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removed pdbx as submodule
install now pdbfilter.py
None-checks in pdbfilter.py
new ffindex commit
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meiermark committed Sep 28, 2016
1 parent e32a89f commit e1f7fe8
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Showing 7 changed files with 10 additions and 16 deletions.
3 changes: 0 additions & 3 deletions .gitmodules
@@ -1,6 +1,3 @@
[submodule "lib/ffindex"]
path = lib/ffindex
url = https://github.com/soedinglab/ffindex_soedinglab.git
[submodule "lib/pdbx"]
path = lib/pdbx
url = https://github.com/soedinglab/pdbx.git
4 changes: 0 additions & 4 deletions CMakeLists.txt
@@ -1,9 +1,6 @@
cmake_minimum_required(VERSION 2.8.12)
project(hhsuite CXX)

option(UserInstallOption "UserInstallOption" OFF)


SET(HAVE_SSSE3 0 CACHE BOOL "Have SSSE3")
SET(HAVE_AVX2 0 CACHE BOOL "Have AVX2")

Expand Down Expand Up @@ -48,7 +45,6 @@ add_subdirectory(scripts)
add_subdirectory(test)
#add_subdirectory(doc)
add_subdirectory(lib/ffindex)
add_subdirectory(lib/pdbx)


SET (CPACK_GENERATOR "DEB;TGZ;ZIP;RPM")
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1 change: 1 addition & 0 deletions README.md
Expand Up @@ -23,6 +23,7 @@ We had to rename our repository for ffindex, so it might be necessary to run the
To compile from source, you will need:
* a recent C/C++ compiler
* [CMake](http://cmake.org/) 2.8.12 or later
* install [pdbx python library](https://github.com/soedinglab/pdbx)


## Installation
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2 changes: 1 addition & 1 deletion lib/ffindex
1 change: 0 additions & 1 deletion lib/pdbx
Submodule pdbx deleted from 7f71d9
1 change: 1 addition & 0 deletions scripts/CMakeLists.txt
Expand Up @@ -27,5 +27,6 @@ INSTALL(PROGRAMS
is_huge_a3m.py
pdbfilter.py
cif2fasta.py
hhmakemodel.py
DESTINATION scripts
)
14 changes: 7 additions & 7 deletions scripts/pdbfilter.py
Expand Up @@ -144,35 +144,35 @@ def select_sequences(clusters, annotations):
# iterate through each entry in nodes while selecting the representative sequence
for node in nodes:

if (node.res != None) and (node.res < best_res):
if (node.res is not None) and (node.res < best_res):
best_res = node.res
best_entry_res = node.entry

if (node.rfr != None) and (node.rfr < best_rfr):
if (node.rfr is not None) and (node.rfr < best_rfr):
best_rfr = node.rfr
best_entry_rfr = node.entry

if (node.comp != None) and (node.comp > best_comp):
if (node.comp is not None) and (node.comp > best_comp):
best_comp = node.comp
best_entry_comp = node.entry

if best_entry_res != None:
if best_entry_res is not None:
selected_sequences.add(best_entry_res)

if DEBUG:
print (' - Selected {n} (best resolution = {r}).'.format(
n = best_entry_res,
r = best_res))

if best_entry_rfr != None:
if best_entry_rfr is not None:
selected_sequences.add(best_entry_rfr)

if DEBUG:
print (' - Selected {n} (best R-free = {r}).'.format(
n = best_entry_rfr,
r = best_rfr))

if best_entry_comp != None:
if best_entry_comp is not None:
selected_sequences.add(best_entry_comp)

if DEBUG:
Expand Down Expand Up @@ -271,4 +271,4 @@ def main():


if __name__ == "__main__":
main()
main()

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