Date: Sat, 25 Oct 2014 19:12:14 +0000 From: bugzilla-noreply@freebsd.org To: freebsd-ports-bugs@FreeBSD.org Subject: [Bug 194599] New: OpenBabel 2.3.2 Python binding pybel does not recognize supported formats Message-ID: <bug-194599-13@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=194599 Bug ID: 194599 Summary: OpenBabel 2.3.2 Python binding pybel does not recognize supported formats Product: Ports Tree Version: Latest Hardware: amd64 OS: Any Status: Needs Triage Severity: Affects Only Me Priority: Normal Component: Individual Port(s) Assignee: freebsd-ports-bugs@FreeBSD.org Reporter: ftorazyne@mail.ru Function readstring() from OpenBabel 2.3.2 Python binding pybel does not recognize any supported format - 'smi','pdb' etc. Code like a import pybel mymol=pybel.readstring('smi','CCOC(=O)C') mymol.addh() mymol.make3D() print mymol.write(format='mol2') receives this error: Traceback (most recent call last): File "./test.py", line 6, in <module> mymol=pybel.readstring('smi','CCOC(=O)C') File "/usr/local/lib/python2.7/site-packages/pybel.py", line 179, in readstring raise ValueError("%s is not a recognised Open Babel format" % format) ValueError: smi is not a recognised Open Babel format But pybel.informats contain 'smi' key: >>> import pybel >>> print sorted(pybel.informats) ['CONFIG', 'CONTCAR', 'HISTORY', 'POSCAR', 'VASP', 'abinit', 'acesout', 'acr', 'adfout', 'alc', 'arc', 'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1', 'c3d2', 'caccrt', 'can', 'car', 'castep', 'ccc', 'cdx', 'cdxml', 'cif', 'ck', 'cml', 'cmlr', 'crk2d', 'crk3d', 'ct', 'cub', 'cube', 'dat', 'dmol', 'dx', 'ent', 'fa', 'fasta', 'fch', 'fchk', 'fck', 'feat', 'fhiaims', 'fract', 'fs', 'fsa', 'g03', 'g09', 'g92', 'g94', 'g98', 'gal', 'gam', 'gamess', 'gamin', 'gamout', 'got', 'gpr', 'gro', 'gukin', 'gukout', 'gzmat', 'hin', 'inchi', 'inp', 'ins', 'jout', 'log', 'mcdl', 'mcif', 'mdl', 'ml2', 'mmcif', 'mmd', 'mmod', 'mol', 'mol2', 'mold', 'molden', 'molf', 'moo', 'mop', 'mopcrt', 'mopin', 'mopout', 'mpc', 'mpo', 'mpqc', 'mrv', 'msi', 'nwo', 'out', 'outmol', 'output', 'pc', 'pcm', 'pdb', 'pdbqt', 'png', 'pos', 'pqr', 'pqs', 'prep', 'pwscf', 'qcout', 'res', 'rsmi', 'rxn', 'sd', 'sdf', 'smi', 'smiles', 'sy2', 't41', 'tdd', 'text', 'therm', 'tmol', 'txt', 'txyz', 'unixyz', 'vmol', 'xml', 'xsf', 'xyz', 'yob'] It was established in discussion at OpenBabel forum (http://forums.openbabel.org/Error-in-Pybel-readstring-smi-format-not-recognized-td4657776.html) that function OBConversion.SetInFormat from openbabel.py returns "False" for any format specificator whenever it is supported or not. I should underline, that OpenBabel was installed from port, i.e. was compilied from sources at my machine, and I do not use any pre-compilied OpenBabel binaries. I used gcc4.2 and gcc4.8. -- You are receiving this mail because: You are the assignee for the bug.
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