putting back into properties.

---

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https://sourceforge.net/p/cdk/bugs/1372/

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[Nina Jeliazkova]

John, is there a replacement of mol.getProperties().clear() in 1.5.11 ?

[John May]

Nope, but we should add a clearProperties() method.

mol.setProperties(new LinkedHashMap<>());

?

Regards,
John W May
john.wilkinsonmay@gmail.com

On 9 September 2015 at 14:17, Nina Jeliazkova vedina@users.sf.net wrote:

John, is there a replacement of mol.getProperties().clear() in 1.5.11 ?

• [bugs:#1372] http://sourceforge.net/p/cdk/bugs/1372/ AtomContainer
  properties are returned as unmodifiable collection in 1.5.11*

Status: closed
Group: cdk-1.6.x
Created: Wed Sep 09, 2015 06:35 AM UTC by Nina Jeliazkova
Last Updated: Wed Sep 09, 2015 09:43 AM UTC
Owner: John May

Since 1.5.11 the atomcontainer properties collection returns unmodifiable
map.

@Override
public Map<Object, Object=""> getProperties() {
return properties == null ? Collections.emptyMap()
: Collections.unmodifiableMap(properties);
}

I've probably missed when this change was discussed.
I can see the reason (and the inefficient workaround through cloning), but
this change is likely to break a lot of code, e.g. in the simple scenario
of reading the structure and properties form SDF file, calculating
something and putting back into properties.

---

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https://sourceforge.net/p/cdk/bugs/1372/

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[Nina Jeliazkova]

+1