diff --git a/.gitignore b/.gitignore
index b2f9571aa2b37baf9283524aacdb0cfb962d921b..e627a39e6ee07c986b54975c9346902de6dc2f4e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,12 @@
/*.txt
/*.psf
/*.pdb
-/*.bd
\ No newline at end of file
+/*.exb
+/*.bd
+/*.namd
+
+output
+potentials
+
+__pycache__
+.backup
diff --git a/CanonicalNucleotideAtoms.py b/CanonicalNucleotideAtoms.py
index 29ffd4810f499ebf615e9838656a288d5aebd897..fb31fa8de77098a4a5ef68a7c53a877e4508bc81 100644
--- a/CanonicalNucleotideAtoms.py
+++ b/CanonicalNucleotideAtoms.py
@@ -17,7 +17,8 @@ def stringToIntTuples(string, tupleLen, offset):
return ret
class CanonicalNucleotide():
- DefaultOrientation = rotationAboutAxis([0,0,1], 68)
+ # DefaultOrientation = rotationAboutAxis([0,0,1], 68)
+ DefaultOrientation = rotationAboutAxis([0,0,1], 68+180)
def __init__(self, prefix):
d = np.loadtxt("%s.dat" % prefix, dtype='i4,S4,S4,f4,f4,f4,f4,f4')
@@ -60,10 +61,18 @@ class CanonicalNucleotide():
## Apply transformation
for i in range(len(c)):
rvec = np.array([c.props[k][i] for k in ('x','y','z')])
- rvec = (scale*rvec).dot( R )
+ rvec = rvec.dot( R )
for k,r,o in zip(('x','y','z'), rvec, translation):
c.props[k][i] = r + o
+ if scale != 1:
+ i0 = self.index("C3'")
+ r0 = np.array([c.props[k][i0] for k in ('x','y','z')])
+ for i in range(len(c)):
+ rvec = np.array([c.props[k][i] for k in ('x','y','z')])
+ rvec = scale*(rvec-r0) + r0
+ for k,r in zip(('x','y','z'), rvec):
+ c.props[k][i] = r
return c
# def __iter__(self):
diff --git a/atomicModel.py b/atomicModel.py
index 243002dd72bd5bd133acfdca3e4a636b62ec01c0..63542339ca01b4a29f4a20fd83c933f33c2c98ea 100644
--- a/atomicModel.py
+++ b/atomicModel.py
@@ -220,8 +220,8 @@ class atomicModel():
random.seed(randomSeed)
+ self.latticeType = atomicModel._determineLatticeType(part)
self._buildModel(part)
- self.latticeType = self._determineLatticeType(part)
def _helixStrandsToEnds(self, helixStrands):
@@ -307,7 +307,8 @@ class atomicModel():
## Loop over oligos/segments
segments = []
ntCount = 0
- for oligo in part.oligos():
+ keyFn = lambda o: (o.length(), o._strand5p.idNum(), o._strand5p.idx5Prime())
+ for oligo in reversed(sorted(part.oligos(), key=keyFn)):
# if oligo.isLoop():
# # print("A loop exists")
# raise Exception("Loop strands are not supported")
@@ -334,6 +335,13 @@ class atomicModel():
bpr,tpr,eulerZ,z = [vh_props[k][hid] for k in keys]
twist_per_base = tpr*360./bpr
+ ## override twist_per_base if square lattice
+ if self.latticeType == "square":
+ # assert(twist_per_base == 360.0*3/32)
+ twist_per_base == 360.0*3/32
+ else:
+ assert(twist_per_base == 360.0/10.5)
+
zIdxToPos = lambda idx: (x*10,y*10,z-3.4*idx)
zIdxToAngle = lambda idx: idx*twist_per_base + eulerZ
@@ -448,13 +456,18 @@ class atomicModel():
node1.addXover(node2, isFwd1)
node2.addXover(node1, isFwd2)
- def _determineLatticeType(self, part):
+ def _getNeighborHelixDict(part):
