[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

Post by JP
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.
HETATM 1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81
O
HETATM 2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65
P
HETATM 3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49
O
HETATM 4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78
N
HETATM 5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97
C
HETATM 6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75
C
HETATM 7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73
C
HETATM 8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70
C
HETATM 9 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
m = Chem.MolFromPDBFile(sys.argv[1])
print Chem.MolToSmiles(m)
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
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Paul Emsley

2014-01-13 19:22:51 UTC

Post by JP
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.
HETATM 1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81
O
HETATM 2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65
P
HETATM 3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49
O
HETATM 4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78
N
HETATM 5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97
C
HETATM 6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75
C
HETATM 7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73
C
HETATM 8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70
C
HETATM 9 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
m = Chem.MolFromPDBFile(sys.argv[1])
print Chem.MolToSmiles(m)
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.

sereina riniker

2014-01-13 19:46:27 UTC

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

2014-01-13 21:02:27 UTC

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

Post by sereina riniker
Hi JP,
If you have also a SMILES of the molecule you want to read from PDB, you
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
Is this what you're looking for?
Best,
Sereina

2014-01-14 12:38:18 UTC

Apologies all -- but I am still having problems with this.

Reading
https://www.mail-archive.com/rdkit-***@lists.sourceforge.net/msg03485.html

"As far as I understood, the PDB reader assigns bond orders to the amino
acids in a protein, but if a ligand is present it puts all bonds of it to
SINGLE bonds as auto bond-type perception is not trivial (see Roger's
comments)."

However I am unable to get bond orders for the protein side - am I doing
something wrong or is this the intended behaviour ?
I imagine I can use AssignBondOrdersFromTemplate() for the 20 amino acids
and set these myself -- or is there a better way to do this?

Also, is there a way to make AssignBondOrdersFromTemplate assign bond
orders to all matches?

import rdkit
from rdkit import Chem
temp = Chem.MolFromSmiles('C=O')
mol = Chem.MolFromSmiles('C(O)CC(O)')
from rdkit.Chem import AllChem
m2 = AllChem.AssignBondOrdersFromTemplate(temp, mol)

[12:24:56] WARNING: More than one matching pattern found - picking one

print Chem.MolToSmiles(m2) # was expecting O=CCC=O

O=CCCO

Also another thing I don't quite understand is in the following below code,
I get a "WARNING: More than one matching pattern found - picking one" but
how can my template match multiple times (this is not symettrical) ?

# (Using RDKit_2013_09_1)
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem

ligand_mol = Chem.MolFromPDBBlock("""HETATM 1 C1 MRC A1993
30.994 82.769 82.139 1.00 18.68 C
HETATM 2 C2 MRC A1993 29.949 82.382 81.280 1.00 18.38
C
HETATM 3 C3 MRC A1993 28.809 83.090 80.875 1.00 16.44
C
HETATM 4 C4 MRC A1993 27.794 82.511 79.886 1.00 17.11
C
HETATM 5 C5 MRC A1993 26.268 82.360 79.965 1.00 16.74
C
HETATM 6 C6 MRC A1993 25.256 81.832 78.911 1.00 17.00
C
HETATM 7 C7 MRC A1993 23.832 81.867 79.556 1.00 17.45
C
HETATM 8 C8 MRC A1993 23.758 81.056 80.927 1.00 16.89
C
HETATM 9 C9 MRC A1993 23.820 79.467 80.419 1.00 17.84
C
HETATM 10 C10 MRC A1993 22.833 78.610 79.550 1.00 19.48
C
HETATM 11 C11 MRC A1993 22.999 78.593 78.193 1.00 20.56
C
HETATM 12 C12 MRC A1993 21.733 78.839 77.305 1.00 20.86
C
HETATM 13 C13 MRC A1993 21.779 78.052 75.821 1.00 20.74
C
HETATM 14 C14 MRC A1993 20.323 77.662 75.537 1.00 22.44
C
HETATM 15 C15 MRC A1993 28.456 84.523 81.348 1.00 12.97
C
HETATM 16 C16 MRC A1993 24.899 81.634 81.814 1.00 16.07
C
HETATM 17 C1' MRC A1993 38.561 75.401 83.188 1.00 53.39
C
HETATM 18 O1P MRC A1993 39.367 74.705 83.841 1.00 53.58
O
HETATM 19 O1Q MRC A1993 38.963 76.034 82.185 1.00 52.93
O
HETATM 20 C2' MRC A1993 37.074 75.480 83.615 1.00 51.57
C
HETATM 21 C3' MRC A1993 36.915 75.997 85.071 1.00 48.41
C
HETATM 22 C4' MRC A1993 35.513 76.588 85.323 1.00 45.07
C
HETATM 23 C5' MRC A1993 35.443 78.068 84.897 1.00 41.55
C
HETATM 24 C6' MRC A1993 34.033 78.631 85.167 1.00 37.19
C
HETATM 25 C7' MRC A1993 33.490 79.356 83.929 1.00 34.17
C
HETATM 26 C8' MRC A1993 33.454 80.886 84.151 1.00 31.34
C
HETATM 27 C9' MRC A1993 32.082 81.519 83.803 1.00 27.63
C
HETATM 28 O1A MRC A1993 32.056 81.880 82.413 1.00 22.28
O
HETATM 29 O1B MRC A1993 31.044 83.885 82.667 1.00 20.31
O
HETATM 30 O5 MRC A1993 26.209 81.625 81.183 1.00 16.19
O
HETATM 31 O7 MRC A1993 23.503 83.224 79.735 1.00 14.98
O
HETATM 32 O6 MRC A1993 25.399 82.787 77.821 1.00 15.00
O
HETATM 33 O10 MRC A1993 22.868 77.384 78.981 1.00 21.90
O
HETATM 34 C17 MRC A1993 21.395 80.405 77.027 1.00 20.53
C
HETATM 35 O13 MRC A1993 22.524 76.868 75.987 1.00 21.25
O
TER
END""")

template_ligand_mol = Chem.MolFromSmiles("C[***@H](O)[***@H](C)[C@@H]1O[***@H
]1C[***@H]2CO[C@@H](C/C(C)=C/C(=O)OCCCCCCCCC(O)=O)[C@@H](O)[***@H]2O")

ligand_mol_with_bonds =
AllChem.AssignBondOrdersFromTemplate(template_ligand_mol, ligand_mol)
# [12:33:39] WARNING: More than one matching pattern found - picking one

print Chem.MolToSmiles(ligand_mol)
# CC(CC(O)OCCCCCCCCC(O)O)CC1OCC(CC2OC2C(C)C(C)O)C(O)C1O
print Chem.MolToSmiles(ligand_mol_with_bonds)
# CC(=CC(=O)OCCCCCCCCC(=O)O)CC1OCC(CC2OC2C(C)C(C)O)C(O)C1O

Any help would be greatly appreciated.

Thanks,
JP

Post by JP
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.

Post by JP
This works for all Chemical Components (or what other fashionable name

they go by these days) in the PDB.

Post by JP
For posterity: I have found a post in the mailing list started by James

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.
HETATM 1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81

HETATM 2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65

HETATM 3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49

HETATM 4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78

HETATM 5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97

HETATM 6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75

HETATM 7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73

HETATM 8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70

HETATM 9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49

HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60

HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17

HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33

HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26

HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39

HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47

HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24

HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28

HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69

HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64

HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80

HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01

HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08

HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10

HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58

HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95

HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27

HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28

HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81

HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85

HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44

HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86

TER
END
m = Chem.MolFromPDBFile(sys.argv[1])
print Chem.MolToSmiles(m)
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

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sereina riniker

2014-01-14 13:30:40 UTC

Hi JP,

However I am unable to get bond orders for the protein side - am I doing

Post by JP
something wrong or is this the intended behaviour ?
I imagine I can use AssignBondOrdersFromTemplate() for the 20 amino acids
and set these myself -- or is there a better way to do this?

I don't know why your protein doesn't get bond orders, the PDBParser should
know the standard amino acids. At least it worked for me when I tried
Chem.MolFromPDB() in the past. Which PDB structure do you try to read?

Post by JP
Also, is there a way to make AssignBondOrdersFromTemplate assign bond
orders to all matches?

The function was meant for assigning bonds based on an entire molecule. It
would probably not be so difficult to change this (with default = match
only one), if it is really needed.

Post by JP
Also another thing I don't quite understand is in the following below
code, I get a "WARNING: More than one matching pattern found - picking one"
but how can my template match multiple times (this is not symettrical) ?

The way the AssignBondOrdersFromTemplate() function works is the following:
1) a copy of the template is generated where all bonds are set to single
bonds
2) this single-bonds copy is used for a substructure match with the query
molecule
3) bond orders are assigned based on this match and the original template

If you get this warning, it means that there is some symmetry in the
"all-single-bonds-stage" of your molecule. In your case, I guess it's the
carboxylic acids which can match two ways when there are only single bonds.

I hope this helps.

Best,
Sereina

Post by JP
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.

Post by JP
This works for all Chemical Components (or what other fashionable name

they go by these days) in the PDB.

