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Updating the documentation and setup.py to reflect that MMCIF now doe…

…s not rely on C code
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1 parent b2bafdf commit aa2bd86baa47b567566e174aeb8d05e4b69b9ecc Michiel de Hoon committed Mar 15, 2013
Showing with 0 additions and 19 deletions.
  1. +0 −5 Doc/Tutorial.tex
  2. +0 −8 Doc/install/Installation.tex
  3. +0 −6 setup.py
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@@ -284,11 +284,6 @@ \section{Frequently Asked Questions (FAQ)}
Second, they are now stricter about how to provide a list of IDs -- Biopython 1.59 onwards
turns a list into a comma separated string automatically.
- \item \emph{Why doesn't} \verb|Bio.PDB.MMCIFParser| \emph{work? I see an import error about} \verb|MMCIFlex| \\
- From Biopython 1.42 to 1.59, the underlying \verb|Bio.PDB.mmCIF.MMCIFlex| module
- was not installed by default. It required a third party tool called flex
- (fast lexical analyzer generator). This should work with Biopython 1.60 onwards.
-
\item \emph{Why doesn't} \verb|Bio.Blast.NCBIWWW.qblast()| \emph{give the same results as the NCBI BLAST website?} \\
You need to specify the same options -- the NCBI often adjust the default settings on the website,
and they do not match the QBLAST defaults anymore. Check things like the gap penalties and expectation threshold.
@@ -398,14 +398,6 @@ \subsection{mxTextTools (no longer needed)}
version is available for download at:
\ahrefurl{\url{http://www.egenix.com/products/python/mxBase/mxTextTools/}}.
-\subsection{flex (fast lexical analyzer generator) (optional)}
-
-The mmCIF parser \verb|Bio.PDB.mmCIF.MMCIFlex| relies on C code which
-uses flex (fast lexical analyzer generator). At the time of writing,
-in order to parse mmCIF files you'll have to install flex, then tweak
-your \verb|setup.py| file to include the \verb|Bio.PDB.mmCIF.MMCIFlex|
-module, before (re)installing Biopython from source.
-
\section{Installing Biopython}
\subsection{Obtaining Biopython}
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@@ -322,7 +322,6 @@ def is_Numpy_installed():
'Bio.Pathway',
'Bio.Pathway.Rep',
'Bio.PDB',
- 'Bio.PDB.mmCIF',
'Bio.PopGen',
'Bio.PopGen.Async',
'Bio.PopGen.FDist',
@@ -390,11 +389,6 @@ def is_Numpy_installed():
'Bio/trie.c'],
include_dirs=["Bio"]
),
- Extension('Bio.PDB.mmCIF.MMCIFlex',
- ['Bio/PDB/mmCIF/lex.yy.c',
- 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
- include_dirs=["Bio"],
- ),
Extension('Bio.Nexus.cnexus',
['Bio/Nexus/cnexus.c']
),

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