add segmentmodel_from_cadnano

mrdna/readers/.gitignore

-libs
 *.swp
 .ipynb*

mrdna/readers/__init__.py

@@ -7,6 +7,11 @@ def read_cadnano(json_file, sequence=None, fill_sequence='T', **model_parameters
     data = read_json_file(json_file)
     return model_from_cadnano_json(data, sequence, fill_sequence, **model_parameters)
 
+def read_cadnano_input(json_file,sequence=None,**model_parameters):
+    from .segmentmodel_from_cadnano import mrdna_model_from_cadnano
+
+    return mrdna_model_from_cadnano(json_file,seq=sequence,**model_parameters)
+
 def read_vhelix(maya_file, **model_parameters):
     from .polygon_mesh import parse_maya_file, convert_maya_bases_to_segment_model
 

mrdna/readers/list.pdb

-CRYST1 5000.000 5000.000 5000.000  90.00  90.00  90.00 P 1           1
-ATOM      1 DNA  DNA A 1       0.50000 0.00000 8.50000  0.00  0.00   0     0
-ATOM      2 DNA  DNA A 2       0.50000 0.00000 15.3000  0.00  0.00   0     1
-ATOM      3 DNA  DNA A 3       0.50000 0.00000 15.3000  0.00  0.00   0     1
-ATOM      4 NAS  NAS A 4       0.00000 0.00000-1.70000  0.00  0.00   0     2
-ATOM      5 NAS  NAS A 5       0.00000 0.00000 1.70000  0.00  0.00   0     2
-ATOM      6 NAS  NAS A 6       0.00000 0.00000 5.10000  0.00  0.00   0     2
-ATOM      7 NAS  NAS A 7       0.00000 0.00000 20.4000  0.00  0.00   0     3

mrdna/readers/list.psf

-PSF NAMD
-
-       0 !NTITLE
-
-       7 !NATOM
-         1 0        1        DNA      DNA      D000   0.000000      225.0000 0
-         2 1        2        DNA      DNA      D001   0.000000      300.0000 0
-         3 1        3        DNA      DNA      D002   0.000000      375.0000 0
-         4 2        4        NAS      NAS      S000   0.000000      150.0000 0
-         5 2        5        NAS      NAS      S000   0.000000      150.0000 0
-         6 2        6        NAS      NAS      S001   0.000000       75.0000 0
-         7 3        7        NAS      NAS      S000   0.000000      150.0000 0
-
-       7 !NBOND
-       1       6        4       5        5       6        4       7
-       1       3        2       3        2       7 
-
-       3 !NTHETA
-       4       5       6        5       4       7        1       3       2
-
-       0 !NPHI
-
-       0 !NIMPHI
-
-
-       0 !NDON: donors
-
-
-
-       0 !NACC: acceptors
-
-
-
-       0 !NNB
-
-      0      0      0      0      0      0      0
-
-       1       0 !NGRP
-

mrdna/readers/segmentmodel_from_cadnano.py

@@ -6,10 +6,16 @@ from glob import glob
 import re
 import pandas as pd
 pd.options.mode.chained_assignment = None  # default='warn'
+from .segmentmodel_from_lists import model_from_basepair_stack_3prime
 
 from ..arbdmodel.coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
 from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
 from ..model.dna_sequence import m13 as m13seq
+import json
+import re
+import cadnano
+from cadnano.document import Document
+
 
 ## Only testing on cadnano2.5
 ## TODO: separate SegmentModel from ArbdModel so multiple parts can be combined
@@ -34,10 +40,6 @@ def get_lattice(part):
 
 
 def read_json_file(filename):
-    import json
-    import re
-    import cadnano
-    from cadnano.document import Document
 
     try:
         with open(filename) as ch:
@@ -138,11 +140,13 @@ def gen_prop_table(json_file):
     tot_id=scaf_id+stap_id
     vhi,zidi=np.where(np.array(scaf_id)==1)
     vhj,zidj=np.where(np.array(stap_id)==1)
+    vhi=vslist.index[vhi]
+    vhj=vslist.index[vhj]
     nt_prop["vh"]=list(vhi)+list(vhj)
     nt_prop["zid"]=list(zidi)+list(zidj)
     vhzid=list(zip(nt_prop["vh"],nt_prop["zid"]))
-    nt_prop["r"]=[part.getCoordinate(i,j) for i,j in zip(nt_prop["vh"],nt_prop["zid"])]
-    nt_prop["orientation"]=[get_helix_angle(part, helix_id, indices) for i,j in zip(nt_prop["vh"],nt_prop["zid"])]
+    nt_prop["r"]=[part.getCoordinate(helix_id, indices) for helix_id, indices in zip(nt_prop["vh"],nt_prop["zid"])]
+    nt_prop["orientation"]=[get_helix_angle(part, helix_id, indices) for helix_id,indices in zip(nt_prop["vh"],nt_prop["zid"])]
     nt_prop=nt_prop.fillna(-1)
     for i in range(int(len(vhzid)/2)):
         try:
@@ -152,6 +156,7 @@ def gen_prop_table(json_file):
         except:
             pass
     tprime_list=-np.ones(len(nt_prop.index),dtype=int)
+    index2=list(zip(vhzid,nt_prop["is_scaf"]))
     for i in range(len(nt_prop.index)):
         ((m,n),p)=list(zip(vhzid,nt_prop["is_scaf"]))[i]
         if p==True:
@@ -169,13 +174,17 @@ def gen_prop_table(json_file):
     (n,)=np.where(nt_prop["threeprime"]==-1)
     stackid=nt_prop["bp"][[list(nt_prop["threeprime"]).index(i) for i in n]]
     nt_prop["stack"][stackid.index[np.where(np.array(stackid)!=-1)]]=nt_prop["threeprime"][stackid.index[np.where(np.array(stackid)!=-1)]]
+    ## Todo: sequence    
     