Post by JP
For posterity: I have found a post in the mailing list started by James

Post by sereina riniker
Hi JP,
If you have also a SMILES of the molecule you want to read from PDB,
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
Is this what you're looking for?
Best,
Sereina

Post by JP
RDKitters!
Finally back on the mailing list!
I am sure we've been through this at the UGM (my mind must have

Post by JP
To the technical details.
I am reading in the following PDB file with a simple MolFromPDBFile()
HETATM 1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81

Post by JP
HETATM 2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65

Post by JP
HETATM 3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49

Post by JP
HETATM 4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78

Post by JP
HETATM 5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97

Post by JP
HETATM 6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75

Post by JP
HETATM 7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73

Post by JP
HETATM 8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70

Post by JP
HETATM 9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49

Post by JP
HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60

Post by JP
HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17

Post by JP
HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33

Post by JP
HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26

Post by JP
HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39

Post by JP
HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47

Post by JP
HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24

Post by JP
HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28

Post by JP
HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69

Post by JP
HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64

Post by JP
HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80

Post by JP
HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01

Post by JP
HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08

Post by JP
HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10

Post by JP
HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58

Post by JP
HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95

Post by JP
HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27

Post by JP
HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28

Post by JP
HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81

Post by JP
HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85

Post by JP
HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44

Post by JP
HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86

Post by JP
TER
END
m = Chem.MolFromPDBFile(sys.argv[1])
print Chem.MolToSmiles(m)
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

------------------------------------------------------------------------------

Post by JP
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Post by JP
_______________________________________________
Rdkit-discuss mailing list
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

2014-01-14 13:50:32 UTC

Post by sereina riniker
Hi JP,
However I am unable to get bond orders for the protein side - am I doing

Post by JP
something wrong or is this the intended behaviour ?
I imagine I can use AssignBondOrdersFromTemplate() for the 20 amino acids
and set these myself -- or is there a better way to do this?

I don't know why your protein doesn't get bond orders, the PDBParser
should know the standard amino acids. At least it worked for me when I
tried Chem.MolFromPDB() in the past. Which PDB structure do you try to read?

The following code for example:

