OBConversion reinitialization for WriteString() and WriteFile()

[adalke]

• [ X] I believe this to be a bug with Open Babel
• This is a feature request

Environment Information

Open Babel version: 2.4.90 (HEAD as of 14 January 2019)
Operating system and version: macOS 10.12.2

Expected Behavior

I expect to be able to write to FPS format using OBConversion without having a segfault. Here are examples of expected behavior:

Example 1 (expected)

>>> import pybel
>>> print(pybel.readstring("smi", "C").write("fps")[:70])
#FPS1
#num_bits=1021
#type=OpenBabel-FP2/1
#software=OpenBabel/2.4.90

Example 2 (expected)

>>> import openbabel as ob
>>> conv = ob.OBConversion()
>>> conv.SetInAndOutFormats("smi", "fps")
True
>>> mol = ob.OBMol()
>>> conv.ReadString(mol, "C")
True
>>> conv.WriteString(mol)
'#FPS1\n#num_bits=1021\n#type=OpenBabel-FP2/1\n#software=OpenBabel/2.4.90\n ...`
>>> conv.WriteFile(mol, "example.fps")
True
>>> print(open("example.fps").read()[:80])
#FPS1
#num_bits=1021
#type=OpenBabel-FP2/1
#software=OpenBabel/2.4.90
#source=
#

Actual Behavior

The above code on the current Open Babel HEAD (and with 2.4.1) causes segmentation faults:

Steps to Reproduce

Example 1 (actual)

>>> import pybel
>>> pybel.readstring("smi", "C").write("fps")
Segmentation fault

Example 2 (actual)

>>> import openbabel as ob
>>> conv = ob.OBConversion()
>>> conv.SetInAndOutFormats("smi", "fps")
True
>>> mol = ob.OBMol()
>>> conv.ReadString(mol, "C")
True
>>> conv.WriteString(mol)
Segmentation fault

(Replace the WriteString() with the WriteFile() and there is still a segmentation fault.)

The problem seems to be that WriteString() and WriteFile() on a newly constructed OBConversion() leave the Index at the initial value of 0.

Some of the formats use GetOutputIndex() and, if it is 1, perform an initialization. For the FPS format, the initialization loads the correct fingerprint type. If it is uninitialized then it will deference an unassigned variable, causing the segfault.

I have patched WriteString() and WriteFile(). I will submit a pull request shortly to demonstrate one possible solution.

Related symptoms

issue #1783

Note that this is likely related to issue #1783 . With an un-patched system:

>>> import pybel
>>> pybel.readstring("smi", "c1ccccc1").write("fpt")
'>\n'

with my patch in place:

>>> import pybel
>>> print(pybel.readstring("smi", "c1ccccc1").write("fpt"))
>   6 bits set
00000000 00000000 00000000 00000200 00000000 00000000
00000000 00000000 00000000 00000840 00000000 00008000
00000000 00000000 00000000 00000000 00000000 00000000
00000000 00000000 00000000 08000000 00000000 00000000
00000000 00000000 00000000 00000000 00000000 00020000
00000000 00000000

The proposed solution in that issue was to enable the 'h' option, which worked because the relevant code sets hexoutput using the following.

    if(pConv->IsOption("h") || (pConv->GetOutputIndex()==1 && pConv->IsLast()))
      hexoutput=true;

It may also be related to issue #852 .

CML output

As another example, the CML output differs between an unpatched system:

>>> print(pybel.readstring("smi", "C").write("cml"))
<molecule>
 <atomArray>
  <atom id="a1" elementType="C"/>
 </atomArray>
</molecule>

and a patched system:

>>> print(pybel.readstring("smi", "C").write("cml"))
<?xml version="1.0"?>
<molecule xmlns="http://www.xml-cml.org/schema">
 <atomArray>
  <atom id="a1" elementType="C" hydrogenCount="4"/>
 </atomArray>
</molecule>

Note the leading XML declaration in the patched version. This is because of the following test in format/xml/cmlformat.cpp :

    if(!_pxmlConv->IsOption("MolsNotStandalone") && _pxmlConv->GetOutputIndex()==1)
     ...
            xmlTextWriterStartDocument(writer(), NULL, NULL, NULL);