Re: [Rdkit-discuss] MolFromXYZ?
Hi, Without information about whether or not atoms are bonded, and the orders of the bonds between them, there's no sensible way to get an XYZ file into the RDKit. If you can combine the XYZ file with a SMILES (or some other format that has bond information), then it should be no problem -greg On Sat, Jan 17, 2015 at 3:57 PM, Naeem Attari naeemraz...@gmail.com wrote: Hi, Is it possible to generate rdkit mol object only from xyz coordinates? It would be useful to connect rdkit with other tools. Was asked earlier: http://sourceforge.net/p/rdkit/mailman/message/31601105/ Thanks Kind Regards Shaikh Naeem -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] MolFromXYZ?
[adding the list back to the recipient list] On Mon, Jan 19, 2015 at 10:02 AM, Naeem Attari naeemraz...@gmail.com wrote: Can't we derive the bond order and connectivity information from distance matrix (which can be derived from coordinates)? Assuming all hydrogens and charges are present in the file, the geometry is a good one, and the structure is made up of octet-complete atoms from the organic subset, getting 90% of the bonds correct is almost certainly doable without too much effort. The last bit will be problematic. If you remove any of the above constraints, you're left with a research problem. Here's a recent publication on the topic: http://pubs.acs.org/doi/abs/10.1021/ci300358c This isn't an attempt to discourage you from doing an implementation for your own purposes, just an explanation of why something that is seemingly simple is not present in the RDKit. -greg -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] MolFromXYZ?
Hi, Is it possible to generate rdkit mol object only from xyz coordinates? It would be useful to connect rdkit with other tools. Was asked earlier: http://sourceforge.net/p/rdkit/mailman/message/31601105/ Thanks Kind Regards Shaikh Naeem -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] MolFromXYZ?
On 1/17/2015 8:57 AM, Naeem Attari wrote: Hi, Is it possible to generate rdkit mol object only from xyz coordinates? It would be useful to connect rdkit with other tools. If you can't transform your xyz coordinates into pdb ATOM line, then probably not. Dima -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] MolFromXYZ?
Dear Sereina, No, I have just a table of 3D coordinates (generated by cclib). This is equivalent to having an xyz file. I know that this conversion is possible with OpenBabel, but I would like to avoid using it for this particular purpose. It seems that the simplest way is to hardcode generation of SDF myself. Thanks, Michal On 4 November 2013 13:52, sereina riniker sereina.rini...@gmail.com wrote: Hi Michal, Well, if you have your 3D coordinates as a PDB file, you can read them in with the new PDB parser and assign the bond orders based on a template (generated from the SMILES of your molecule): tmp = Chem.MolFromPDBFile(yourfilename) template = Chem.MolFromSmiles(yoursmiles) mol = AllChem.AssignBondOrdersFromTemplate(template, tmp) I don't know if this is what you were looking for. Best, Sereina 2013/11/4 Michal Krompiec michal.kromp...@gmail.com Hello, Is it possible to construct a Mol (or EditableMol) object out of a list of 3D coordinates? I am trying to write a bridge between cclib and RDKit, and I need a function to convert 3D geometries to SDF. Thanks, Michal -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] MolFromXYZ?
Hi Michal, Well, if you have your 3D coordinates as a PDB file, you can read them in with the new PDB parser and assign the bond orders based on a template (generated from the SMILES of your molecule): tmp = Chem.MolFromPDBFile(yourfilename) template = Chem.MolFromSmiles(yoursmiles) mol = AllChem.AssignBondOrdersFromTemplate(template, tmp) I don't know if this is what you were looking for. Best, Sereina 2013/11/4 Michal Krompiec michal.kromp...@gmail.com Hello, Is it possible to construct a Mol (or EditableMol) object out of a list of 3D coordinates? I am trying to write a bridge between cclib and RDKit, and I need a function to convert 3D geometries to SDF. Thanks, Michal -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