# (Using RDKit_2013_09_1)
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem

prot_mol = Chem.MolFromPDBBlock("""ATOM 1 P C T 70 36.833
83.840 76.703 1.00 24.64 P
ATOM 2 OP1 C T 70 36.424 82.808 77.694 1.00 26.34
O
ATOM 3 OP2 C T 70 37.969 83.555 75.781 1.00 26.16
O
ATOM 4 O5' C T 70 35.587 84.229 75.793 1.00 22.26
O
ATOM 5 C5' C T 70 34.303 84.408 76.358 1.00 24.59
C
ATOM 6 C4' C T 70 33.305 84.740 75.281 1.00 24.33
C
ATOM 7 O4' C T 70 33.668 86.014 74.692 1.00 26.24
O
ATOM 8 C3' C T 70 33.307 83.794 74.087 1.00 26.50
C
ATOM 9 O3' C T 70 32.552 82.619 74.333 1.00 28.61
O
ATOM 10 C2' C T 70 32.707 84.664 72.988 1.00 26.61
C
ATOM 11 O2' C T 70 31.303 84.800 73.078 1.00 28.08
O
ATOM 12 C1' C T 70 33.336 86.016 73.311 1.00 25.28
C
ATOM 13 N1 C T 70 34.551 86.235 72.522 1.00 25.48
N
ATOM 14 C2 C T 70 34.409 86.756 71.233 1.00 22.70
C
ATOM 15 O2 C T 70 33.269 87.032 70.831 1.00 20.93
O
ATOM 16 N3 C T 70 35.506 86.948 70.471 1.00 21.93
N
ATOM 17 C4 C T 70 36.713 86.654 70.961 1.00 22.94
C
ATOM 18 N4 C T 70 37.774 86.874 70.181 1.00 22.99
N
ATOM 19 C5 C T 70 36.888 86.122 72.276 1.00 23.81
C
ATOM 20 C6 C T 70 35.791 85.931 73.015 1.00 23.64
C
TER
ATOM 21 N GLY A 55 16.572 81.800 79.047 1.00 24.32
N
ATOM 22 CA GLY A 55 17.264 80.922 78.115 1.00 21.44
C
ATOM 23 C GLY A 55 17.511 79.665 78.938 1.00 19.98
C
ATOM 24 O GLY A 55 17.960 79.782 80.070 1.00 18.32
O
ATOM 25 N PRO A 56 17.248 78.456 78.415 1.00 19.67
N
ATOM 26 CA PRO A 56 17.452 77.216 79.178 1.00 19.71
C
ATOM 27 C PRO A 56 18.863 76.711 79.438 1.00 20.15
C
ATOM 28 O PRO A 56 19.515 76.211 78.529 1.00 20.52
O
ATOM 29 CB PRO A 56 16.654 76.195 78.378 1.00 19.65
C
ATOM 30 CG PRO A 56 16.917 76.637 76.970 1.00 19.83
C
ATOM 31 CD PRO A 56 16.737 78.158 77.064 1.00 18.98
C
ATOM 32 N PRO A 57 19.341 76.795 80.694 1.00 20.23
N
ATOM 33 CA PRO A 57 20.695 76.307 80.976 1.00 20.02
C
ATOM 34 C PRO A 57 20.732 74.811 80.752 1.00 19.70
C
ATOM 35 O PRO A 57 19.699 74.155 80.795 1.00 18.65
O
ATOM 36 CB PRO A 57 20.913 76.687 82.449 1.00 21.28
C
ATOM 37 CG PRO A 57 19.546 76.673 83.017 1.00 19.57
C
ATOM 38 CD PRO A 57 18.722 77.336 81.916 1.00 21.61
C
ATOM 39 N TYR A 58 21.922 74.273 80.518 1.00 20.78
N
ATOM 40 CA TYR A 58 22.068 72.854 80.267 1.00 20.66
C
ATOM 41 C TYR A 58 22.037 72.020 81.538 1.00 22.45
C
ATOM 42 O TYR A 58 22.782 72.273 82.491 1.00 21.68
O
ATOM 43 CB TYR A 58 23.359 72.591 79.515 1.00 21.91
C
ATOM 44 CG TYR A 58 23.343 71.252 78.831 1.00 23.30
C
ATOM 45 CD1 TYR A 58 22.483 71.010 77.751 1.00 21.40
C
ATOM 46 CD2 TYR A 58 24.165 70.217 79.269 1.00 22.13
C
ATOM 47 CE1 TYR A 58 22.447 69.773 77.127 1.00 20.96
C
ATOM 48 CE2 TYR A 58 24.133 68.975 78.652 1.00 23.29
C
ATOM 49 CZ TYR A 58 23.274 68.758 77.581 1.00 21.33
C
ATOM 50 OH TYR A 58 23.249 67.522 76.976 1.00 22.48
O
ATOM 51 N HIS A 64 28.134 77.876 87.356 1.00 16.16
N
ATOM 52 CA HIS A 64 29.370 78.628 87.473 1.00 16.18
C
ATOM 53 C HIS A 64 28.951 80.089 87.685 1.00 15.24
C
ATOM 54 O HIS A 64 27.767 80.402 87.639 1.00 13.81
O
ATOM 55 CB HIS A 64 30.227 78.469 86.209 1.00 15.17
C
ATOM 56 CG HIS A 64 29.501 78.777 84.939 1.00 17.43
C
ATOM 57 ND1 HIS A 64 29.378 77.862 83.913 1.00 17.53
N
ATOM 58 CD2 HIS A 64 28.901 79.912 84.508 1.00 15.04
C
ATOM 59 CE1 HIS A 64 28.737 78.422 82.902 1.00 17.82
C
ATOM 60 NE2 HIS A 64 28.436 79.666 83.236 1.00 21.06
N
ATOM 61 N MET A 65 29.912 80.969 87.928 1.00 15.38
N
ATOM 62 CA MET A 65 29.630 82.383 88.171 1.00 16.74
C
ATOM 63 C MET A 65 28.774 83.047 87.075 1.00 17.60
C
ATOM 64 O MET A 65 28.042 84.004 87.338 1.00 17.28
O
ATOM 65 CB MET A 65 30.951 83.142 88.332 1.00 16.05
C
ATOM 66 CG MET A 65 30.917 84.201 89.423 1.00 19.05
C
ATOM 67 SD MET A 65 30.477 83.491 91.028 1.00 21.29
S
ATOM 68 CE MET A 65 29.105 84.522 91.457 1.00 19.14
C
ATOM 69 N GLY A 66 28.877 82.545 85.849 1.00 16.38
N
ATOM 70 CA GLY A 66 28.087 83.097 84.759 1.00 16.17
C
ATOM 71 C GLY A 66 26.596 82.870 84.978 1.00 16.45
C
ATOM 72 O GLY A 66 25.777 83.744 84.690 1.00 16.27
O
ATOM 73 N HIS A 67 26.229 81.694 85.480 1.00 15.53
N
ATOM 74 CA HIS A 67 24.817 81.415 85.737 1.00 17.28
C
ATOM 75 C HIS A 67 24.292 82.388 86.781 1.00 15.79
C
ATOM 76 O HIS A 67 23.162 82.858 86.683 1.00 17.54
O
ATOM 77 CB HIS A 67 24.609 79.990 86.270 1.00 17.57
C
ATOM 78 CG HIS A 67 24.902 78.914 85.270 1.00 19.11
C
ATOM 79 ND1 HIS A 67 26.071 78.183 85.284 1.00 17.88
N
ATOM 80 CD2 HIS A 67 24.163 78.426 84.245 1.00 17.47
C
ATOM 81 CE1 HIS A 67 26.036 77.287 84.314 1.00 19.15
C
ATOM 82 NE2 HIS A 67 24.889 77.413 83.670 1.00 16.21
N
ATOM 83 N ALA A 68 25.125 82.663 87.783 1.00 13.71
N
ATOM 84 CA ALA A 68 24.782 83.558 88.878 1.00 13.53
C
ATOM 85 C ALA A 68 24.592 84.990 88.389 1.00 12.34
C
ATOM 86 O ALA A 68 23.585 85.621 88.695 1.00 12.93
O
ATOM 87 CB ALA A 68 25.872 83.497 89.959 1.00 14.07
C
ATOM 88 N LEU A 69 25.561 85.484 87.622 1.00 10.80
N
ATOM 89 CA LEU A 69 25.499 86.828 87.065 1.00 11.73
C
ATOM 90 C LEU A 69 24.203 86.998 86.269 1.00 12.69
C
ATOM 91 O LEU A 69 23.421 87.932 86.503 1.00 11.38
O
ATOM 92 CB LEU A 69 26.687 87.077 86.124 1.00 9.60
C
ATOM 93 CG LEU A 69 26.543 88.339 85.268 1.00 8.37
C
ATOM 94 CD1 LEU A 69 26.584 89.536 86.171 1.00 6.65
C
ATOM 95 CD2 LEU A 69 27.667 88.439 84.222 1.00 9.77
C
ATOM 96 N ASN A 70 23.993 86.066 85.340 1.00 13.60
N
ATOM 97 CA ASN A 70 22.839 86.051 84.454 1.00 14.47
C
ATOM 98 C ASN A 70 21.485 85.948 85.150 1.00 14.28
C
ATOM 99 O ASN A 70 20.544 86.653 84.787 1.00 15.95
O
ATOM 100 CB ASN A 70 22.968 84.895 83.450 1.00 14.15
C
ATOM 101 CG ASN A 70 21.689 84.678 82.654 1.00 14.47
C
ATOM 102 OD1 ASN A 70 20.811 83.910 83.057 1.00 12.26
O
ATOM 103 ND2 ASN A 70 21.563 85.384 81.530 1.00 16.87
N
ATOM 104 N LYS A 74 18.580 88.964 85.786 1.00 13.79
N
ATOM 105 CA LYS A 74 17.192 88.703 85.412 1.00 15.44
C
ATOM 106 C LYS A 74 16.237 89.035 86.558 1.00 15.10
C
ATOM 107 O LYS A 74 15.203 89.674 86.348 1.00 13.82
O
ATOM 108 CB LYS A 74 17.014 87.228 85.028 1.00 13.86
C
ATOM 109 CG LYS A 74 17.639 86.879 83.700 1.00 14.38
C
ATOM 110 CD LYS A 74 17.573 85.399 83.415 1.00 11.34
C
ATOM 111 CE LYS A 74 17.974 85.153 81.964 1.00 9.22
C
ATOM 112 NZ LYS A 74 18.226 83.726 81.726 1.00 6.91
N
ATOM 113 N ASP A 95 17.612 72.846 79.490 1.00 22.31
N
ATOM 114 CA ASP A 95 18.000 72.193 78.250 1.00 20.84
C
ATOM 115 C ASP A 95 18.382 70.774 78.687 1.00 19.47
C
ATOM 116 O ASP A 95 19.348 70.597 79.422 1.00 18.03
O
ATOM 117 CB ASP A 95 19.195 72.946 77.667 1.00 20.82
C
ATOM 118 CG ASP A 95 19.219 72.925 76.153 1.00 23.49
C
ATOM 119 OD1 ASP A 95 18.142 72.737 75.550 1.00 21.52
O
ATOM 120 OD2 ASP A 95 20.315 73.118 75.569 1.00 23.96
O
ATOM 121 N TRP A 528 20.582 73.020 69.677 1.00 23.71
N
ATOM 122 CA TRP A 528 20.332 74.440 69.457 1.00 23.24
C
ATOM 123 C TRP A 528 18.905 74.570 68.935 1.00 21.85
C
ATOM 124 O TRP A 528 18.220 75.556 69.214 1.00 20.38
O
ATOM 125 CB TRP A 528 21.316 75.036 68.435 1.00 22.52
C
ATOM 126 CG TRP A 528 22.700 75.272 68.988 1.00 24.85
C
ATOM 127 CD1 TRP A 528 23.873 74.792 68.486 1.00 25.49
C
ATOM 128 CD2 TRP A 528 23.050 76.047 70.151 1.00 23.69
C
ATOM 129 NE1 TRP A 528 24.931 75.213 69.259 1.00 26.56
N
ATOM 130 CE2 TRP A 528 24.456 75.986 70.286 1.00 25.78
C
ATOM 131 CE3 TRP A 528 22.310 76.786 71.088 1.00 24.37
C
ATOM 132 CZ2 TRP A 528 25.146 76.638 71.326 1.00 25.91
C
ATOM 133 CZ3 TRP A 528 22.995 77.439 72.123 1.00 23.91
C
ATOM 134 CH2 TRP A 528 24.399 77.358 72.230 1.00 25.34
C
ATOM 135 N SER A 531 16.450 74.372 72.143 1.00 20.16
N
ATOM 136 CA SER A 531 16.319 75.621 72.893 1.00 19.65
C
ATOM 137 C SER A 531 15.786 76.708 71.993 1.00 19.35
C
ATOM 138 O SER A 531 14.973 77.537 72.407 1.00 19.32
O
ATOM 139 CB SER A 531 17.671 76.055 73.479 1.00 17.88
C
ATOM 140 OG SER A 531 18.648 76.204 72.467 1.00 17.02
O
ATOM 141 N GLY A 532 16.245 76.691 70.751 1.00 20.07
N
ATOM 142 CA GLY A 532 15.809 77.687 69.799 1.00 20.95
C
ATOM 143 C GLY A 532 14.309 77.708 69.592 1.00 21.44
C
ATOM 144 O GLY A 532 13.786 78.667 69.041 1.00 22.61
O
ATOM 145 N LEU A 553 17.820 87.851 77.715 1.00 16.25
N
ATOM 146 CA LEU A 553 19.029 88.343 78.371 1.00 18.27
C
ATOM 147 C LEU A 553 19.950 87.160 78.639 1.00 17.66
C
ATOM 148 O LEU A 553 19.612 86.289 79.436 1.00 20.05
O
ATOM 149 CB LEU A 553 18.680 89.040 79.695 1.00 16.91
C
ATOM 150 CG LEU A 553 19.848 89.378 80.637 1.00 18.24