props, origins = part.helixPropertiesAndOrigins()
- origins = [np.array(o) for o in origins]
+ neighborHelices = dict()
+ for i in range(len(origins)):
+ neighborHelices[i] = [int(j.strip('[,]')) for j in props['neighbors'][i].split() if j != '[]']
+ return neighborHelices
+ def _determineLatticeType(part):
+ props, origins = part.helixPropertiesAndOrigins()
+ origins = [np.array(o) for o in origins]
neighborVecs = []
- for i in range(len(props['neighbors'])):
- js = [int(j.strip('[,]')) for j in props['neighbors'][i].split()]
+ for i,js in atomicModel._getNeighborHelixDict(part).items():
for j in js:
neighborVecs.append( origins[j]-origins[i] )
@@ -591,10 +604,12 @@ class atomicModel():
def setScaffoldSeq(self,sequence):
## get longest segment
- segs = sort( [(len(s),s) for s in self.segments], key=lambda x: x[0] )
+ segs = sorted( [(len(s),s) for s in self.segments], key=lambda x: x[0] )
seg = segs[-1][1]
assert( len(seg) > len(segs[-2][1]) )
- assert( len(sequence) >= len(seg) )
+ if len(seg) < len(sequence):
+ raise Exception("Sequence (%d) too short for scaffold (%d)!" % (len(sequence),len(seg)))
+
for nt,seq in zip(seg,sequence):
assert(seq in ("A","T","C","G"))
nt.sequence = seq
@@ -925,14 +940,12 @@ class atomicModel():
raise Exception("Not implemented")
else:
props, origins = self.part.helixPropertiesAndOrigins()
- neighborHelices = dict()
- for hid in helixIds:
- neighborHelices[hid] = [int(j.strip('[,]')) for j in props['neighbors'][hid].split()]
+ neighborHelices = atomicModel._getNeighborHelixDict(self.part)
if self.latticeType == 'honeycomb':
- minDist = 7
+ minDist = 8 # TODO: test against server
elif self.latticeType == 'square':
- minDist = 10
+ minDist = 11
for seg in self.segments:
for nt in seg:
diff --git a/resources/cadnano2pdb.seq.m13mp18.dat b/resources/cadnano2pdb.seq.m13mp18.dat
new file mode 100644
index 0000000000000000000000000000000000000000..edfc67497262cd16c2ffc711859b0231deb96549
--- /dev/null
+++ b/resources/cadnano2pdb.seq.m13mp18.dat
@@ -0,0 +1,122 @@
+;m13mp18 from http://genome-www.stanford.edu/vectordb/vector_descrip/COMPLETE/M13MP18.SEQ.html
+aatgctacta ctattagtag aattgatgcc accttttcag ctcgcgcccc aaatgaaaat
+atagctaaac aggttattga ccatttgcga aatgtatcta atggtcaaac taaatctact
+cgttcgcaga attgggaatc aactgttaca tggaatgaaa cttccagaca ccgtacttta
+gttgcatatt taaaacatgt tgagctacag caccagattc agcaattaag ctctaagcca
+tccgcaaaaa tgacctctta tcaaaaggag caattaaagg tactctctaa tcctgacctg
+ttggagtttg cttccggtct ggttcgcttt gaagctcgaa ttaaaacgcg atatttgaag
+tctttcgggc ttcctcttaa tctttttgat gcaatccgct ttgcttctga ctataatagt
+cagggtaaag acctgatttt tgatttatgg tcattctcgt tttctgaact gtttaaagca
+tttgaggggg attcaatgaa tatttatgac gattccgcag tattggacgc tatccagtct
+aaacatttta ctattacccc ctctggcaaa acttcttttg caaaagcctc tcgctatttt
+ggtttttatc gtcgtctggt aaacgagggt tatgatagtg ttgctcttac tatgcctcgt
