On Feb 18, 2013, at 5:50 PM, [email protected] wrote:
> My issue2solve: read in a sdf.gz & simply extract the SD tags.
If you don't mind digging into the undocumented chemfp API
(which mean that it may change in the future), then you can
use the simple-minded SDF reader I wrote for it.
It's "simple-minded" because there are valid SD files which will
cause it to break. However, it should work for the large majority
of SD files that you'll come across.
from chemfp import sdf_reader
import re
# Match the tag and its data lines. Data lines include the newlines.
tag_pattern = re.compile(r"""
^> # start of line (using re.MULTILINE mode)
\s* # ignore whitespace
<([^>]+)> # tag field (allow any character except '>')
.*\n # skip junk to the end of line
( # zero or more data lines
(?:[^\n].*\n)* # data lines start with something other than a newline then
can have anything
)
\n # data must end with a blank line
""", re.MULTILINE | re.VERBOSE )
# For each record, extract the title and (tag, data) fields
def read_tags(records):
for record in records:
title = record[:record.find("\n")]
ct_end = record.find("\nM END\n")
assert ct_end != -1, "Missing 'M END' for record %r" % (title,)
yield title, tag_pattern.findall(record, ct_end), record
# This iterates over the records in the SD file. Ignore any errors.
reader = sdf_reader.open_sdf("/Users/dalke/databases/chembl_14.sdf.gz",
errors = "ignore")
# Extract the tag data for each record and print it out
for title, tag_fields, record in read_tags(reader):
print "Title:", title
for tag, data in tag_fields:
if len(data) > 40:
data_repr = repr(data[:38] + " ...")
else:
data_repr = repr(data)
print tag, "=>", data_repr
Andrew
[email protected]
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