C
ATOM 151 CD1 LEU A 553 20.878 90.214 79.890 1.00 16.80
C
ATOM 152 CD2 LEU A 553 19.329 90.145 81.873 1.00 15.80
C
ATOM 153 N GLU A 554 21.098 87.122 77.964 1.00 15.85
N
ATOM 154 CA GLU A 554 22.061 86.030 78.140 1.00 16.57
C
ATOM 155 C GLU A 554 23.489 86.499 77.856 1.00 16.47
C
ATOM 156 O GLU A 554 23.720 87.652 77.501 1.00 17.84
O
ATOM 157 CB GLU A 554 21.758 84.849 77.197 1.00 16.61
C
ATOM 158 CG GLU A 554 20.352 84.229 77.266 1.00 15.10
C
ATOM 159 CD GLU A 554 20.011 83.656 78.630 1.00 14.16
C
ATOM 160 OE1 GLU A 554 20.937 83.311 79.379 1.00 15.15
O
ATOM 161 OE2 GLU A 554 18.814 83.533 78.953 1.00 13.71
O
ATOM 162 N GLY A 555 24.434 85.578 77.993 1.00 16.15
N
ATOM 163 CA GLY A 555 25.837 85.870 77.751 1.00 17.28
C
ATOM 164 C GLY A 555 26.171 86.089 76.281 1.00 19.04
C
ATOM 165 O GLY A 555 25.394 85.716 75.389 1.00 17.28
O
ATOM 166 N SER A 556 27.346 86.676 76.049 1.00 19.19
N
ATOM 167 CA SER A 556 27.849 87.034 74.725 1.00 20.00
C
ATOM 168 C SER A 556 27.979 85.883 73.742 1.00 21.08
C
ATOM 169 O SER A 556 27.951 86.103 72.532 1.00 22.40
O
ATOM 170 CB SER A 556 29.207 87.727 74.859 1.00 21.49
C
ATOM 171 OG SER A 556 30.190 86.828 75.366 1.00 22.33
O
ATOM 172 N ASP A 557 28.130 84.668 74.264 1.00 19.85
N
ATOM 173 CA ASP A 557 28.263 83.472 73.437 1.00 18.54
C
ATOM 174 C ASP A 557 26.922 83.091 72.832 1.00 19.50
C
ATOM 175 O ASP A 557 26.859 82.227 71.950 1.00 18.23
O
ATOM 176 CB ASP A 557 28.787 82.298 74.276 1.00 16.94
C
ATOM 177 CG ASP A 557 27.976 82.086 75.562 1.00 14.92
C
ATOM 178 OD1 ASP A 557 27.515 83.084 76.141 1.00 15.85
O
ATOM 179 OD2 ASP A 557 27.814 80.936 76.008 1.00 14.87
O
ATOM 180 N GLN A 558 25.845 83.717 73.309 1.00 18.73
N
ATOM 181 CA GLN A 558 24.530 83.404 72.767 1.00 19.22
C
ATOM 182 C GLN A 558 24.226 84.122 71.453 1.00 19.40
C
ATOM 183 O GLN A 558 23.206 83.848 70.824 1.00 21.91
O
ATOM 184 CB GLN A 558 23.427 83.673 73.794 1.00 17.66
C
ATOM 185 CG GLN A 558 23.528 82.787 75.041 1.00 17.18
C
ATOM 186 CD GLN A 558 23.873 81.345 74.703 1.00 18.87
C
ATOM 187 OE1 GLN A 558 23.247 80.723 73.843 1.00 21.59
O
ATOM 188 NE2 GLN A 558 24.871 80.805 75.383 1.00 18.35
N
ATOM 189 N GLY A 561 24.701 81.509 69.675 1.00 22.35
N
ATOM 190 CA GLY A 561 23.864 80.475 70.253 1.00 20.34
C
ATOM 191 C GLY A 561 22.359 80.673 70.259 1.00 18.88
C
ATOM 192 O GLY A 561 21.733 80.797 69.209 1.00 21.58
O
ATOM 193 N TRP A 562 21.780 80.712 71.452 1.00 16.94
N
ATOM 194 CA TRP A 562 20.339 80.823 71.618 1.00 16.53
C
ATOM 195 C TRP A 562 19.687 82.026 70.963 1.00 17.05
C
ATOM 196 O TRP A 562 18.547 81.930 70.508 1.00 16.05
O
ATOM 197 CB TRP A 562 19.989 80.795 73.111 1.00 17.20
C
ATOM 198 CG TRP A 562 18.523 80.627 73.414 1.00 15.01
C
ATOM 199 CD1 TRP A 562 17.718 79.574 73.056 1.00 15.82
C
ATOM 200 CD2 TRP A 562 17.717 81.480 74.232 1.00 15.18
C
ATOM 201 NE1 TRP A 562 16.469 79.717 73.615 1.00 12.60
N
ATOM 202 CE2 TRP A 562 16.441 80.877 74.340 1.00 14.20
C
ATOM 203 CE3 TRP A 562 17.949 82.690 74.890 1.00 14.72
C
ATOM 204 CZ2 TRP A 562 15.407 81.448 75.082 1.00 14.81
C
ATOM 205 CZ3 TRP A 562 16.921 83.254 75.630 1.00 14.59
C
ATOM 206 CH2 TRP A 562 15.665 82.633 75.719 1.00 14.04
C
ATOM 207 N HIS A 585 25.223 90.175 78.319 1.00 20.31
N
ATOM 208 CA HIS A 585 26.253 90.543 79.282 1.00 18.60
C
ATOM 209 C HIS A 585 27.523 89.785 78.933 1.00 17.39
C
ATOM 210 O HIS A 585 27.500 88.884 78.093 1.00 17.25
O
ATOM 211 CB HIS A 585 25.807 90.216 80.722 1.00 19.36
C
ATOM 212 CG HIS A 585 25.492 88.770 80.953 1.00 18.17
C
ATOM 213 ND1 HIS A 585 24.200 88.288 81.001 1.00 19.77
N
ATOM 214 CD2 HIS A 585 26.300 87.697 81.127 1.00 17.82
C
ATOM 215 CE1 HIS A 585 24.225 86.980 81.193 1.00 17.60
C
ATOM 216 NE2 HIS A 585 25.486 86.597 81.273 1.00 20.27
N
ATOM 217 N GLY A 586 28.625 90.149 79.576 1.00 16.78
N
ATOM 218 CA GLY A 586 29.884 89.493 79.294 1.00 15.81
C
ATOM 219 C GLY A 586 30.079 88.299 80.202 1.00 17.98
C
ATOM 220 O GLY A 586 29.152 87.888 80.909 1.00 16.92
O
ATOM 221 N PHE A 587 31.287 87.739 80.162 1.00 16.05
N
ATOM 222 CA PHE A 587 31.649 86.596 80.976 1.00 15.59
C
ATOM 223 C PHE A 587 32.348 87.079 82.246 1.00 16.58
C
ATOM 224 O PHE A 587 32.816 88.225 82.323 1.00 15.87
O
ATOM 225 CB PHE A 587 32.607 85.691 80.205 1.00 15.92
C
ATOM 226 CG PHE A 587 31.931 84.705 79.303 1.00 15.13
C
ATOM 227 CD1 PHE A 587 30.846 85.083 78.516 1.00 16.16
C
ATOM 228 CD2 PHE A 587 32.395 83.395 79.228 1.00 13.25
C
ATOM 229 CE1 PHE A 587 30.225 84.162 77.660 1.00 16.73
C
ATOM 230 CE2 PHE A 587 31.785 82.471 78.380 1.00 15.11
C
ATOM 231 CZ PHE A 587 30.696 82.856 77.592 1.00 14.64
C
ATOM 232 N VAL A 588 32.432 86.189 83.229 1.00 13.22
N
ATOM 233 CA VAL A 588 33.075 86.500 84.494 1.00 12.41
C
ATOM 234 C VAL A 588 34.553 86.120 84.429 1.00 15.09
C
ATOM 235 O VAL A 588 34.897 84.959 84.180 1.00 16.46
O
ATOM 236 CB VAL A 588 32.400 85.726 85.624 1.00 11.13
C
ATOM 237 CG1 VAL A 588 33.002 86.106 86.971 1.00 10.18
C
ATOM 238 CG2 VAL A 588 30.913 85.983 85.591 1.00 6.06
C
ATOM 239 N MET A 589 35.421 87.106 84.629 1.00 16.18
N
ATOM 240 CA MET A 589 36.868 86.889 84.618 1.00 18.53
C
ATOM 241 C MET A 589 37.412 86.965 86.040 1.00 19.09
C
ATOM 242 O MET A 589 36.678 87.288 86.980 1.00 18.77
O
ATOM 243 CB MET A 589 37.580 87.968 83.789 1.00 19.91
C
ATOM 244 CG MET A 589 37.122 88.063 82.351 1.00 21.94
C
ATOM 245 SD MET A 589 37.172 86.454 81.594 1.00 25.18
S
ATOM 246 CE MET A 589 38.767 86.360 81.249 1.00 25.22
C
ATOM 247 N MET A 596 39.062 82.269 84.124 1.00 24.94
N
ATOM 248 CA MET A 596 39.182 81.456 85.322 1.00 25.58
C
ATOM 249 C MET A 596 39.496 80.071 84.788 1.00 26.30
C
ATOM 250 O MET A 596 38.873 79.612 83.836 1.00 25.93
O
ATOM 251 CB MET A 596 37.875 81.453 86.097 1.00 25.72
C
ATOM 252 CG MET A 596 37.335 82.848 86.332 1.00 28.37
C
ATOM 253 SD MET A 596 36.277 82.918 87.762 1.00 31.56
S
ATOM 254 CE MET A 596 34.906 81.961 87.180 1.00 30.37
C
ATOM 255 N SER A 597 40.472 79.413 85.394 1.00 28.56
N
ATOM 256 CA SER A 597 40.898 78.107 84.926 1.00 31.63
C
ATOM 257 C SER A 597 40.689 76.969 85.927 1.00 33.21
C
ATOM 258 O SER A 597 39.664 76.298 85.899 1.00 35.61
O
ATOM 259 CB SER A 597 42.373 78.202 84.507 1.00 30.61
C
ATOM 260 OG SER A 597 42.882 76.945 84.115 1.00 33.37
O
ATOM 261 N LYS A 598 41.668 76.764 86.798 1.00 33.92
N
ATOM 262 CA LYS A 598 41.665 75.714 87.824 1.00 35.55
C
ATOM 263 C LYS A 598 43.117 75.321 87.972 1.00 35.95
C
ATOM 264 O LYS A 598 43.605 75.093 89.077 1.00 38.29
O
ATOM 265 CB LYS A 598 40.838 74.489 87.422 1.00 36.06
C
ATOM 266 CG LYS A 598 39.620 74.288 88.314 1.00 36.99
C
ATOM 267 CD LYS A 598 38.755 73.116 87.874 1.00 38.45
C
ATOM 268 CE LYS A 598 37.472 73.054 88.699 1.00 39.45
C
ATOM 269 NZ LYS A 598 37.734 73.063 90.175 1.00 38.75
N
ATOM 270 N SER A 599 43.809 75.247 86.842 1.00 34.93
N
ATOM 271 CA SER A 599 45.223 74.950 86.867 1.00 34.79
C
ATOM 272 C SER A 599 45.861 76.230 87.397 1.00 33.98
C
ATOM 273 O SER A 599 46.978 76.217 87.912 1.00 35.72
O
ATOM 274 CB SER A 599 45.730 74.621 85.460 1.00 34.95
C
ATOM 275 OG SER A 599 45.226 75.537 84.501 1.00 39.80
O
ATOM 276 N VAL A 603 39.460 80.454 90.177 1.00 22.65
N
ATOM 277 CA VAL A 603 38.067 80.203 89.849 1.00 24.86
C
ATOM 278 C VAL A 603 36.981 80.941 90.633 1.00 25.80
C
ATOM 279 O VAL A 603 36.405 81.894 90.130 1.00 28.02
O
ATOM 280 CB VAL A 603 37.762 78.677 89.864 1.00 25.42
C
ATOM 281 CG1 VAL A 603 36.308 78.428 89.498 1.00 25.09
C
ATOM 282 CG2 VAL A 603 38.670 77.963 88.862 1.00 26.76
C
ATOM 283 N ILE A 604 36.698 80.535 91.859 1.00 24.62
N
ATOM 284 CA ILE A 604 35.611 81.182 92.589 1.00 23.04
C
ATOM 285 C ILE A 604 34.308 80.742 91.940 1.00 23.54
C
ATOM 286 O ILE A 604 34.030 81.047 90.773 1.00 23.65
O
ATOM 287 CB ILE A 604 35.662 82.714 92.531 1.00 21.95
C
ATOM 288 CG1 ILE A 604 36.861 83.221 93.339 1.00 20.26
C
ATOM 289 CG2 ILE A 604 34.335 83.291 93.075 1.00 20.23
C
ATOM 290 CD1 ILE A 604 36.957 84.718 93.390 1.00 19.36
C
ATOM 291 N VAL A 605 33.516 80.033 92.729 1.00 22.57
N
ATOM 292 CA VAL A 605 32.251 79.465 92.311 1.00 23.55
C
ATOM 293 C VAL A 605 31.103 80.074 93.118 1.00 25.03
C
ATOM 294 O VAL A 605 31.293 80.458 94.270 1.00 25.64
O
ATOM 295 CB VAL A 605 32.338 77.929 92.516 1.00 23.58
C
ATOM 296 CG1 VAL A 605 31.008 77.340 92.974 1.00 22.36
C
ATOM 297 CG2 VAL A 605 32.831 77.291 91.226 1.00 22.17
C
TER
END""")