+aattcctttt ggcgttatgt atctgcatta gttgaatgtg gtattcctaa atctcaactg
+atgaatcttt ctacctgtaa taatgttgtt ccgttagttc gttttattaa cgtagatttt
+tcttcccaac gtcctgactg gtataatgag ccagttctta aaatcgcata aggtaattca
+caatgattaa agttgaaatt aaaccatctc aagcccaatt tactactcgt tctggtgttc
+tcgtcagggc aagccttatt cactgaatga gcagctttgt tacgttgatt tgggtaatga
+atatccggtt cttgtcaaga ttactcttga tgaaggtcag ccagcctatg cgcctggtct
+gtacaccgtt catctgtcct ctttcaaagt tggtcagttc ggttccctta tgattgaccg
+tctgcgcctc gttccggcta agtaacatgg agcaggtcgc ggatttcgac acaatttatc
+aggcgatgat acaaatctcc gttgtacttt gtttcgcgct tggtataatc gctgggggtc
+aaagatgagt gttttagtgt attctttcgc ctctttcgtt ttaggttggt gccttcgtag
+tggcattacg tattttaccc gtttaatgga aacttcctca tgaaaaagtc tttagtcctc
+aaagcctctg tagccgttgc taccctcgtt ccgatgctgt ctttcgctgc tgagggtgac
+gatcccgcaa aagcggcctt taactccctg caagcctcag cgaccgaata tatcggttat
+gcgtgggcga tggttgttgt cattgtcggc gcaactatcg gtatcaagct gtttaagaaa
+ttcacctcga aagcaagctg ataaaccgat acaattaaag gctccttttg gagccttttt
+ttttggagat tttcaacgtg aaaaaattat tattcgcaat tcctttagtt gttcctttct
+attctcactc cgctgaaact gttgaaagtt gtttagcaaa accccataca gaaaattcat
+ttactaacgt ctggaaagac gacaaaactt tagatcgtta cgctaactat gagggttgtc
+tgtggaatgc tacaggcgtt gtagtttgta ctggtgacga aactcagtgt tacggtacat
+gggttcctat tgggcttgct atccctgaaa atgagggtgg tggctctgag ggtggcggtt
+ctgagggtgg cggttctgag ggtggcggta ctaaacctcc tgagtacggt gatacaccta
+ttccgggcta tacttatatc aaccctctcg acggcactta tccgcctggt actgagcaaa
+accccgctaa tcctaatcct tctcttgagg agtctcagcc tcttaatact ttcatgtttc
+agaataatag gttccgaaat aggcaggggg cattaactgt ttatacgggc actgttactc
+aaggcactga ccccgttaaa acttattacc agtacactcc tgtatcatca aaagccatgt
+atgacgctta ctggaacggt aaattcagag actgcgcttt ccattctggc tttaatgaag
+atccattcgt ttgtgaatat caaggccaat cgtctgacct gcctcaacct cctgtcaatg
+ctggcggcgg ctctggtggt ggttctggtg gcggctctga gggtggtggc tctgagggtg
+gcggttctga gggtggcggc tctgagggag gcggttccgg tggtggctct ggttccggtg
+attttgatta tgaaaagatg gcaaacgcta ataagggggc tatgaccgaa aatgccgatg
+aaaacgcgct acagtctgac gctaaaggca aacttgattc tgtcgctact gattacggtg
+ctgctatcga tggtttcatt ggtgacgttt ccggccttgc taatggtaat ggtgctactg
+gtgattttgc tggctctaat tcccaaatgg ctcaagtcgg tgacggtgat aattcacctt
+taatgaataa tttccgtcaa tatttacctt ccctccctca atcggttgaa tgtcgccctt
+ttgtctttag cgctggtaaa ccatatgaat tttctattga ttgtgacaaa ataaacttat
+tccgtggtgt ctttgcgttt cttttatatg ttgccacctt tatgtatgta ttttctacgt
+ttgctaacat actgcgtaat aaggagtctt aatcatgcca gttcttttgg gtattccgtt
+attattgcgt ttcctcggtt tccttctggt aactttgttc ggctatctgc ttacttttct
+taaaaagggc ttcggtaaga tagctattgc tatttcattg tttcttgctc ttattattgg
+gcttaactca attcttgtgg gttatctctc tgatattagc gctcaattac cctctgactt
+tgttcagggt gttcagttaa ttctcccgtc taatgcgctt ccctgttttt atgttattct
+ctctgtaaag gctgctattt tcatttttga cgttaaacaa aaaatcgttt cttatttgga
+ttgggataaa taatatggct gtttattttg taactggcaa attaggctct ggaaagacgc
