Hi Andrew,
Many thanks for your detailed answer!
Yes, I use Python. I will give your suggested solution a try.
Best regards,
Rudy
On Sun, Feb 27, 2022 at 4:27 PM Andrew Dalke <da...@dalkescientific.com>
wrote:
> Hi Rudy,
>
>
>
> > On Feb 27, 2022, at 20:55, Rudy Richardson <rjr...@umich.edu> wrote:
> >
> > I have a library of ~1000 compounds as SMILES strings with an appended
> name code and a property. For example:
> >
> > c1ccc(c2ccccc2)cc1 0001 -2.52
> >
> > Where "0001" is the name code and "-2.52" is a physicochemical property
> of the molecule.
> >
> > I would like to convert these strings to a concatenated SDF file,
>
>
> If you're comfortable working with Python, here's an example using the
> pybel interface.
>
> First, here's how to get the name code and property
>
> >>> from openbabel import pybel
> >>> mol = pybel.readstring("smi", "c1ccc(c2ccccc2)cc1\t0001\t-2.52")
> >>> mol
> <openbabel.pybel.Molecule object at 0x1101dece0>
> >>> mol.title
> '0001\t-2.52'
>
> In that case I used tabs (represented as "\t"), because I believe that's
> what's in your file. That would explain the extra space between the fields.
>
> I'll use Python's string.split() to split on any whitespace (which
> includes both spaces and tabs)
>
> >>> mol.title.split()
> ['0001', '-2.52']
>
> and assign them to the variables "name_code" and "value".
>
> >>> name_code, value = mol.title.split()
>
> The pybel API has a "write()" method on molecules which formats it into a
> given format. Here's what it looks like in "sdf".
>
> >>> print(mol.write("sdf"))
> 0001 -2.52
> OpenBabel02272221522D
>
> 12 13 0 0 0 0 0 0 0 0999 V2000
> ...
>
> I need to change the title and add a "logX" data item, which I can do with:
>
> >>> mol.title = name_code
> >>> mol.data["logX"] = value
>
> giving most of what you wanted.
>
> >>> print(mol.write("sdf"))
> 0001
> OpenBabel02272221552D
>
> 12 13 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 12 2 0 0 0 0
> 1 2 1 0 0 0 0
> 2 3 2 0 0 0 0
> 3 4 1 0 0 0 0
> 4 5 1 0 0 0 0
> 4 11 2 0 0 0 0
> 5 10 2 0 0 0 0
> 5 6 1 0 0 0 0
> 6 7 2 0 0 0 0
> 7 8 1 0 0 0 0
> 8 9 2 0 0 0 0
> 9 10 1 0 0 0 0
> 11 12 1 0 0 0 0
> M END
> > <logX>
> -2.52
>
> $$$$
>
> You also had a "No." field. I don't know if that is the index of the input
> record, or the integer value of the name_code, like:
>
> >>> int(name_code)
> 1
>
> I'll assume it's the input index.
>
> I'll use Python's built-in "enumerate()" function. What it does is it add
> an index for each element of an iterator. For example, I can iterate
> through the characters of "ABCD" like this:
>
> >>> for c in "ABCD":
> ... print(c)
> ...
> A
> B
> C
> D
>
> What enumerate() does is for each X in the input iterator, it returns
> (index, X)
>
> >>> for i, c in enumerate("ABCD"):
> ... print(i, c)
> ...
> 0 A
> 1 B
> 2 C
> 3 D
>
> I can also specify the initial index, for example, to start at 1:
>
> >>> for i, c in enumerate("ABCD", 1):
> ... print(i, c)
> ...
> 1 A
> 2 B
> 3 C
> 4 D
>
> The last bit to know is that pybel's "readfile" gives a way to iterate
> over all molecules in a file.
>
> >>> from openbabel import pybel
> >>> for i, mol in enumerate(pybel.readfile("smi", "wikipedia2.smi"), 1):
> ... print("Entry#:", i, repr(mol.title))
> ... if i == 10:
> ... break
> ...
> Entry#: 1 'Ammonia'
> Entry#: 2 'Aspirin'
> Entry#: 3 'Acetylene'
> Entry#: 4 'Adenosine triphosphate'
> Entry#: 5 'Ampicillin'
> Entry#: 6 'Ascorbic acid'
> Entry#: 7 'Ascorbic acid'
> Entry#: 8 'Amphetamine'
> Entry#: 9 'Aspartame'
> Entry#: 10 'Amoxicillin'
>
> Finally, all the coordinates were 0.0. To make things a bit nicer, use the
> "make2D()" or "make3D()" methods to add 2D or 3D coordinates, respectively.
> Your example uses 3D, so I'll do that.
>
> Putting it all together, along with some use of Python's "argparse"
> molecule to handle command-line processing (which I won't discuss here)
> gives the "rjrich.py" program, attached.
>
> It's used like this:
>
> % python rjrich.py test.smi
>
> You can also change the output tag, and the output file name, like this:
>
> % python rjrich.py test.smi --tag Cacao2 -o cacao2.sdf
>
> (I believe if you're using Open Babel under Windows, with Python
> installed, then you should use "py" instead of "python" to run the program.)
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
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