[Rdkit-discuss] PDB reader and bond perception
RDKitters! Finally back on the mailing list! I am sure we've been through this at the UGM (my mind must have wandered off!), but a quick question about the PDB reader and bond perception. Is this supported with the current PDB reader? I remember that someone (PaulE, perhaps?) was saying bond perception was painful, but there was some dictionary for PDB ligands which helps (any idea the name of this dictionary?). To the technical details. I am reading in the following PDB file with a simple MolFromPDBFile() call: HETATM1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81 O HETATM2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65 P HETATM3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49 O HETATM4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78 N HETATM5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97 C HETATM6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75 C HETATM7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73 C HETATM8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70 C HETATM9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49 C HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60 C HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17 O HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33 O HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26 O HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39 O HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47 C HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24 C HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28 C HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69 C HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64 O HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80 O HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01 C HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08 N HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10 C HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58 N HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95 C HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27 C HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28 N HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81 C HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85 C HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44 N HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86 N TER END But I am losing all the double bond (and aromatic) information: m = Chem.MolFromPDBFile(sys.argv[1]) print Chem.MolToSmiles(m) Gives me: CC(C)C(O)C(O)C(O)NP(O)(O)OCC1CC(O)C(N2CNC3C2NCNC3N)O1 As usual, many thanks for your time, - Jean-Paul Ebejer Early Stage Researcher -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PDB reader and bond perception
Hi JP I use this file from PDB Europe: ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/pdb.tar.gz Useful links followed from http://www.ebi.ac.uk/pdbe-srv/pdbechem/ The pdb.tar.gz file has the standard residues and LOTS of others with specific CONNECT records. TJ On Mon, Jan 13, 2014 at 9:54 AM, JP jeanpaul.ebe...@inhibox.com wrote: RDKitters! Finally back on the mailing list! I am sure we've been through this at the UGM (my mind must have wandered off!), but a quick question about the PDB reader and bond perception. Is this supported with the current PDB reader? I remember that someone (PaulE, perhaps?) was saying bond perception was painful, but there was some dictionary for PDB ligands which helps (any idea the name of this dictionary?). To the technical details. I am reading in the following PDB file with a simple MolFromPDBFile() call: HETATM1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81 O HETATM2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65 P HETATM3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49 O HETATM4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78 N HETATM5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97 C HETATM6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75 C HETATM7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73 C HETATM8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70 C HETATM9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49 C HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60 C HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17 O HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33 O HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26 O HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39 O HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47 C HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24 C HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28 C HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69 C HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64 O HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80 O HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01 C HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08 N HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10 C HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58 N HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95 C HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27 C HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28 N HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81 C HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85 C HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44 N HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86 N TER END But I am losing all the double bond (and aromatic) information: m = Chem.MolFromPDBFile(sys.argv[1]) print Chem.MolToSmiles(m) Gives me: CC(C)C(O)C(O)C(O)NP(O)(O)OCC1CC(O)C(N2CNC3C2NCNC3N)O1 As usual, many thanks for your time, - Jean-Paul Ebejer Early Stage Researcher -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PDB reader and bond perception
On 13/01/14 17:54, JP wrote: RDKitters! Finally back on the mailing list! I am sure we've been through this at the UGM (my mind must have wandered off!), but a quick question about the PDB reader and bond perception. Is this supported with the current PDB reader? I remember that someone (PaulE, perhaps?) was saying bond perception was painful, but there was some dictionary for PDB ligands which helps (any idea the name of this dictionary?). To the technical details. I am reading in the following PDB file with a simple MolFromPDBFile() call: HETATM1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81 O HETATM2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65 P HETATM3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49 O HETATM4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78 N HETATM5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97 C HETATM6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75 C HETATM7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73 C HETATM8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70 C HETATM9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49 C HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60 C HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17 O HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33 O HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26 O HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39 O HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47 C HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24 C HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28 C HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69 C HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64 O HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80 O HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01 C HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08 N HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10 C HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58 N HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95 C HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27 C HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28 N HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81 C HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85 C HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44 N HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86 N TER END But I am losing all the double bond (and aromatic) information: m = Chem.MolFromPDBFile(sys.argv[1]) print Chem.MolToSmiles(m) Gives me: CC(C)C(O)C(O)C(O)NP(O)(O)OCC1CC(O)C(N2CNC3C2NCNC3N)O1 As usual, many thanks for your time, 84T is a reference to chemical description: http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/84T This (mmcif) is what I parse, either from the local dictionary or downloading the file on the fly: ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/84T.cif Does that help? Paul. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PDB reader and bond perception
