Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
On Wed, Dec 7, 2011 at 5:06 AM, Greg Landrum greg.land...@gmail.com wrote: Dear JP, I do not see how AddHs will help me when replacing [OH] with [O-], but that might just be me being thick. My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl, replaceAll=True) in my original attached code throws away the 3D coordinates (ps[0] atoms are all on 0,0,0) - and I don't know of a way to regain the original co-ordinates back. You need two things here: 1) the coordinates of the input molecule should be copied to the result molecule 2) some way to generate sensible coordinates for the new atoms. The first is already supposed to be happening; the fact that it's not is a bug which I will fix (https://sourceforge.net/tracker/?func=detailaid=3453144group_id=160139atid=814650). This bug is now fixed in svn. -greg -- Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
Just bumping this up ... On 29 November 2011 16:47, JP jeanpaul.ebe...@inhibox.com wrote: Dear Greg, I am not sure that is what I need/I explained myself well. My question is: If you have a 3D molecule, and you replace a part of it with a new group based on some SMARTS expression (with no 3D coorinates) - what is the best way to keep all the 3D info for the atoms in the molecule which have not changed while creating some sensible co-cordinates (in the current frame) for the newly appended atoms to the molecule. I do not see how AddHs will help me when replacing [OH] with [O-], but that might just be me being thick. My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl, replaceAll=True) in my original attached code throws away the 3D coordinates (ps[0] atoms are all on 0,0,0) - and I don't know of a way to regain the original co-ordinates back. Is this still a rumble? Many thanks - Jean-Paul Ebejer Early Stage Researcher On 29 November 2011 16:10, Greg Landrum greg.land...@gmail.com wrote: Dear JP, On Tue, Nov 29, 2011 at 3:36 PM, JP jeanpaul.ebe...@inhibox.com wrote: Sorry for the repeated posting -- I had asked a similar question for 2D some time ago (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html), but now I need the 3D case and I am stuck. Using RDKit 2011_09_01. I am simply protonating a molecule via some simple SMART replacements. I would like the final output molecule to have the same 3D co ordinates as the input one. I have code which works for the 2D case, (basically the below but using GenerateDepictionMatching2DStructure(...) instead. I think you're overcomplicating things. Once you have the molecule ready to be protonated, try doing: Chem.AddHs(mol,addCoords=True) That is *supposed* to do the right thing (assuming I've understood the request correctly). If it doesn't let me know and I will propose a more complicated solution. -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
Sorry for the repeated posting -- I had asked a similar question for
2D some time ago
(http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html),
but now I need the 3D case and I am stuck.
Using RDKit 2011_09_01.
I am simply protonating a molecule via some simple SMART replacements.
I would like the final output molecule to have the same 3D co
ordinates as the input one. I have code which works for the 2D case,
(basically the below but using
GenerateDepictionMatching2DStructure(...) instead.
A copy and paste example:
#!/usr/bin/env python
Protonates the input molecules...
@author: JP
from rdkit import Chem
from rdkit.Chem import AllChem
orig_mol = LIGAND
Insight 3D 0
47 48 0 0 0 0 0
16.1500 22.3350 42.8110 C 0 0 0 0 0 0
15.3160 21.8930 41.9800 O 0 0 0 0 0 0
16.9980 23.2070 42.5060 O 0 0 0 0 0 0
16.1410 21.7710 44.2030 C 0 0 0 0 0 0
15.1160 22.5540 45.0230 C 0 0 0 0 0 0
15.0619 22.1799 46.0577 H 0 0 0 0 0 0
15.3649 23.6269 45.0656 H 0 0 0 0 0 0
14.1065 22.4630 44.5883 H 0 0 0 0 0 0
17.5310 21.9290 44.8610 C 0 0 0 0 0 0