print Chem.MolToSmiles(prot_mol)

# Outputs: (note no double bonds)

CCC(C)C(NC(O)C(N)C(C)C)C(O)NC(CO)C(C)C.CSCCC(CO)NC(O)C(NC(O)C(CC1CCCCC1)NC(O)CNC(O)C(N)CC1CNCN1)C(C)C.CSCCC(N)C(O)NC(CO)C(O)NC(CCCCN)C(O)NC(CO)CO.CSCCC(NC(O)C(N)CC1CNCN1)C(O)NCC(O)NC(CC1CNCN1)C(O)NC(C)C(O)NC(CC(C)C)C(O)NC(CO)CC(N)O.CC(C)CC(N)C(O)NC(CCC(O)O)C(O)NCC(O)NC(CO)C(O)NC(CC(O)O)C(O)NC(CO)CCC(N)O.NCCCCC(N)CO.NCC(O)NC(CO)CC1CNC2CCCCC12.NCC(O)N1CCCC1C(O)N1CCCC1C(O)NC(CO)CC1CCC(O)
CC1.NC(CO)CC(O)O.NC(CO)CC1CNC2CCCCC12.NC
(CO)C(O)NCCO.NC1CCN(C2OC(COP(O)O)C(O)C2O)C(O)N1

Post by JP
Also, is there a way to make AssignBondOrdersFromTemplate assign bond
orders to all matches?

The function was meant for assigning bonds based on an entire molecule. It
would probably not be so difficult to change this (with default = match
only one), if it is really needed.

1) a copy of the template is generated where all bonds are set to single
bonds
2) this single-bonds copy is used for a substructure match with the query
molecule
3) bond orders are assigned based on this match and the original template
If you get this warning, it means that there is some symmetry in the
"all-single-bonds-stage" of your molecule. In your case, I guess it's the
carboxylic acids which can match two ways when there are only single bonds.

Thanks for the explanation. This part is clear now.

Greg Landrum

2014-01-14 16:48:01 UTC

ok, it looks like something bad happened[1] when the PDB branch was merged
into trunk before the last release. Here's an example that worked properly
at the time of the UGM:

In [5]: m =Chem.MolFromPDBFile('data/2FVD.pdb')
In [6]: Chem.MolToSmiles(m,canonical=False)
Out[6]: 'NC(C(O)NC(C .... '

Here's the notebook showing what's supposed to happen:
http://nbviewer.ipython.org/github/rdkit/UGM_2013/blob/master/Notebooks/Whats_new.ipynb

I'll look into this as soon as I can and get it fixed.

-greg
[1] in other words: I seem to have screwed something up.

Post by sereina riniker
Hi JP,
However I am unable to get bond orders for the protein side - am I

doing something wrong or is this the intended behaviour ?
I imagine I can use AssignBondOrdersFromTemplate() for the 20 amino
acids and set these myself -- or is there a better way to do this?

I don't know why your protein doesn't get bond orders, the PDBParser
should know the standard amino acids. At least it worked for me when I
tried Chem.MolFromPDB() in the past. Which PDB structure do you try to read?