+tcgttagcgt tggtaagatt caggataaaa ttgtagctgg gtgcaaaata gcaactaatc
+ttgatttaag gcttcaaaac ctcccgcaag tcgggaggtt cgctaaaacg cctcgcgttc
+ttagaatacc ggataagcct tctatatctg atttgcttgc tattgggcgc ggtaatgatt
+cctacgatga aaataaaaac ggcttgcttg ttctcgatga gtgcggtact tggtttaata
+cccgttcttg gaatgataag gaaagacagc cgattattga ttggtttcta catgctcgta
+aattaggatg ggatattatt tttcttgttc aggacttatc tattgttgat aaacaggcgc
+gttctgcatt agctgaacat gttgtttatt gtcgtcgtct ggacagaatt actttacctt
+ttgtcggtac tttatattct cttattactg gctcgaaaat gcctctgcct aaattacatg
+ttggcgttgt taaatatggc gattctcaat taagccctac tgttgagcgt tggctttata
+ctggtaagaa tttgtataac gcatatgata ctaaacaggc tttttctagt aattatgatt
+ccggtgttta ttcttattta acgccttatt tatcacacgg tcggtatttc aaaccattaa
+atttaggtca gaagatgaaa ttaactaaaa tatatttgaa aaagttttct cgcgttcttt
+gtcttgcgat tggatttgca tcagcattta catatagtta tataacccaa cctaagccgg
+aggttaaaaa ggtagtctct cagacctatg attttgataa attcactatt gactcttctc
+agcgtcttaa tctaagctat cgctatgttt tcaaggattc taagggaaaa ttaattaata
+gcgacgattt acagaagcaa ggttattcac tcacatatat tgatttatgt actgtttcca
+ttaaaaaagg taattcaaat gaaattgtta aatgtaatta attttgtttt cttgatgttt
+gtttcatcat cttcttttgc tcaggtaatt gaaatgaata attcgcctct gcgcgatttt
+gtaacttggt attcaaagca atcaggcgaa tccgttattg tttctcccga tgtaaaaggt
+actgttactg tatattcatc tgacgttaaa cctgaaaatc tacgcaattt ctttatttct
+gttttacgtg ctaataattt tgatatggtt ggttcaattc cttccataat tcagaagtat
+aatccaaaca atcaggatta tattgatgaa ttgccatcat ctgataatca ggaatatgat
+gataattccg ctccttctgg tggtttcttt gttccgcaaa atgataatgt tactcaaact
+tttaaaatta ataacgttcg ggcaaaggat ttaatacgag ttgtcgaatt gtttgtaaag
+tctaatactt ctaaatcctc aaatgtatta tctattgacg gctctaatct attagttgtt
+agtgcaccta aagatatttt agataacctt cctcaattcc tttctactgt tgatttgcca
+actgaccaga tattgattga gggtttgata tttgaggttc agcaaggtga tgctttagat
+ttttcatttg ctgctggctc tcagcgtggc actgttgcag gcggtgttaa tactgaccgc
+ctcacctctg ttttatcttc tgctggtggt tcgttcggta tttttaatgg cgatgtttta
+gggctatcag ttcgcgcatt aaagactaat agccattcaa aaatattgtc tgtgccacgt
+attcttacgc tttcaggtca gaagggttct atctctgttg gccagaatgt cccttttatt
+actggtcgtg tgactggtga atctgccaat gtaaataatc catttcagac gattgagcgt
+caaaatgtag gtatttccat gagcgttttt cctgttgcaa tggctggcgg taatattgtt
+ctggatatta ccagcaaggc cgatagtttg agttcttcta ctcaggcaag tgatgttatt
+actaatcaaa gaagtattgc tacaacggtt aatttgcgtg atggacagac tcttttactc
+ggtggcctca ctgattataa aaacacttct caagattctg gcgtaccgtt cctgtctaaa
+atccctttaa tcggcctcct gtttagctcc cgctctgatt ccaacgagga aagcacgtta
+tacgtgctcg tcaaagcaac catagtacgc gccctgtagc ggcgcattaa gcgcggcggg
+tgtggtggtt acgcgcagcg tgaccgctac acttgccagc gccctagcgc ccgctccttt
+cgctttcttc ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg
+ggggctccct ttagggttcc gatttagtgc tttacggcac ctcgacccca aaaaacttga
+tttgggtgat ggttcacgta gtgggccatc gccctgatag acggtttttc gccctttgac
+gttggagtcc acgttcttta atagtggact cttgttccaa actggaacaa cactcaaccc
+tatctcgggc tattcttttg atttataagg gattttgccg atttcggaac caccatcaaa
+caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc
+caggcggtga agggcaatca gctgttgccc gtctcgctgg tgaaaagaaa aaccaccctg
+gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca
+cgacaggttt cccgactgga aagcgggcag tgagcgcaac gcaattaatg tgagttagct
+cactcattag gcaccccagg ctttacactt tatgcttccg gctcgtatgt tgtgtggaat
+tgtgagcgga taacaatttc acacaggaaa cagctatgac catgattacg aattcgagct
+cggtacccgg ggatcctcta gagtcgacct gcaggcatgc aagcttggca ctggccgtcg
+ttttacaacg tcgtgactgg gaaaaccctg gcgttaccca acttaatcgc cttgcagcac
+atcccccttt cgccagctgg cgtaatagcg aagaggcccg caccgatcgc ccttcccaac
+agttgcgcag cctgaatggc gaatggcgct ttgcctggtt tccggcacca gaagcggtgc
+cggaaagctg gctggagtgc gatcttcctg aggccgatac ggtcgtcgtc ccctcaaact
+ggcagatgca cggttacgat gcgcccatct acaccaacgt aacctatccc attacggtca
+atccgccgtt tgttcccacg gagaatccga cgggttgtta ctcgctcaca tttaatgttg
+atgaaagctg gctacaggaa ggccagacgc gaattatttt tgatggcgtt cctattggtt
+aaaaaatgag ctgatttaac aaaaatttaa cgcgaatttt aacaaaatat taacgtttac
+aatttaaata tttgcttata caatcttcct gtttttgggg cttttctgat tatcaaccgg
+ggtacatatg attgacatgc tagttttacg attaccgttc atcgattctc ttgtttgctc
+cagactctca ggcaatgacc tgatagcctt tgtagatctc tcaaaaatag ctaccctctc
+cggcattaat ttatcagcta gaacggttga atatcatatt gatggtgatt tgactgtctc
+cggcctttct cacccttttg aatctttacc tacacattac tcaggcattg catttaaaat
+atatgagggt tctaaaaatt tttatccttg cgttgaaata aaggcttctc ccgcaaaagt
+attacagggt cataatgttt ttggtacaac cgatttagct ttatgctctg aggctttatt
+gcttaatttt gctaattctt tgccttgcct gtatgattta ttggatgtt
diff --git a/run.py b/run.py
index 0eb760c6adf031ff448befff8a2d0fa2024de5b9..19c6006fb0f43110e4fad1cfc0b49cfd03eb0797 100644
--- a/run.py
+++ b/run.py
@@ -14,7 +14,25 @@ import sys
# twistLp = 1e-6
twistLp = 90
-def simulateDesign(inFile, outPrefix, gpu=0, shiftEulerZ=0):
+
+def readSequenceFile(sequenceFile='resources/cadnano2pdb.seq.m13mp18.dat'):
+ seq = []
+ with open(sequenceFile) as ch:
+ for l in ch:
+ l = l.strip().replace(" ", "")
+ if l[0] in (";","#"): continue
+ seq.extend([c.upper() for c in l])
+ return seq
+
+def readArbdCoords(fname):
+ coords = []
+ with open(fname) as fh:
+ for line in fh:
+ coords.append([float(x) for x in line.split()[1:]])
+ return np.array(coords)
+
+def simulateDesign(inFile, outPrefix, numCoarsestSteps=5000000, gpu=0, shiftEulerZ=0,
+ sequenceFile='resources/cadnano2pdb.seq.m13mp18.dat'):
# ----------------- #
# Read cadnano file #
# ----------------- #
@@ -43,14 +61,6 @@ def simulateDesign(inFile, outPrefix, gpu=0, shiftEulerZ=0):
cadnano.fileio.v2decode.decode(doc, data)
- def readArbdCoords(fname):
- coords = []
- with open(fname) as fh:
- for line in fh:
- coords.append([float(x) for x in line.split()[1:]])
- return np.array(coords)
-
-
parts = [p for p in doc.getParts()]
if len(parts) != 1:
raise Exception("Only documents containing a single 'part' are implemented at this time.")