Hi JP, If you have also a SMILES of the molecule you want to read from PDB, you can assign the bond orders based on this template: tmp = Chem.MolFromPDBFile(yourfilename) template = Chem.MolFromSmiles(yoursmiles) mol = AllChem.AssignBondOrdersFromTemplate(template, tmp) Is this what you're looking for? Best, Sereina 2014/1/13 JP jeanpaul.ebe...@inhibox.com RDKitters! Finally back on the mailing list! I am sure we've been through this at the UGM (my mind must have wandered off!), but a quick question about the PDB reader and bond perception. Is this supported with the current PDB reader? I remember that someone (PaulE, perhaps?) was saying bond perception was painful, but there was some dictionary for PDB ligands which helps (any idea the name of this dictionary?). To the technical details. I am reading in the following PDB file with a simple MolFromPDBFile() call: HETATM1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81 O HETATM2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65 P HETATM3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49 O HETATM4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78 N HETATM5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97 C HETATM6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75 C HETATM7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73 C HETATM8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70 C HETATM9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49 C HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60 C HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17 O HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33 O HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26 O HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39 O HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47 C HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24 C HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28 C HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69 C HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64 O HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80 O HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01 C HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08 N HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10 C HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58 N HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95 C HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27 C HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28 N HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81 C HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85 C HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44 N HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86 N TER END But I am losing all the double bond (and aromatic) information: m = Chem.MolFromPDBFile(sys.argv[1]) print Chem.MolToSmiles(m) Gives me: CC(C)C(O)C(O)C(O)NP(O)(O)OCC1CC(O)C(N2CNC3C2NCNC3N)O1 As usual, many thanks for your time, - Jean-Paul Ebejer Early Stage Researcher -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PDB reader and bond perception
Thanks All - I think I am in a good place now. I can get the SMILES from Paul's mmcif links and then I can use Sereina magic three lines to do what I want. I'd cross my fingers - but with RDKit you don't need to. This works for all Chemical Components (or what other fashionable name they go by these days) in the PDB. For posterity: I have found a post in the mailing list started by James which sheds some light on this: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03481.html On 13 January 2014 19:46, sereina riniker sereina.rini...@gmail.com wrote: Hi JP, If you have also a SMILES of the molecule you want to read from PDB, you can assign the bond orders based on this template: tmp = Chem.MolFromPDBFile(yourfilename) template = Chem.MolFromSmiles(yoursmiles) mol = AllChem.AssignBondOrdersFromTemplate(template, tmp) Is this what you're looking for? Best, Sereina 2014/1/13 JP jeanpaul.ebe...@inhibox.com RDKitters! Finally back on the mailing list! I am sure we've been through this at the UGM (my mind must have wandered off!), but a quick question about the PDB reader and bond perception. Is this supported with the current PDB reader? I remember that someone (PaulE, perhaps?) was saying bond perception was painful, but there was some dictionary for PDB ligands which helps (any idea the name of this dictionary?). To the technical details. I am reading in the following PDB file with a simple MolFromPDBFile() call: HETATM1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81 O HETATM2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65 P HETATM3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49 O HETATM4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78 N HETATM5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97 C HETATM6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75 C HETATM7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73 C HETATM8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70 C HETATM9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49 C HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60 C HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17 O HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33 O HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26 O HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39 O HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47 C HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24 C HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28 C HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69 C HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64 O HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80 O HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01 C HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08 N HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10 C HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58 N HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95 C HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27 C HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28 N HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81 C HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85 C HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44 N HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86 N TER END But I am losing all the double bond (and aromatic) information: m = Chem.MolFromPDBFile(sys.argv[1]) print Chem.MolToSmiles(m) Gives me: CC(C)C(O)C(O)C(O)NP(O)(O)OCC1CC(O)C(N2CNC3C2NCNC3N)O1 As usual, many thanks for your time, - Jean-Paul Ebejer Early Stage Researcher -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today.
