Re: [Rdkit-discuss] PyObject * - RDKit::ROMol *
Hi,
Am 29.04.2012 16:19, schrieb Paul Emsley:
I am trying to write a C++ function to examine an RDKit::ROMol... but
running it from a python script:
m = Chem.MolFromSmilesString('Oc1c1')
do_cool_stuff(m)
my C++ (which gets swigged) is:
PyObject *do_cool_stuff(PyObject *pyo) {
RDKit::ROMol *mol = magic(pyo);
using a reference instead of pointer access:
RDKit::ROMol mol = boost::python::extractRDKit::ROMol(m);
via pointer access:
RDKit::ROMol *mol;
mol=boost::python::extractRDKit::ROMol*(m);
inner_cool_stuff(mol);
...
Regards
Uwe
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Re: [Rdkit-discuss] PyObject * - RDKit::ROMol *
On 30/04/12 08:39, Uwe Hoffmann wrote:
Hi,
Am 29.04.2012 16:19, schrieb Paul Emsley:
I am trying to write a C++ function to examine an RDKit::ROMol... but
running it from a python script:
m = Chem.MolFromSmilesString('Oc1c1')
do_cool_stuff(m)
my C++ (which gets swigged) is:
PyObject *do_cool_stuff(PyObject *pyo) {
RDKit::ROMol *mol = magic(pyo);
using a reference instead of pointer access:
RDKit::ROMolmol = boost::python::extractRDKit::ROMol(m);
Ah! Magic! Just what I wanted.
(actually, I forgot that Greg was away, or I would have held back on
sending this :-)
Cheers,
Paul.
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Re: [Rdkit-discuss] Molecule with no atoms, so is it valid?
On 2012-04-30 13:41, Paul Emsley wrote: On 30/04/12 01:03, Eddie Cao wrote: Hi Andrew, I also prefer #2. #1 is not quite sensible because many readers like MolFromSmiles will return None on failure and it will be hard to distinguish bad input from an empty one if we choose to do #1. Semantically, in many RDKit use cases, None and Empty Mol are as different as a webpage not found (HTTP 404) and a blank web page. FWIW, I agree to #2 too. Paul. My humble opinion would also be that #2 is the best option. In line with the analogy given by Eddie, treating an empty molecule as an error is equivalent to saying that a blank string is equal to NULL - which would be unfortunate, since there is a big semantic difference. Also, imagine that you delete all atoms and bonds in a molecule in order to replace them. Enforcing the semantics of empty molecules are invalid should then cause your code to break half-way through the process ? Cheers -- Jan Holst Jensen -- 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
[Rdkit-discuss] Failed Expression: pick = 0
I'm desalting the ChEMBL data set and generating the corresponding de-salted SD and SMILES files. I found a problem in the conversion step, and found that the problem has nothing to do with the de-salting. My code failed with CHEMBL1269997, which is record ~750,200 out of 1,142,974. (In other words, it took a while to get to this point.) Here's a reproducible: from rdkit import Chem writer = Chem.SDWriter(/dev/stdout) for mol in Chem.ForwardSDMolSupplier(CHEMBL1269997.sdf): ... writer.write(mol) ... [22:11:05] Invariant Violation Violation occurred on line 388 in file /tmp/homebrew-rdkit-HEAD-Ebdo/Code/GraphMol/FileParsers/MolFileStereochem.cpp Failed Expression: pick = 0 Traceback (most recent call last): File stdin, line 2, in module RuntimeError: Invariant Violation Chem.MolToSmiles(mol) 'OCC1=CC2OC(CC(C)C)(CC(C)C)C3C456C(OC(C)(C)O5)C1(O)C46C23' Chem.MolToSmiles(mol, isomericSmiles=True) 'OCC1=C[C@@H]2OC(CC(C)C)(CC(C)C)[C@@H]3[C@H]4CCC[C@@]56[C@@H](OC(C)(C)O5)[C@]1(O)[C@]46[C@H]23' You can see that the molecule was read in, is not None, and can be used to generate a SMILES. The CHEMBL1269997.sdf is attached. This error was previously reported in the thread JP started, titled Invariant violation..., dated July 6, 2011. Greg replied: Wow that is certainly an error I never expected to see. From the code, I guess the molecule has a stereocenter that is surrounded by other stereocenters and something extremely unfortunate is happening with the way decisions are being made about which bonds to wedge. As Eddie requested in an earlier message, it would be helpful to have the input that produced the error so that it can be added to the test cases (and so that I can be sure the problem is fixed once I figure out how to). but I see no posting of a failing structure. I hope the attached structure helps resolve this problem. Andrew da...@dalkescientific.com CHEMBL1269997.sdf Description: Binary data -- 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
