Does standardizer always keep atoms sequence?

User a216001020

02-10-2006 12:02:45

If the input file is in sdf format, and the output file too, does standardizer always keep the sequence of atoms, i.e. will atom numbering never change? Even if H atoms are added?

ChemAxon d76e6e95eb

02-10-2006 12:31:10

Standardization does not keep the order of the atoms, so do not count on their numbering. If you need to identify the atoms in the resulting structure try using atom maps.

User a216001020

02-10-2006 12:36:14

Thanks. Is there other way to add H atoms keeping the original atom numbering?

ChemAxon d76e6e95eb

02-10-2006 12:58:51

Adding H atoms keeps the original atomic order by default.

Draw a molecule in Marvin and turn on the display of atom numbers (View/Misc/Atom Numbers). Then press Edit/Add/Explicit H Atoms. The new H atoms are appended.

User a216001020

02-10-2006 15:03:28

I meant adding H atoms in batch mode. Is it possible to addexplicitH with standardize without standardizing, i.e. keeping atomic order ?

ChemAxon d76e6e95eb

02-10-2006 15:28:59

Have you tried it and didn't work?

With the standardize tool:

Code:

standardize in.sdf -c "addexplicitH" -f sdf -o out.sdf

Alternatively with molconvert:

Code:

molconvert sdf:+H in.sdf -o out.sdf

User a216001020

02-10-2006 15:48:25

Gyuri wrote:

With the standardize tool:

Code:

standardize in.sdf -c "addexplicitH" -f sdf -o out.sdf

Alternatively with molconvert:

Code:

molconvert sdf:+H in.sdf -o out.sdf

My question is: will both of these commands ALWAYS keep the atomic order of in.sdf?

ChemAxon d76e6e95eb

02-10-2006 17:03:50

Both calls the same function. As I said the atom order does not change during this function. However, other standardization tasks can change the atom order. Did you experience something else?

User a216001020

03-10-2006 08:54:52

Gyuri wrote:

Both calls the same function. As I said the atom order does not change during this function. However, other standardization tasks can change the atom order. Did you experience something else?

No, I'd just wanted to be sure. Thanks.