Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record
Hi JP, Not sure if this is of any help. If it's an pdb file from rcsb or an in-house one where you have a corresponding smiles available maybe you could use this information to properly setup the bond types using bond matches? I know the components.cif file still has quite a few errors - however, maybe it could be of help. Cheers Nik Maybe you could use the smiles information ion On 7/6/12 5:04 AM, Greg Landrum greg.land...@gmail.com wrote: Hi JP, On Thu, Jul 5, 2012 at 7:07 PM, JP jeanpaul.ebe...@inhibox.com wrote: I generate a RWMol instance from the HETATM portion of a PDB file. My atoms are currently only joined by a single bond as defined in the connect portion of the pdb file, e.g. CONECT 2235 2234 2236 CONECT 2236 2231 2235 2251 CONECT 2237 2238 2242 ah, yes, the missing bond orders, one of the many reasons that I have never done a PDB parser for the RDKit. :-S I think you're doing this work in C++, so I'm going to answer the rest of the questions accordingly. Are there any obvious rdkit ways how to detect :- 0. rings Sure. If you just want to know if each atom/ring is in a ring you can use MolOps::fastFindRings and then mol.getRingInfo().numAtomRings(idx)0 or mol.getRingInfo().numBondRings(idx)0 If you want to know what the SSSR rings are, then you should use MolOps::symmetrizeSSSR(). You can pass that an extra argument where it will return the rings as defined by atom indices. After calling this, you can also get the set of atom rings using mol.getRingInfo().atomRings() or the bond rings with mol.getRingInfo().bondRings(); 1. aromatic rings/atoms 2. double/triple bonds 3. charges (if any) Here's where the trouble starts. I guess you want to perceive the bond types and atom hybridizations from the geometry. From there you can get the charges. The RDKit does not currently have anything to do this. There was a discussion on the mailing list last year: http://comments.gmane.org/gmane.science.chemistry.rdkit.user/85 where Geoff Hutchinson very kindly offered to donate the OpenBabel bond perception code to the RDKit. He sent the code, but I've never had the time to port it from OpenBabel to RDKit. If you're interested in implementing this and were willing to do it in a way that could be integrated into the main RDKit, I can send you the donated code; it's about 300 lines of well-commented C++. I would like to set these properties on every atom instance contained in my RWMol - so I generate a correct molecule representation. I assume sanitize would not clean these up for me? Correct? Correct. Sanitize uses the bond information that's there. -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record
Steifl -- that is a really crafty and less painful way how to go about it. The SMILES is in fact, a wget call away - since I am processing PDB deposited structures. http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG Of course, this approach is not generally applicable (and for this you'd need the perception code Greg mentioned). Can I have a look at that code, just to see the amount of work involved -- if nothing else? For the protein I can somehow guess the bonds. SanitizeMol takes around 20 mins on my machine (I assume this is because of the massive size of the molecule ~ 2000 atoms). - Jean-Paul Ebejer Early Stage Researcher On 6 July 2012 07:33, Stiefl, Nikolaus nikolaus.sti...@novartis.com wrote: Hi JP, Not sure if this is of any help. If it's an pdb file from rcsb or an in-house one where you have a corresponding smiles available maybe you could use this information to properly setup the bond types using bond matches? I know the components.cif file still has quite a few errors - however, maybe it could be of help. Cheers Nik Maybe you could use the smiles information ion On 7/6/12 5:04 AM, Greg Landrum greg.land...@gmail.com wrote: Hi JP, On Thu, Jul 5, 2012 at 7:07 PM, JP jeanpaul.ebe...@inhibox.com wrote: I generate a RWMol instance from the HETATM portion of a PDB file. My atoms are currently only joined by a single bond as defined in the connect portion of the pdb file, e.g. CONECT 2235 2234 2236 CONECT 2236 2231 2235 2251 CONECT 2237 2238 2242 ah, yes, the missing bond orders, one of the many reasons that I have never done a PDB parser for the RDKit. :-S I think you're doing this work in C++, so I'm going to answer the rest of the questions accordingly. Are there any obvious rdkit ways how to detect :- 0. rings Sure. If you just want to know if each atom/ring is in a ring you can use MolOps::fastFindRings and then mol.getRingInfo().numAtomRings(idx)0 or mol.getRingInfo().numBondRings(idx)0 If you want to know what the SSSR rings are, then you should use MolOps::symmetrizeSSSR(). You can pass that an extra argument where it will return the rings as defined by atom indices. After calling this, you can also get the set of atom rings using mol.getRingInfo().atomRings() or the bond rings with mol.getRingInfo().bondRings(); 1. aromatic rings/atoms 2. double/triple bonds 3. charges (if any) Here's where the trouble starts. I guess you want to perceive the bond types and atom hybridizations from the geometry. From