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authorUrmi Majumder <urmi@nanorex.com>2008-06-26 20:52:29 +0000
committerUrmi Majumder <urmi@nanorex.com>2008-06-26 20:52:29 +0000
commitfa1662718c6918a0bf8508d246691b3db75ce784 (patch)
treea3aeb57fc2c281321f0ac3ac70d21112e0743aea
parent75f55077c5e77becd84d03912f5f52f77610f8f8 (diff)
downloadnanoengineer-fa1662718c6918a0bf8508d246691b3db75ce784.tar.gz
nanoengineer-fa1662718c6918a0bf8508d246691b3db75ce784.zip
Ignorable except from Bruce and Piotr
-rw-r--r--cad/src/files/ios/files_ios.py14
1 files changed, 10 insertions, 4 deletions
diff --git a/cad/src/files/ios/files_ios.py b/cad/src/files/ios/files_ios.py
index 2380904c6..fb876b433 100644
--- a/cad/src/files/ios/files_ios.py
+++ b/cad/src/files/ios/files_ios.py
@@ -189,7 +189,7 @@ def railImplementation(assy):
for strand in strandList:
strandID = strand.name
- #Note: Ninad needs to look at this, what do the indices in
+ #Note: Ninad/Bruce needs to look at this, what do the indices in
#wholechain_baseindex_range_for_rail(rail) for each rail of the wholechain
#coresspond to? When you sort them, and arrange the corresponding basestrings
#accordinly, it does not yield the original sequence. The error is, however
@@ -197,6 +197,7 @@ def railImplementation(assy):
#from one or more strands.
#Also rails and chunks cannot be used since they are not in the same order
#as the sequence string
+ #Piotr has used this method before successfully, how?
print "Strand Name =", strand.name
strand_wholechain = strand.get_strand_wholechain()
@@ -204,7 +205,7 @@ def railImplementation(assy):
indexTupleListInOrder = []
if strand_wholechain:
for rail in strand_wholechain.rails():
- #print "Rail baseatoms", rail.baseatoms
+
baseList = []
for a in rail.baseatoms:
bases = a.getDnaBaseName()
@@ -234,6 +235,7 @@ def railImplementation(assy):
else:
#locate place in the list where to insert basestring and index
#tuple
+ oldListLength = len(indexTupleListInOrder)
for i in range(len(indexTupleListInOrder)):
if i == 0 and indexTuple[1] < indexTupleListInOrder[i][0]:
#insert this string at index 0
@@ -245,6 +247,10 @@ def railImplementation(assy):
baseStringListInOrder.insert(i,baseStringFinal)
else:
continue
+ if oldListLength == len(indexTupleListInOrder):
+ indexTupleListInOrder.insert(oldListLength, indexTuple)
+ baseStringListInOrder.insert(oldListLength,baseStringFinal)
+
print "BaseString List=", baseStringListInOrder
print "Index Tuple List= ", indexTupleListInOrder
@@ -599,8 +605,8 @@ def createStrands(doc,elemDoc, assy):
"""
#Run by Ninad/Bruce: UM 20080624
- #railImplementation(assy)
- atomByAtomImplementation(assy)
+ railImplementation(assy)
+ #atomByAtomImplementation(assy)
"""
#old implementation for getting strand information