@@ -77,7 +87,7 @@ def simulateDesign(inFile, outPrefix, gpu=0, shiftEulerZ=0):
finerModel = beadModelTwist(part, twistPersistenceLength=twistLp,
maxBpsPerDNode=1, maxNtsPerSNode=1)
- finestModel = atomicModel(part, ntScale=1.0)
+ finestModel = atomicModel(part, ntScale=0.5)
models = [coarsestModel, coarseModel, fineModel, finerModel, finestModel]
@@ -123,7 +133,7 @@ def simulateDesign(inFile, outPrefix, gpu=0, shiftEulerZ=0):
# ------------------------------- #
out = outPrefix + "-1"
- coarsestModel.simulate(out, outputDirectory='output', numSteps=15000000, timestep=200e-6,
+ coarsestModel.simulate(out, outputDirectory='output', numSteps=numCoarsestSteps, timestep=200e-6,
arbd="/home/cmaffeo2/development/cuda/arbd.dev/src/arbd", gpu=gpu)
coarsestModelCoords = readArbdCoords( "output/%s.0.restart" % out )
@@ -131,7 +141,7 @@ def simulateDesign(inFile, outPrefix, gpu=0, shiftEulerZ=0):
coarseModel.backmap( coarsestModel, coarsestModelCoords,
dsDnaHelixNeighborDist=100, dsDnaAllNeighborDist=50,
ssDnaHelixNeighborDist=50)
- coarseModel.simulate( out, outputDirectory='output', numSteps=1000000,
+ coarseModel.simulate( out, outputDirectory='output', numSteps=100000,
arbd="/home/cmaffeo2/development/cuda/arbd.dev/src/arbd", gpu=gpu)
coarseModelCoords = readArbdCoords( "output/%s.0.restart" % out )
@@ -139,7 +149,7 @@ def simulateDesign(inFile, outPrefix, gpu=0, shiftEulerZ=0):
fineModel.backmap( coarseModel, coarseModelCoords,
dsDnaHelixNeighborDist=100, dsDnaAllNeighborDist=50,
ssDnaHelixNeighborDist=50)
- fineModel.simulate( out, outputDirectory='output', numSteps=1000000,
+ fineModel.simulate( out, outputDirectory='output', numSteps=100000,
arbd="/home/cmaffeo2/development/cuda/arbd.dev/src/arbd", gpu=gpu)
fineModelCoords = readArbdCoords( "output/%s.0.restart" % out )
@@ -147,21 +157,21 @@ def simulateDesign(inFile, outPrefix, gpu=0, shiftEulerZ=0):
finerModel.backmap( fineModel, fineModelCoords,
dsDnaHelixNeighborDist=100, dsDnaAllNeighborDist=50,
ssDnaHelixNeighborDist=50)
- finerModel.simulate( out, outputDirectory='output', numSteps=1000000,
+ finerModel.simulate(out, outputDirectory='output', numSteps=100000, timestep=50e-6,
arbd="/home/cmaffeo2/development/cuda/arbd.dev/src/arbd", gpu=gpu)
finerModelCoords = readArbdCoords( "output/%s.0.restart" % out )
out = outPrefix + "-5"
+ finestModel.setScaffoldSeq(readSequenceFile(sequenceFile))
finestModel.randomizeUnassignedNtSeqs()
+ # finestModel.setUnassignedNtSeqs("T")
finestModel.writePdbPsf( out + ".ideal" )
finestModel.backmap( finerModel, finerModelCoords )
- finestModel.writePdbPsf( out )
-
+ finestModel.writeNamdFiles( out )
# def simulateDesign(f,out,gpu=0,shiftEulerZ=180):
# print(out)
-
if len(sys.argv) > 1:
files = sys.argv[1:]
else:
@@ -169,9 +179,9 @@ else:
print(files)
-gpu=0
+gpu=1
for f in files[:]:
# f = files
print(f)
out = re.match('json/(.*).json',f).group(1)
- simulateDesign(f,out,gpu=gpu)
+ simulateDesign(f, out, numCoarsestSteps=5000000, gpu=gpu)
diff --git a/test.py b/test.py
deleted file mode 100644
index 8b15a12138c3ceffffd900402f3a9bdb6710b01a..0000000000000000000000000000000000000000
--- a/test.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import json
-import cadnano
-from cadnano.document import Document
-from encode import encodeDocument
-
-with open('input.json') as ch:
- data = json.load(ch)
-
-try:
- doc = Document()
- cadnano.fileio.v3decode.decode(doc, data)
-except:
- doc = Document()
- cadnano.fileio.v2decode.decode(doc, data)
-
-encodeDocument(doc)