there you can get the charges. The RDKit does not currently have anything to do this. There was a discussion on the mailing list last year: http://comments.gmane.org/gmane.science.chemistry.rdkit.user/85 where Geoff Hutchinson very kindly offered to donate the OpenBabel bond perception code to the RDKit. He sent the code, but I've never had the time to port it from OpenBabel to RDKit. If you're interested in implementing this and were willing to do it in a way that could be integrated into the main RDKit, I can send you the donated code; it's about 300 lines of well-commented C++. I would like to set these properties on every atom instance contained in my RWMol - so I generate a correct molecule representation. I assume sanitize would not clean these up for me? Correct? Correct. Sanitize uses the bond information that's there. -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled
I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... - Jean-Paul Ebejer Early Stage Researcher On 4 July 2012 16:52, Greg Landrum greg.land...@gmail.com wrote: On Wed, Jul 4, 2012 at 3:38 PM, JP jeanpaul.ebe...@inhibox.com wrote: A suggestion, if I'm allowed. suggestions are always allowed. They may, of course, be ignored. ;-) I am trying to build a PDB file parser to return an rdkit mol (representing a protein) from a pdb file. I have battled and partially won the glue code between C++ and python. This was by far the most difficult bit extending rdkit. But there have been casualties and I am not sure I 100% understand what is going on (how is my code automatically residing in the Chem package? why do you need this struct anyway?). If I may suggest a hands on/tutorial session at the RDKit user meeting on this -- I think it will be a topic worth broaching. If there is enough interest, a free slot in the programme and someone with the capabilities to explain of course. Capabilities to explain is, of course, not a problem. I'm also happy to do it, but the topic is pretty specialized, so I wonder how many others would be interested. -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled
On Fri, Jul 6, 2012 at 11:06 AM, JP jeanpaul.ebe...@inhibox.com wrote: I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... eh, that depends. C++ users of the code are also users. I'm more concerned about having a session that only 2 people are interested in. To accommodate that we would have to do breakout sessions, and we hadn't planned to do such a thing. I will see if I can come up with a sensible demo that shows how to create a new python extension module using RDKit functionality. This should at least make some stuff easier for others in the future. -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled
I have the question connected with the topic, Is there any temporary plan of the meeting or topics which will be discussed during this event? If yes where I can find it? If no will it be announced and when? I suggest to publish such a list of topics and to vote for most interesting of them. 2012/7/6 Greg Landrum greg.land...@gmail.com: On Fri, Jul 6, 2012 at 11:06 AM, JP jeanpaul.ebe...@inhibox.com wrote: I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... eh, that depends. C++ users of the code are also users. I'm more concerned about having a session that only 2 people are interested in. To accommodate that we would have to do breakout sessions, and we hadn't planned to do such a thing. I will see if I can come up with a sensible demo that shows how to create a new python extension module using RDKit functionality. This should at least make some stuff easier for others in the future. -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record
On Fri, Jul 6, 2012 at 10:27 AM, JP jeanpaul.ebe...@inhibox.com wrote: Steifl -- that is a really crafty and less painful way how to go about it. The SMILES is in fact, a wget call away - since I am processing PDB deposited structures. http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG Do you want ideal ligand structures or those from the experimental PDB file? The ideal ones you can just download from PDBeChem (SDF). The Credo web service has a REST resource for downloading ligand structures in different formats (including SDF) - hopefully I will have a web server soon to make this publicly available. Of course, this approach is not generally applicable (and for this you'd need the perception code Greg mentioned). Can I have a look at that code, just to see the amount of work involved -- if nothing else? Just remember that those ligand structures are often far from perfect - the most common problems are missing atoms and dodgy geometries that affect bond order perception. Here are the two ligands (FRG) from PDB entry 1M48 for example: COC(=O)[C@H](Cc1ccc(cc1)C#Cc2c2)NC(=O)C[C@H]3CCCN(C3)C(=[NH2+])N COC(=O)[C@H](Cc1ccc(cc1)C#Cc2c2)NC(=O)C[C@H]3CC=CN(C3)C(=[NH2+])N The second one has a double bond because one of the rings does not have the same geometry as it does in the other ligand. For the protein I can somehow guess the bonds. SanitizeMol takes around 20 mins on my machine (I assume this is because of the massive size of the molecule ~ 2000 atoms). Jean-Paul Ebejer Early Stage Researcher It might be easier to use Open Babel to load the PDB structure and extract just the binding site, which you could safe in a different format and use afterwards in RDKit. On 6 July 2012 07:33, Stiefl, Nikolaus nikolaus.sti...