date:20131202

Re: [Rdkit-discuss] Joining Fragments

2013-12-02 Thread Nicholas Firth

Thanks for the replies.

I was looking for the combine molecules function. I use the reaction based
joining for ordered connections I want to make. I was looking for something a
bit more basic though.

Best,
Nick

[cid:image001.gif@01CE053D.51D3C4E0]

On 1 Dec 2013, at 04:40, Greg Landrum
greg.land...@gmail.commailto:greg.land...@gmail.com wrote:

This is the approach I would use. It allows you to skip the SMILES generation
and parsing steps.

On Fri, Nov 29, 2013 at 5:31 PM, Markus Hartenfeller
markus.hartenfel...@molecularhealth.commailto:markus.hartenfel...@molecularhealth.com
wrote:
Hi Nick,

I'm not 100% sure, but this might do what you are looking for:

Chem.CombineMols(molFrags[i], molFrags[i+1])

Best,
Markus

On 11/29/2013 05:03 PM, Nicholas Firth wrote:
Hi RDKitters,

This may be a silly question, but I'm wondering if there's any functionality
in RDKit to add two molecules together? I've been writing to SMILES and
joining with a '.' and then reading back in. This feels very cludgy.

Basically I have two fragments of molecules and I want to add them into one
EditableMol and join these fragments to construct a single molecule.

Thanks in advance.

Best,
Nick

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Re: [Rdkit-discuss] Joining Fragments

2013-12-02 Thread Michal Krompiec

Dear Greg,
But does CombineMols create any new bonds?
What is the simplest/fastest way of joining two molecules (fragments)
together? (i.e. is there anything simpler than using
ReplaceSubstructs)
Best wishes,
Michal



On 1 December 2013 04:40, Greg Landrum greg.land...@gmail.com wrote:
 This is the approach I would use. It allows you to skip the SMILES
 generation and parsing steps.



 On Fri, Nov 29, 2013 at 5:31 PM, Markus Hartenfeller
 markus.hartenfel...@molecularhealth.com wrote:

 Hi Nick,

 I'm not 100% sure, but this might do what you are looking for:

 Chem.CombineMols(molFrags[i], molFrags[i+1])

 Best,
 Markus


 On 11/29/2013 05:03 PM, Nicholas Firth wrote:
  Hi RDKitters,
 
  This may be a silly question, but I'm wondering if there's any
  functionality in RDKit to add two molecules together? I've been writing to
  SMILES and joining with a '.' and then reading back in. This feels very
  cludgy.
 
  Basically I have two fragments of molecules and I want to add them into
  one EditableMol and join these fragments to construct a single molecule.
 
  Thanks in advance.
 
  Best,
  Nick
 
  Nicholas C. Firth | PhD Student | Cancer Therapeutics
  The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
  Surrey | SM2 5NG
  T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter
  @ICRnews
 
  The Institute of Cancer Research: Royal Cancer Hospital, a charitable
  Company Limited by Guarantee, Registered in England under Company No. 
  534147
  with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
 
  This e-mail message is confidential and for use by the addressee only.
  If the message is received by anyone other than the addressee, please 
  return
  the message to the sender by replying to it and then delete the message 
  from
  your computer and network.
 
 
  --
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  your
  Java,.NET,  PHP application. Start your 15-day FREE TRIAL of
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Re: [Rdkit-discuss] Joining Fragments

2013-12-02 Thread Greg Landrum

On Mon, Dec 2, 2013 at 1:03 PM, Michal Krompiec
michal.kromp...@gmail.comwrote:


  ReplaceSubstructs() is designed for the very simple case of replacing a
  piece of the molecule that is connected via one bond. It has the
 significant
  limitation that it (currently) assumes that the bond will be formed to
 the
  first atom in the replacement.
 It would be useful to remove this limitation, that is to add the index
 of the bonding atom in the replacement to the arguments.


Yeah, there's a feature request in github for this already:
https://github.com/rdkit/rdkit/issues/171
It will almost certainly make it into the next release.


   The most general and flexible approach to this is almost definitely to
 use
  reactions. However, these are somewhat trickier to encode and do not
  preserve conformations.

 In my project (combinatorial library), joining molecules with reaction
 smarts is much (10x?) slower than using ReplaceSubstructs (with
 renumbering of atoms in the replacement).


Interesting. I'm not surprised that the reaction code is somewhat slower
(there's plenty of room for optimization there), but it's suprising that
the difference would be that large.

-greg
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Re: [Rdkit-discuss] Joining Fragments

Re: [Rdkit-discuss] Joining Fragments

Re: [Rdkit-discuss] Joining Fragments

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