17.5541 21.4127 45.8334 H 0 0 0 0 0 0
18.3473 21.5168 44.2477 H 0 0 0 0 0 0
17.7642 22.9903 45.0477 H 0 0 0 0 0 0
15.7170 20.3840 44.1390 O 0 0 0 0 0 0
16.5230 19.2430 43.6250 C 0 0 0 0 0 0
16.2460 17.9700 44.1170 C 0 0 0 0 0 0
15.4668 17.8367 44.8675 H 0 0 0 0 0 0
16.9520 16.8770 43.6600 C 0 0 0 0 0 0
16.7273 15.8853 44.0527 H 0 0 0 0 0 0
17.9400 17.0290 42.7100 C 0 0 0 0 0 0
17.5250 19.4050 42.6630 C 0 0 0 0 0 0
17.7525 20.3959 42.2701 H 0 0 0 0 0 0
18.2350 18.2860 42.2070 C 0 0 0 0 0 0
19.0179 18.4043 41.4579 H 0 0 0 0 0 0
18.6450 15.8760 42.2400 C 0 0 0 0 0 0
18.9367 15.2468 43.1044 H 0 0 0 0 0 0
19.6099 16.1765 41.7887 H 0 0 0 0 0 0
17.8550 15.0410 41.2140 C 0 0 0 0 0 0
16.7450 15.4130 40.8360 O 0 0 0 0 0 0
18.2860 13.8040 41.0020 N 0 0 0 0 0 0
19.1093 13.4965 41.5391 H 0 0 0 0 0 0
17.7310 12.8920 40.1270 C 0 0 0 0 0 0
16.3370 12.7960 39.9850 C 0 0 0 0 0 0
15.6892 13.5478 40.4357 H 0 0 0 0 0 0
15.7870 11.7440 39.2710 C 0 0 0 0 0 0
16.6210 10.7910 38.7010 C 0 0 0 0 0 0
16.19299.9591 38.1417 H 0 0 0 0 0 0
18.5490 11.9350 39.5470 C 0 0 0 0 0 0
19.6312 12.0105 39.6525 H 0 0 0 0 0 0
18.0040 10.8950 38.8420 C 0 0 0 0 0 0
14.3030 11.6400 39.1100 C 0 0 0 0 0 0
13.8285 12.6314 39.1672 H 0 0 0 0 0 0
14.0383 11.1938 38.1399 H 0 0 0 0 0 0
13.8615 11.0120 39.9008 H 0 0 0 0 0 0
18.90909.8760 38.2190 C 0 0 0 0 0 0
18.47289.4727 37.2928 H 0 0 0 0 0 0
19.8880 10.3114 37.9693 H 0 0 0 0 0 0
19.08119.0290 38.9030 H 0 0 0 0 0 0
1 2 1 0 0 0
1 3 2 0 0 0
1 4 1 0 0 0
4 5 1 0 0 0
4 9 1 0 0 0
4 13 1 0 0 0
5 6 1 0 0 0
5 7 1 0 0 0
5 8 1 0 0 0
9 10 1 0 0 0
9 11 1 0 0 0
9 12 1 0 0 0
13 14 1 0 0 0
14 15 2 0 0 0
14 20 1 0 0 0
15 17 1 0 0 0
15 16 1 0 0 0
17 19 2 0 0 0
17 18 1 0 0 0
19 22 1 0 0 0
19 24 1 0 0 0
20 22 2 0 0 0
20 21 1 0 0 0
22 23 1 0 0 0
24 27 1 0 0 0
24 25 1 0 0 0
24 26 1 0 0 0
27 28 2 0 0 0
27 29 1 0 0 0
29 31 1 0 0 0
29 30 1 0 0 0
31 32 1 0 0 0
31 37 2 0 0 0
32 34 2 0 0 0
32 33 1 0 0 0
34 35 1 0 0 0
34 40 1 0 0 0
35 39 2 0 0 0
35 36 1 0 0 0
37 39 1 0 0 0
37 38 1 0 0 0
39 44 1 0 0 0
40 41 1 0 0 0
40 42 1 0 0 0
40 43 1 0 0 0
44 45 1 0 0 0
44 46 1 0 0 0
44 47 1 0 0 0
M END
rules=(
# Carboxylic Acid ionization
('[O-]','[$([OH]C(=O))]'),
)
def protonate(mol):
Chem.SanitizeMol(mol)
orig = Chem.MolToSmiles(mol)
for repl, patt in rules:
repl = Chem.MolFromSmiles(repl, sanitize=False)
patt = Chem.MolFromSmarts(patt)
ps = AllChem.ReplaceSubstructs(mol, patt, repl, replaceAll=True)
ps[0].UpdatePropertyCache(False)
Chem.GetSymmSSSR(ps[0])
new = Chem.MolToSmiles(ps[0])
modified = Chem.MolToSmiles(mol) != Chem.MolToSmiles(ps[0])
print Input: %s,Output: %s,Deprotonated: %s % (orig,
new, modified)
if modified:
# emebed these as
# the following keeps the co ordinates in mol, and just
adds co ordinates
# for the new (replaced) atoms
Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
Dear JP, On Tue, Nov 29, 2011 at 3:36 PM, JP jeanpaul.ebe...@inhibox.com wrote: Sorry for the repeated posting -- I had asked a similar question for 2D some time ago (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html), but now I need the 3D case and I am stuck. Using RDKit 2011_09_01. I am simply protonating a molecule via some simple SMART replacements. I would like the final output molecule to have the same 3D co ordinates as the input one. I have code which works for the 2D case, (basically the below but using GenerateDepictionMatching2DStructure(...) instead. I think you're overcomplicating things. Once you have the molecule ready to be protonated, try doing: Chem.AddHs(mol,addCoords=True) That is *supposed* to do the right thing (assuming I've understood the request correctly). If it doesn't let me know and I will propose a more complicated solution. -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