@novartis.com wrote: Hi JP, Not sure if this is of any help. If it's an pdb file from rcsb or an in-house one where you have a corresponding smiles available maybe you could use this information to properly setup the bond types using bond matches? I know the components.cif file still has quite a few errors - however, maybe it could be of help. Cheers Nik Maybe you could use the smiles information ion On 7/6/12 5:04 AM, Greg Landrum greg.land...@gmail.com wrote: Hi JP, On Thu, Jul 5, 2012 at 7:07 PM, JP jeanpaul.ebe...@inhibox.com wrote: I generate a RWMol instance from the HETATM portion of a PDB file. My atoms are currently only joined by a single bond as defined in the connect portion of the pdb file, e.g. CONECT 2235 2234 2236 CONECT 2236 2231 2235 2251 CONECT 2237 2238 2242 ah, yes, the missing bond orders, one of the many reasons that I have never done a PDB parser for the RDKit. :-S I think you're doing this work in C++, so I'm going to answer the rest of the questions accordingly. Are there any obvious rdkit ways how to detect :- 0. rings Sure. If you just want to know if each atom/ring is in a ring you can use MolOps::fastFindRings and then mol.getRingInfo().numAtomRings(idx)0 or mol.getRingInfo().numBondRings(idx)0 If you want to know what the SSSR rings are, then you should use MolOps::symmetrizeSSSR(). You can pass that an extra argument where it will return the rings as defined by atom indices. After calling this, you can also get the set of atom rings using mol.getRingInfo().atomRings() or the bond rings with mol.getRingInfo().bondRings(); 1. aromatic rings/atoms 2. double/triple bonds 3. charges (if any) Here's where the trouble starts. I guess you want to perceive the bond types and atom hybridizations from the geometry. From there you can get the charges. The RDKit does not currently have anything to do this. There was a discussion on the mailing list last year: http://comments.gmane.org/gmane.science.chemistry.rdkit.user/85 where Geoff Hutchinson very kindly offered to donate the OpenBabel bond perception code to the RDKit. He sent the code, but I've never had the time to port it from OpenBabel to RDKit. If you're interested in implementing this and were willing to do it in a way that could be integrated into the main RDKit, I can send you the donated code; it's about 300 lines of well-commented C++. I would like to set these properties on every atom instance contained in my RWMol - so I generate a correct molecule representation. I assume sanitize would not clean these up for me? Correct? Correct. Sanitize uses the bond information that's there. -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list
Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled
On 06/07/12 10:06, JP wrote: I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... What's the difference? A user uses python and a dev uses python, boost.python and c++? Anyway, I too (AFAICS ATM) would be interested in your suggestion (FWIW). Paul. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Announcement: 1st RDKit User Group Meeting scheduled
IMHO I think the main difference is that a user is a consumer of the API (so just calling the available methods), while a developer is one who builds new functionality and extends RDKit's API and internals. That the user in this case is also a software developer somewhat blurs this distinction. The python wrapper is an example of something which a developer of RDKit would be interested in. But for the end user of RDKit, be it C++ or python, this layer is transparent and of no interest. HAGD! - Jean-Paul Ebejer Early Stage Researcher On 6 July 2012 13:05, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 06/07/12 10:06, JP wrote: I just noticed that this is a user meeting and not a dev one - so perhaps such a topic is out of scope... What's the difference? A user uses python and a dev uses python, boost.python and c++? Anyway, I too (AFAICS ATM) would be interested in your suggestion (FWIW). Paul. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record
On 06/07/12 10:27, JP wrote: Steifl -- that is a really crafty and less painful way how to go about it. The SMILES is in fact, a wget call away - since I am processing PDB deposited structures. http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG It is not clear to me how the SMILES helps you. You still have to map between rdkit atoms and PDB atom names, do you not? How about using the monomer library? http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html Of course, this approach is not generally applicable (and for this you'd need the perception code Greg mentioned). Hmm... I am unconvinced that you want to be doing chemistry perception. For the protein I can somehow guess the bonds. What do you mean by guess here? Are you worried about histidine protonation? -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
