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update interface pybel.py (#2509)

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* update interface pybel.py & testpybel.py
This commit is contained in:
Xiang Zhong 2022-08-04 22:23:50 +08:00 committed by GitHub
parent 90df8ddbd6
commit 7702b2bc44
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 48 additions and 11 deletions
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4
scripts/python/examples/testpybel.py
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@ -19,9 +19,9 @@ try:
cinfony = None
try:
from openbabel import pybel
rdkit = cdk = None
except ImportError:
pybel = None
rdkit = cdk = None
except AttributeError:
from cinfony import cdk
pybel = rdkit = None
@ -192,7 +192,7 @@ M END
self.assertRaises(OSError, self.RFreaderror)
def RFformaterror(self):
mol = getattr(self.toolkit.readfile("noel", "head.sdf"), nextmethod)()
mol = getattr(self.toolkit.readfile("noel", os.path.join(here,"head.sdf")), nextmethod)()
def testRFformaterror(self):
"""Test that invalid formats raise an error"""

55
scripts/python/openbabel/pybel.py
View File

@ -116,12 +116,15 @@ ipython_3d = False
"""Toggles 2D vs 3D molecule representations in IPython notebook"""
def readfile(format, filename, opt=None):
def readfile(format=None, filename=None, opt=None):
"""Iterate over the molecules in a file.
Required parameters:
format - see the informats variable for a list of available
input formats
input formats.
If omitted, format will be guessed from filename,
specially, compressed gzip type with hints '.tar.gz' or
'.tgz' or '.gz' will also be accepted.
filename
Optional parameters:
@ -145,21 +148,55 @@ def readfile(format, filename, opt=None):
...
>>> print atomtotal
43
>>> atomtotal = 0
>>> for mol in readfile(filename="head.sdf.tgz"):
... atomtotal += len(mol.atoms)
...
>>> print atomtotal
43
"""
if opt is None:
opt = {}
# To be compitable with testing work inside `python/examples/testpybel.py`,
# "format" has to be checked first, ValueError should be raised, if it does
# not work, whether it's defined by user-input or guessed from filename.
#
# If filename does not exist, OSError should be raised instead.
if not os.path.isfile(filename):
# use a very unusual string to clarify errors when format not works
filename = '>>/NONE'
if not format:
if filename.endswith('.tgz'):
new = filename[:-4]
elif filename.endswith('.tar.gz'):
new = filename[:-7]
elif filename.endswith('.gz'):
# note: .gz has to be after .tar.gz
new = filename[:-3]
else:
new = filename
format = os.path.splitext(new)[1].lstrip('.')
obconversion = ob.OBConversion()
formatok = obconversion.SetInFormat(format)
if not formatok:
if format:
raise ValueError("%s is not a recognised Open Babel format" % format)
else:
if filename == '>>/NONE':
raise ValueError("Input file does not exist")
else:
raise ValueError(
"File format (%s) guessed from file (%s) "
"is not a recognised Open Babel format" % (format,filename)
)
if not os.path.isfile(filename):
raise OSError("Input file does not exist")
if opt is None:
opt = {}
for k, v in opt.items():
if v is None:
obconversion.AddOption(k, obconversion.INOPTIONS)
else:
obconversion.AddOption(k, obconversion.INOPTIONS, str(v))
if not formatok:
raise ValueError("%s is not a recognised Open Babel format" % format)
if not os.path.isfile(filename):
raise OSError("No such file: '%s'" % filename)
def filereader():
obmol = ob.OBMol()
notatend = obconversion.ReadFile(obmol, filename)