Dear Greg, I am not sure that is what I need/I explained myself well. My question is: If you have a 3D molecule, and you replace a part of it with a new group based on some SMARTS expression (with no 3D coorinates) - what is the best way to keep all the 3D info for the atoms in the molecule which have not changed while creating some sensible co-cordinates (in the current frame) for the newly appended atoms to the molecule. I do not see how AddHs will help me when replacing [OH] with [O-], but that might just be me being thick. My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl, replaceAll=True) in my original attached code throws away the 3D coordinates (ps[0] atoms are all on 0,0,0) - and I don't know of a way to regain the original co-ordinates back. Is this still a rumble? Many thanks - Jean-Paul Ebejer Early Stage Researcher On 29 November 2011 16:10, Greg Landrum greg.land...@gmail.com wrote: Dear JP, On Tue, Nov 29, 2011 at 3:36 PM, JP jeanpaul.ebe...@inhibox.com wrote: Sorry for the repeated posting -- I had asked a similar question for 2D some time ago (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html), but now I need the 3D case and I am stuck. Using RDKit 2011_09_01. I am simply protonating a molecule via some simple SMART replacements. I would like the final output molecule to have the same 3D co ordinates as the input one. I have code which works for the 2D case, (basically the below but using GenerateDepictionMatching2DStructure(...) instead. I think you're overcomplicating things. Once you have the molecule ready to be protonated, try doing: Chem.AddHs(mol,addCoords=True) That is *supposed* to do the right thing (assuming I've understood the request correctly). If it doesn't let me know and I will propose a more complicated solution. -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generating 3D coordinates
It's kind of interesting (and encouraging) that the optimizer doesn't completely freak out when you hand it a 2D conformer. :-) Ah... :) What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...) It is indeed a one-liner (two lines with a bit of error checking). To get a 3D conformer, you need to include GraphMol/DistGeomHelpers/Embedder.h and do the following: int cid = DGeomHelpers::EmbedMolecule(*m); if(cid0) // embedding failed, do something There are a bunch of optional arguments to EmbedMolecule, but the defaults normally work reasonably well. So it seems! Fantastic, that did it. It's pretty jaw dropping that so much power can be added with so little code (on my part :) More later. Cheers, Paul. -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing http://p.sf.net/sfu/novell-sfdev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Generating 3D coordinates
Hi All,
I've been tinkering a bit more with RDKit and having fun.
I have hit a problem though. I am trying to reproduce Greg's Generating
3D coordinates in RDKit-overview.pdf in C++:
This is what I have (mostly via cut 'n paste):
int
main(int argc, char **argv) {
std::string smiles_string = C1CCC1;
RDKit::RWMol *mol=new RDKit::RWMol();
mol = RDKit::SmilesToMol(smiles_string);
RDDepict::compute2DCoords(*mol);
double vdwThresh=10.0;
int confId = -1;
bool ignoreInterfragInteractions=true;
int maxIters = 200;
ForceFields::ForceField *ff =
RDKit::UFF::constructForceField(*mol,
vdwThresh, confId,
ignoreInterfragInteractions);
ff-initialize();
int res=ff-minimize(maxIters);
delete ff;
std::cout RDKit::MolToMolBlock(*mol, true, -1) std::endl;
return 0;
}
But I get 2D coordinates:
RDKit 2D
5 5 0 0 0 0 0 0 0 0999 V2000
1.28790.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.39801.22490. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.04190.75700. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0419 -0.75700. C 0 0 0 0 0 0 0 0 0 0 0 0
0.3980 -1.22490. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 1 0
5 1 1 0
M END
What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...)
Cheers,
Paul.
--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing
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