# (Using RDKit_2013_09_1)
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
prot_mol = Chem.MolFromPDBBlock("""ATOM 1 P C T 70 36.833
83.840 76.703 1.00 24.64 P
ATOM 2 OP1 C T 70 36.424 82.808 77.694 1.00 26.34
O
ATOM 3 OP2 C T 70 37.969 83.555 75.781 1.00 26.16
O
ATOM 4 O5' C T 70 35.587 84.229 75.793 1.00 22.26
O
ATOM 5 C5' C T 70 34.303 84.408 76.358 1.00 24.59
C
ATOM 6 C4' C T 70 33.305 84.740 75.281 1.00 24.33
C
ATOM 7 O4' C T 70 33.668 86.014 74.692 1.00 26.24
O
ATOM 8 C3' C T 70 33.307 83.794 74.087 1.00 26.50
C
ATOM 9 O3' C T 70 32.552 82.619 74.333 1.00 28.61
O
ATOM 10 C2' C T 70 32.707 84.664 72.988 1.00 26.61
C
ATOM 11 O2' C T 70 31.303 84.800 73.078 1.00 28.08
O
ATOM 12 C1' C T 70 33.336 86.016 73.311 1.00 25.28
C
ATOM 13 N1 C T 70 34.551 86.235 72.522 1.00 25.48
N
ATOM 14 C2 C T 70 34.409 86.756 71.233 1.00 22.70
C
ATOM 15 O2 C T 70 33.269 87.032 70.831 1.00 20.93
O
ATOM 16 N3 C T 70 35.506 86.948 70.471 1.00 21.93
N
ATOM 17 C4 C T 70 36.713 86.654 70.961 1.00 22.94
C
ATOM 18 N4 C T 70 37.774 86.874 70.181 1.00 22.99
N
ATOM 19 C5 C T 70 36.888 86.122 72.276 1.00 23.81
C
ATOM 20 C6 C T 70 35.791 85.931 73.015 1.00 23.64
C
TER
ATOM 21 N GLY A 55 16.572 81.800 79.047 1.00 24.32
N
ATOM 22 CA GLY A 55 17.264 80.922 78.115 1.00 21.44
C
ATOM 23 C GLY A 55 17.511 79.665 78.938 1.00 19.98
C
ATOM 24 O GLY A 55 17.960 79.782 80.070 1.00 18.32
O
ATOM 25 N PRO A 56 17.248 78.456 78.415 1.00 19.67
N
ATOM 26 CA PRO A 56 17.452 77.216 79.178 1.00 19.71
C
ATOM 27 C PRO A 56 18.863 76.711 79.438 1.00 20.15
C
ATOM 28 O PRO A 56 19.515 76.211 78.529 1.00 20.52
O
ATOM 29 CB PRO A 56 16.654 76.195 78.378 1.00 19.65
C
ATOM 30 CG PRO A 56 16.917 76.637 76.970 1.00 19.83
C
ATOM 31 CD PRO A 56 16.737 78.158 77.064 1.00 18.98
C
ATOM 32 N PRO A 57 19.341 76.795 80.694 1.00 20.23
N
ATOM 33 CA PRO A 57 20.695 76.307 80.976 1.00 20.02
C
ATOM 34 C PRO A 57 20.732 74.811 80.752 1.00 19.70
C
ATOM 35 O PRO A 57 19.699 74.155 80.795 1.00 18.65
O
ATOM 36 CB PRO A 57 20.913 76.687 82.449 1.00 21.28
C
ATOM 37 CG PRO A 57 19.546 76.673 83.017 1.00 19.57
C
ATOM 38 CD PRO A 57 18.722 77.336 81.916 1.00 21.61
C
ATOM 39 N TYR A 58 21.922 74.273 80.518 1.00 20.78
N
ATOM 40 CA TYR A 58 22.068 72.854 80.267 1.00 20.66
C
ATOM 41 C TYR A 58 22.037 72.020 81.538 1.00 22.45
C
ATOM 42 O TYR A 58 22.782 72.273 82.491 1.00 21.68
O
ATOM 43 CB TYR A 58 23.359 72.591 79.515 1.00 21.91
C
ATOM 44 CG TYR A 58 23.343 71.252 78.831 1.00 23.30
C
ATOM 45 CD1 TYR A 58 22.483 71.010 77.751 1.00 21.40
C
ATOM 46 CD2 TYR A 58 24.165 70.217 79.269 1.00 22.13
C
ATOM 47 CE1 TYR A 58 22.447 69.773 77.127 1.00 20.96
C
ATOM 48 CE2 TYR A 58 24.133 68.975 78.652 1.00 23.29
C
ATOM 49 CZ TYR A 58 23.274 68.758 77.581 1.00 21.33
C
ATOM 50 OH TYR A 58 23.249 67.522 76.976 1.00 22.48
O
ATOM 51 N HIS A 64 28.134 77.876 87.356 1.00 16.16
N
ATOM 52 CA HIS A 64 29.370 78.628 87.473 1.00 16.18
C
ATOM 53 C HIS A 64 28.951 80.089 87.685 1.00 15.24
C
ATOM 54 O HIS A 64 27.767 80.402 87.639 1.00 13.81
O
ATOM 55 CB HIS A 64 30.227 78.469 86.209 1.00 15.17
C
ATOM 56 CG HIS A 64 29.501 78.777 84.939 1.00 17.43
C
ATOM 57 ND1 HIS A 64 29.378 77.862 83.913 1.00 17.53
N
ATOM 58 CD2 HIS A 64 28.901 79.912 84.508 1.00 15.04
C
ATOM 59 CE1 HIS A 64 28.737 78.422 82.902 1.00 17.82
C
ATOM 60 NE2 HIS A 64 28.436 79.666 83.236 1.00 21.06
N
ATOM 61 N MET A 65 29.912 80.969 87.928 1.00 15.38
N
ATOM 62 CA MET A 65 29.630 82.383 88.171 1.00 16.74
C
ATOM 63 C MET A 65 28.774 83.047 87.075 1.00 17.60
C
ATOM 64 O MET A 65 28.042 84.004 87.338 1.00 17.28
O
ATOM 65 CB MET A 65 30.951 83.142 88.332 1.00 16.05
C
ATOM 66 CG MET A 65 30.917 84.201 89.423 1.00 19.05
C
ATOM 67 SD MET A 65 30.477 83.491 91.028 1.00 21.29
S
ATOM 68 CE MET A 65 29.105 84.522 91.457 1.00 19.14
C
ATOM 69 N GLY A 66 28.877 82.545 85.849 1.00 16.38
N
ATOM 70 CA GLY A 66 28.087 83.097 84.759 1.00 16.17
C
ATOM 71 C GLY A 66 26.596 82.870 84.978 1.00 16.45
C
ATOM 72 O GLY A 66 25.777 83.744 84.690 1.00 16.27
O
ATOM 73 N HIS A 67 26.229 81.694 85.480 1.00 15.53
N
ATOM 74 CA HIS A 67 24.817 81.415 85.737 1.00 17.28
C
ATOM 75 C HIS A 67 24.292 82.388 86.781 1.00 15.79
C
ATOM 76 O HIS A 67 23.162 82.858 86.683 1.00 17.54
O
ATOM 77 CB HIS A 67 24.609 79.990 86.270 1.00 17.57
C
ATOM 78 CG HIS A 67 24.902 78.914 85.270 1.00 19.11
C
ATOM 79 ND1 HIS A 67 26.071 78.183 85.284 1.00 17.88
N
ATOM 80 CD2 HIS A 67 24.163 78.426 84.245 1.00 17.47
C
ATOM 81 CE1 HIS A 67 26.036 77.287 84.314 1.00 19.15
C
ATOM 82 NE2 HIS A 67 24.889 77.413 83.670 1.00 16.21
N
ATOM 83 N ALA A 68 25.125 82.663 87.783 1.00 13.71
N
ATOM 84 CA ALA A 68 24.782 83.558 88.878 1.00 13.53
C
ATOM 85 C ALA A 68 24.592 84.990 88.389 1.00 12.34
C
ATOM 86 O ALA A 68 23.585 85.621 88.695 1.00 12.93
O
ATOM 87 CB ALA A 68 25.872 83.497 89.959 1.00 14.07
C
ATOM 88 N LEU A 69 25.561 85.484 87.622 1.00 10.80
N
ATOM 89 CA LEU A 69 25.499 86.828 87.065 1.00 11.73
C
ATOM 90 C LEU A 69 24.203 86.998 86.269 1.00 12.69
C
ATOM 91 O LEU A 69 23.421 87.932 86.503 1.00 11.38
O
ATOM 92 CB LEU A 69 26.687 87.077 86.124 1.00 9.60
C
ATOM 93 CG LEU A 69 26.543 88.339 85.268 1.00 8.37
C
ATOM 94 CD1 LEU A 69 26.584 89.536 86.171 1.00 6.65
C
ATOM 95 CD2 LEU A 69 27.667 88.439 84.222 1.00 9.77
C
ATOM 96 N ASN A 70 23.993 86.066 85.340 1.00 13.60
N
ATOM 97 CA ASN A 70 22.839 86.051 84.454 1.00 14.47
C
ATOM 98 C ASN A 70 21.485 85.948 85.150 1.00 14.28
C
ATOM 99 O ASN A 70 20.544 86.653 84.787 1.00 15.95
O
ATOM 100 CB ASN A 70 22.968 84.895 83.450 1.00 14.15
C
ATOM 101 CG ASN A 70 21.689 84.678 82.654 1.00 14.47
C
ATOM 102 OD1 ASN A 70 20.811 83.910 83.057 1.00 12.26
O
ATOM 103 ND2 ASN A 70 21.563 85.384 81.530 1.00 16.87
N
ATOM 104 N LYS A 74 18.580 88.964 85.786 1.00 13.79
N
ATOM 105 CA LYS A 74 17.192 88.703 85.412 1.00 15.44
C
ATOM 106 C LYS A 74 16.237 89.035 86.558 1.00 15.10
C
ATOM 107 O LYS A 74 15.203 89.674 86.348 1.00 13.82
O
ATOM 108 CB LYS A 74 17.014 87.228 85.028 1.00 13.86
C
ATOM 109 CG LYS A 74 17.639 86.879 83.700 1.00 14.38
C
ATOM 110 CD LYS A 74 17.573 85.399 83.415 1.00 11.34
C
ATOM 111 CE LYS A 74 17.974 85.153 81.964 1.00 9.22
C
ATOM 112 NZ LYS A 74 18.226 83.726 81.726 1.00 6.91
N
ATOM 113 N ASP A 95 17.612 72.846 79.490 1.00 22.31
N
ATOM 114 CA ASP A 95 18.000 72.193 78.250 1.00 20.84
C
ATOM 115 C ASP A 95 18.382 70.774 78.687 1.00 19.47
C
ATOM 116 O ASP A 95 19.348 70.597 79.422 1.00 18.03
O
ATOM 117 CB ASP A 95 19.195 72.946 77.667 1.00 20.82
C
ATOM 118 CG ASP A 95 19.219 72.925 76.153 1.00 23.49
C
ATOM 119 OD1 ASP A 95 18.142 72.737 75.550 1.00 21.52
O
ATOM 120 OD2 ASP A 95 20.315 73.118 75.569 1.00 23.96
O
ATOM 121 N TRP A 528 20.582 73.020 69.677 1.00 23.71
N
ATOM 122 CA TRP A 528 20.332 74.440 69.457 1.00 23.24
C
ATOM 123 C TRP A 528 18.905 74.570 68.935 1.00 21.85
C
ATOM 124 O TRP A 528 18.220 75.556 69.214 1.00 20.38
O
ATOM 125 CB TRP A 528 21.316 75.036 68.435 1.00 22.52
C
ATOM 126 CG TRP A 528 22.700 75.272 68.988 1.00 24.85
C
ATOM 127 CD1 TRP A 528 23.873 74.792 68.486 1.00 25.49
C
ATOM 128 CD2 TRP A 528 23.050 76.047 70.151 1.00 23.69
C
ATOM 129 NE1 TRP A 528 24.931 75.213 69.259 1.00 26.56
N
ATOM 130 CE2 TRP A 528 24.456 75.986 70.286 1.00 25.78
C
ATOM 131 CE3 TRP A 528 22.310 76.786 71.088 1.00 24.37
C
ATOM 132 CZ2 TRP A 528 25.146 76.638 71.326 1.00 25.91
C
ATOM 133 CZ3 TRP A 528 22.995 77.439 72.123 1.00 23.91
C
ATOM 134 CH2 TRP A 528 24.399 77.358 72.230 1.00 25.34
C
ATOM 135 N SER A 531 16.450 74.372 72.143 1.00 20.16
N
ATOM 136 CA SER A 531 16.319 75.621 72.893 1.00 19.65
C
ATOM 137 C SER A 531 15.786 76.708 71.993 1.00 19.35
C
ATOM 138 O SER A 531 14.973 77.537 72.407 1.00 19.32
O
ATOM 139 CB SER A 531 17.671 76.055 73.479 1.00 17.88
C
ATOM 140 OG SER A 531 18.648 76.204 72.467 1.00 17.02
O
ATOM 141 N GLY A 532 16.245 76.691 70.751 1.00 20.07
N
ATOM 142 CA GLY A 532 15.809 77.687 69.799 1.00 20.95
C
ATOM 143 C GLY A 532 14.309 77.708 69.592 1.00 21.44
C
ATOM 144 O GLY A 532 13.786 78.667 69.041 1.00 22.61
O
ATOM 145 N LEU A 553 17.820 87.851 77.715 1.00 16.25
N
ATOM 146 CA LEU A 553 19.029 88.343 78.371 1.00 18.27
C
ATOM 147 C LEU A 553 19.950 87.160 78.639 1.00 17.66
C
ATOM 148 O LEU A 553 19.612 86.289 79.436 1.00 20.05
O
ATOM 149 CB LEU A 553 18.680 89.040 79.695 1.00 16.91
C
ATOM 150 CG LEU A 553 19.848 89.378 80.637 1.00 18.24
C
ATOM 151 CD1 LEU A 553 20.878 90.214 79.890 1.00 16.80
C
ATOM 152 CD2 LEU A 553 19.329 90.145 81.873 1.00 15.80
C
ATOM 153 N GLU A 554 21.098 87.122 77.964 1.00 15.85
N
ATOM 154 CA GLU A 554 22.061 86.030 78.140 1.00 16.57
C
ATOM 155 C GLU A 554 23.489 86.499 77.856 1.00 16.47
C
ATOM 156 O GLU A 554 23.720 87.652 77.501 1.00 17.84
O
ATOM 157 CB GLU A 554 21.758 84.849 77.197 1.00 16.61
C
ATOM 158 CG GLU A 554 20.352 84.229 77.266 1.00 15.10
C
ATOM 159 CD GLU A 554 20.011 83.656 78.630 1.00 14.16
C
ATOM 160 OE1 GLU A 554 20.937 83.311 79.379 1.00 15.15
O
ATOM 161 OE2 GLU A 554 18.814 83.533 78.953 1.00 13.71
O
ATOM 162 N GLY A 555 24.434 85.578 77.993 1.00 16.15
N
ATOM 163 CA GLY A 555 25.837 85.870 77.751 1.00 17.28
C
ATOM 164 C GLY A 555 26.171 86.089 76.281 1.00 19.04
C
ATOM 165 O GLY A 555 25.394 85.716 75.389 1.00 17.28
O
ATOM 166 N SER A 556 27.346 86.676 76.049 1.00 19.19
N
ATOM 167 CA SER A 556 27.849 87.034 74.725 1.00 20.00
C
ATOM 168 C SER A 556 27.979 85.883 73.742 1.00 21.08
C
ATOM 169 O SER A 556 27.951 86.103 72.532 1.00 22.40
O
ATOM 170 CB SER A 556 29.207 87.727 74.859 1.00 21.49
C
ATOM 171 OG SER A 556 30.190 86.828 75.366 1.00 22.33
O
ATOM 172 N ASP A 557 28.130 84.668 74.264 1.00 19.85
N
ATOM 173 CA ASP A 557 28.263 83.472 73.437 1.00 18.54
C
ATOM 174 C ASP A 557 26.922 83.091 72.832 1.00 19.50
C
ATOM 175 O ASP A 557 26.859 82.227 71.950 1.00 18.23
O
ATOM 176 CB ASP A 557 28.787 82.298 74.276 1.00 16.94
C
ATOM 177 CG ASP A 557 27.976 82.086 75.562 1.00 14.92
C
ATOM 178 OD1 ASP A 557 27.515 83.084 76.141 1.00 15.85
O
ATOM 179 OD2 ASP A 557 27.814 80.936 76.008 1.00 14.87
O
ATOM 180 N GLN A 558 25.845 83.717 73.309 1.00 18.73
N
ATOM 181 CA GLN A 558 24.530 83.404 72.767 1.00 19.22
C
ATOM 182 C GLN A 558 24.226 84.122 71.453 1.00 19.40
C
ATOM 183 O GLN A 558 23.206 83.848 70.824 1.00 21.91
O
ATOM 184 CB GLN A 558 23.427 83.673 73.794 1.00 17.66
C
ATOM 185 CG GLN A 558 23.528 82.787 75.041 1.00 17.18
C
ATOM 186 CD GLN A 558 23.873 81.345 74.703 1.00 18.87
C
ATOM 187 OE1 GLN A 558 23.247 80.723 73.843 1.00 21.59
O
ATOM 188 NE2 GLN A 558 24.871 80.805 75.383 1.00 18.35
N
ATOM 189 N GLY A 561 24.701 81.509 69.675 1.00 22.35
N
ATOM 190 CA GLY A 561 23.864 80.475 70.253 1.00 20.34
C
ATOM 191 C GLY A 561 22.359 80.673 70.259 1.00 18.88
C
ATOM 192 O GLY A 561 21.733 80.797 69.209 1.00 21.58
O
ATOM 193 N TRP A 562 21.780 80.712 71.452 1.00 16.94
N
ATOM 194 CA TRP A 562 20.339 80.823 71.618 1.00 16.53
C
ATOM 195 C TRP A 562 19.687 82.026 70.963 1.00 17.05
C
ATOM 196 O TRP A 562 18.547 81.930 70.508 1.00 16.05
O
ATOM 197 CB TRP A 562 19.989 80.795 73.111 1.00 17.20
C
ATOM 198 CG TRP A 562 18.523 80.627 73.414 1.00 15.01
C
ATOM 199 CD1 TRP A 562 17.718 79.574 73.056 1.00 15.82
C
ATOM 200 CD2 TRP A 562 17.717 81.480 74.232 1.00 15.18
C
ATOM 201 NE1 TRP A 562 16.469 79.717 73.615 1.00 12.60
N
ATOM 202 CE2 TRP A 562 16.441 80.877 74.340 1.00 14.20
C
ATOM 203 CE3 TRP A 562 17.949 82.690 74.890 1.00 14.72
C
ATOM 204 CZ2 TRP A 562 15.407 81.448 75.082 1.00 14.81
C
ATOM 205 CZ3 TRP A 562 16.921 83.254 75.630 1.00 14.59
C
ATOM 206 CH2 TRP A 562 15.665 82.633 75.719 1.00 14.04
C
ATOM 207 N HIS A 585 25.223 90.175 78.319 1.00 20.31
N
ATOM 208 CA HIS A 585 26.253 90.543 79.282 1.00 18.60
C
ATOM 209 C HIS A 585 27.523 89.785 78.933 1.00 17.39
C
ATOM 210 O HIS A 585 27.500 88.884 78.093 1.00 17.25
O
ATOM 211 CB HIS A 585 25.807 90.216 80.722 1.00 19.36
C
ATOM 212 CG HIS A 585 25.492 88.770 80.953 1.00 18.17
C
ATOM 213 ND1 HIS A 585 24.200 88.288 81.001 1.00 19.77
N
ATOM 214 CD2 HIS A 585 26.300 87.697 81.127 1.00 17.82
C
ATOM 215 CE1 HIS A 585 24.225 86.980 81.193 1.00 17.60
C
ATOM 216 NE2 HIS A 585 25.486 86.597 81.273 1.00 20.27
N
ATOM 217 N GLY A 586 28.625 90.149 79.576 1.00 16.78
N
ATOM 218 CA GLY A 586 29.884 89.493 79.294 1.00 15.81
C
ATOM 219 C GLY A 586 30.079 88.299 80.202 1.00 17.98
C
ATOM 220 O GLY A 586 29.152 87.888 80.909 1.00 16.92
O
ATOM 221 N PHE A 587 31.287 87.739 80.162 1.00 16.05
N
ATOM 222 CA PHE A 587 31.649 86.596 80.976 1.00 15.59
C
ATOM 223 C PHE A 587 32.348 87.079 82.246 1.00 16.58
C
ATOM 224 O PHE A 587 32.816 88.225 82.323 1.00 15.87
O
ATOM 225 CB PHE A 587 32.607 85.691 80.205 1.00 15.92
C
ATOM 226 CG PHE A 587 31.931 84.705 79.303 1.00 15.13
C
ATOM 227 CD1 PHE A 587 30.846 85.083 78.516 1.00 16.16
C
ATOM 228 CD2 PHE A 587 32.395 83.395 79.228 1.00 13.25
C
ATOM 229 CE1 PHE A 587 30.225 84.162 77.660 1.00 16.73
C
ATOM 230 CE2 PHE A 587 31.785 82.471 78.380 1.00 15.11
C
ATOM 231 CZ PHE A 587 30.696 82.856 77.592 1.00 14.64
C
ATOM 232 N VAL A 588 32.432 86.189 83.229 1.00 13.22
N
ATOM 233 CA VAL A 588 33.075 86.500 84.494 1.00 12.41
C
ATOM 234 C VAL A 588 34.553 86.120 84.429 1.00 15.09
C
ATOM 235 O VAL A 588 34.897 84.959 84.180 1.00 16.46
O
ATOM 236 CB VAL A 588 32.400 85.726 85.624 1.00 11.13
C
ATOM 237 CG1 VAL A 588 33.002 86.106 86.971 1.00 10.18
C
ATOM 238 CG2 VAL A 588 30.913 85.983 85.591 1.00 6.06
C
ATOM 239 N MET A 589 35.421 87.106 84.629 1.00 16.18
N
ATOM 240 CA MET A 589 36.868 86.889 84.618 1.00 18.53
C
ATOM 241 C MET A 589 37.412 86.965 86.040 1.00 19.09
C
ATOM 242 O MET A 589 36.678 87.288 86.980 1.00 18.77
O
ATOM 243 CB MET A 589 37.580 87.968 83.789 1.00 19.91
C
ATOM 244 CG MET A 589 37.122 88.063 82.351 1.00 21.94
C
ATOM 245 SD MET A 589 37.172 86.454 81.594 1.00 25.18
S
ATOM 246 CE MET A 589 38.767 86.360 81.249 1.00 25.22
C
ATOM 247 N MET A 596 39.062 82.269 84.124 1.00 24.94
N
ATOM 248 CA MET A 596 39.182 81.456 85.322 1.00 25.58
C
ATOM 249 C MET A 596 39.496 80.071 84.788 1.00 26.30
C
ATOM 250 O MET A 596 38.873 79.612 83.836 1.00 25.93
O
ATOM 251 CB MET A 596 37.875 81.453 86.097 1.00 25.72
C
ATOM 252 CG MET A 596 37.335 82.848 86.332 1.00 28.37
C
ATOM 253 SD MET A 596 36.277 82.918 87.762 1.00 31.56
S
ATOM 254 CE MET A 596 34.906 81.961 87.180 1.00 30.37
C
ATOM 255 N SER A 597 40.472 79.413 85.394 1.00 28.56
N
ATOM 256 CA SER A 597 40.898 78.107 84.926 1.00 31.63
C
ATOM 257 C SER A 597 40.689 76.969 85.927 1.00 33.21
C
ATOM 258 O SER A 597 39.664 76.298 85.899 1.00 35.61
O
ATOM 259 CB SER A 597 42.373 78.202 84.507 1.00 30.61
C
ATOM 260 OG SER A 597 42.882 76.945 84.115 1.00 33.37
O
ATOM 261 N LYS A 598 41.668 76.764 86.798 1.00 33.92
N
ATOM 262 CA LYS A 598 41.665 75.714 87.824 1.00 35.55
C
ATOM 263 C LYS A 598 43.117 75.321 87.972 1.00 35.95
C
ATOM 264 O LYS A 598 43.605 75.093 89.077 1.00 38.29
O
ATOM 265 CB LYS A 598 40.838 74.489 87.422 1.00 36.06
C
ATOM 266 CG LYS A 598 39.620 74.288 88.314 1.00 36.99
C
ATOM 267 CD LYS A 598 38.755 73.116 87.874 1.00 38.45
C
ATOM 268 CE LYS A 598 37.472 73.054 88.699 1.00 39.45
C
ATOM 269 NZ LYS A 598 37.734 73.063 90.175 1.00 38.75
N
ATOM 270 N SER A 599 43.809 75.247 86.842 1.00 34.93
N
ATOM 271 CA SER A 599 45.223 74.950 86.867 1.00 34.79
C
ATOM 272 C SER A 599 45.861 76.230 87.397 1.00 33.98
C
ATOM 273 O SER A 599 46.978 76.217 87.912 1.00 35.72
O
ATOM 274 CB SER A 599 45.730 74.621 85.460 1.00 34.95
C
ATOM 275 OG SER A 599 45.226 75.537 84.501 1.00 39.80
O
ATOM 276 N VAL A 603 39.460 80.454 90.177 1.00 22.65
N
ATOM 277 CA VAL A 603 38.067 80.203 89.849 1.00 24.86
C
ATOM 278 C VAL A 603 36.981 80.941 90.633 1.00 25.80
C
ATOM 279 O VAL A 603 36.405 81.894 90.130 1.00 28.02
O
ATOM 280 CB VAL A 603 37.762 78.677 89.864 1.00 25.42
C
ATOM 281 CG1 VAL A 603 36.308 78.428 89.498 1.00 25.09
C
ATOM 282 CG2 VAL A 603 38.670 77.963 88.862 1.00 26.76
C
ATOM 283 N ILE A 604 36.698 80.535 91.859 1.00 24.62
N
ATOM 284 CA ILE A 604 35.611 81.182 92.589 1.00 23.04
C
ATOM 285 C ILE A 604 34.308 80.742 91.940 1.00 23.54
C
ATOM 286 O ILE A 604 34.030 81.047 90.773 1.00 23.65
O
ATOM 287 CB ILE A 604 35.662 82.714 92.531 1.00 21.95
C
ATOM 288 CG1 ILE A 604 36.861 83.221 93.339 1.00 20.26
C
ATOM 289 CG2 ILE A 604 34.335 83.291 93.075 1.00 20.23
C
ATOM 290 CD1 ILE A 604 36.957 84.718 93.390 1.00 19.36
C
ATOM 291 N VAL A 605 33.516 80.033 92.729 1.00 22.57
N
ATOM 292 CA VAL A 605 32.251 79.465 92.311 1.00 23.55
C
ATOM 293 C VAL A 605 31.103 80.074 93.118 1.00 25.03
C
ATOM 294 O VAL A 605 31.293 80.458 94.270 1.00 25.64
O
ATOM 295 CB VAL A 605 32.338 77.929 92.516 1.00 23.58
C
ATOM 296 CG1 VAL A 605 31.008 77.340 92.974 1.00 22.36
C
ATOM 297 CG2 VAL A 605 32.831 77.291 91.226 1.00 22.17
C
TER
END""")
print Chem.MolToSmiles(prot_mol)
# Outputs: (note no double bonds)
CCC(C)C(NC(O)C(N)C(C)C)C(O)NC(CO)C(C)C.CSCCC(CO)NC(O)C(NC(O)C(CC1CCCCC1)NC(O)CNC(O)C(N)CC1CNCN1)C(C)C.CSCCC(N)C(O)NC(CO)C(O)NC(CCCCN)C(O)NC(CO)CO.CSCCC(NC(O)C(N)CC1CNCN1)C(O)NCC(O)NC(CC1CNCN1)C(O)NC(C)C(O)NC(CC(C)C)C(O)NC(CO)CC(N)O.CC(C)CC(N)C(O)NC(CCC(O)O)C(O)NCC(O)NC(CO)C(O)NC(CC(O)O)C(O)NC(CO)CCC(N)O.NCCCCC(N)CO.NCC(O)NC(CO)CC1CNC2CCCCC12.NCC(O)N1CCCC1C(O)N1CCCC1C(O)NC(CO)CC1CCC(O)
CC1.NC(CO)CC(O)O.NC(CO)CC1CNC2CCCCC12.NC
(CO)C(O)NCCO.NC1CCN(C2OC(COP(O)O)C(O)C2O)C(O)N1

Also, is there a way to make AssignBondOrdersFromTemplate assign bond
orders to all matches?

The function was meant for assigning bonds based on an entire molecule.
It would probably not be so difficult to change this (with default = match
only one), if it is really needed.

Also another thing I don't quite understand is in the following below
code, I get a "WARNING: More than one matching pattern found - picking one"
but how can my template match multiple times (this is not symettrical) ?

Thanks for the explanation. This part is clear now.
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Greg Landrum

2014-01-15 08:38:15 UTC

Post by Greg Landrum
ok, it looks like something bad happened[1] when the PDB branch was merged
into trunk before the last release. Here's an example that worked properly
In [5]: m =Chem.MolFromPDBFile('data/2FVD.pdb')
In [6]: Chem.MolToSmiles(m,canonical=False)
Out[6]: 'NC(C(O)NC(C .... '
http://nbviewer.ipython.org/github/rdkit/UGM_2013/blob/master/Notebooks/Whats_new.ipynb
I'll look into this as soon as I can and get it fixed.

I just tracked this down and fixed it. The changes are checked into github.
Details about what happened are below.

Here's my example from above now:

In [3]: m = Chem.MolFromPDBFile('./2FVD.pdb')
In [4]: Chem.MolToSmiles(m,canonical=False)
Out[4]: 'NC(C(=O)NC(C(=O)NC(C(=O....'

This is, IMO, a major enough problem that it's worth doing a patch release
to address it. Over the next few days, I will put together a list of fixes
(not new features) that should be in the 2013_09_2 release and adjust the
milestones for those issues. Please feel free to suggest additions. The
list (currently empty) can be found here:
https://github.com/rdkit/rdkit/issues?milestone=6

For those who care, here's how the bug came about.
The bond-type assignment code for standard PDB residues tests bonded atoms
to make sure they are in the same residue. This code compares the two
atoms' AtomPDBResidueInfo structures. Shortly before the 2013_09_1 release,
I added an explicit residueNumber property to the AtomPDBResidueInfo class
and switched the serialNumber property (previously used to store the
residueNumber) to capture the actual serial number of the atom. I forgot to
update the residue comparison code to reflect this change, so
the SamePDBResidue() function was returning false unless the two atoms were
the same. silly mistake.

Best,
-greg

2014-01-15 09:50:25 UTC