 
     return nt_prop
 
-def mrdna_model_from_cadnano(json_file,**model_parameters):
+def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
     nt_prop=gen_prop_table(json_file)
-    model = model_from_basepair_stack_3prime( nt_prop["r"], nt_prop["bp"], stack, three_prime, seq, orientation, **model_parameters )
-
-if __name__ == '__main__':
-    
+    if seq is None:
+        if nt_prop["seq"][0]==-1:
+            seq=None
+        else:
+            seq=nt_prop["seq"]
+    model = model_from_basepair_stack_3prime( nt_prop["r"], nt_prop["bp"], nt_prop["stack"], nt_prop["threeprime"], seq,nt_prop["orientation"], **model_parameters )
+ 

mrdna/readers/test.json

-{"name":"test.json","vstrands":[{"row":12,"col":16,"num":0,"scaf":[[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[1,5,0,6],[0,5,0,7],[0,6,0,8],[0,7,0,9],[0,8,0,10],[0,9,0,11],[0,10,0,12],[0,11,0,13],[0,12,0,14],[0,13,0,15],[0,14,0,16],[0,15,0,17],[0,16,0,18],[0,17,0,19],[0,18,0,20],[0,19,0,21],[0,20,0,22],[0,21,0,23],[0,22,0,24],[0,23,0,25],[0,24,0,26],[0,25,0,27],[0,26,0,28],[0,27,0,29],[0,28,0,30],[0,29,0,31],[0,30,0,32],[0,31,0,33],[0,32,0,34],[0,33,0,35],[0,34,0,36],[0,35,1,36],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,0,40],[0,39,0,41],[0,40,-1,-1]],"stap":[[-1,-1,-1,-1],[-1,-1,-1,-1],[0,3,-1,-1],[0,4,0,2],[0,5,0,3],[0,6,0,4],[0,7,0,5],[0,8,0,6],[0,9,0,7],[0,10,0,8],[0,11,0,9],[0,12,0,10],[0,13,0,11],[0,14,0,12],[0,15,0,13],[0,16,0,14],[0,17,0,15],[0,18,0,16],[0,19,0,17],[0,20,0,18],[1,20,0,19],[0,22,1,21],[0,23,0,21],[-1,-1,0,22],[0,25,-1,-1],[0,26,0,24],[0,27,0,25],[5,27,0,26],[0,29,5,28],[0,30,0,28],[0,31,0,29],[0,32,0,30],[0,33,0,31],[0,34,0,32],[0,35,0,33],[0,36,0,34],[0,37,0,35],[0,38,0,36],[-1,-1,0,37],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1]],"loop":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"skip":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"scafLoop":[],"stapLoop":[],"stap_colors":[[23,13369809],[38,12060012]]},{"row":12,"col":15,"num":1,"scaf":[[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[1,6,0,5],[1,7,1,5],[1,8,1,6],[1,9,1,7],[1,10,1,8],[1,11,1,9],[1,12,1,10],[1,13,1,11],[1,14,1,12],[1,15,1,13],[1,16,1,14],[1,17,1,15],[1,18,1,16],[2,18,1,17],[1,20,2,19],[1,21,1,19],[1,22,1,20],[1,23,1,21],[1,24,1,22],[1,25,1,23],[1,26,1,24],[1,27,1,25],[1,28,1,26],[1,29,1,27],[1,30,1,28],[1,31,1,29],[1,32,1,30],[1,33,1,31],[1,34,1,32],[1,35,1,33],[1,36,1,34],[0,36,1,35],[-1,-1,-1,-1],[-1,-1,-1,-1],[1,40,-1,-1],[1,41,1,39],[-1,-1,1,40]],"stap":[[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,1,4],[1,3,1,5],[1,4,1,6],[1,5,1,7],[1,6,1,8],[1,7,1,9],[1,8,1,10],[1,9,1,11],[1,10,1,12],[1,11,1,13],[1,12,1,14],[1,13,1,15],[1,14,1,16],[1,15,1,17],[1,16,1,18],[1,17,1,19],[1,18,1,20],[1,19,0,20],[0,21,1,22],[1,21,1,23],[1,22,1,24],[1,23,1,25],[1,24,1,26],[1,25,1,27],[1,26,1,28],[1,27,1,29],[1,28,1,30],[1,29,1,31],[1,30,1,32],[1,31,1,33],[1,32,1,34],[1,33,1,35],[1,34,1,36],[1,35,1,37],[1,36,1,38],[1,37,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1]],"loop":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"skip":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"scafLoop":[],"stapLoop":[],"stap_colors":[[3,1501302]]},{"row":13,"col":15,"num":2,"scaf":[[-1,-1,-1,-1],[-1,-1,-1,-1],[3,2,2,3],[2,2,2,4],[2,3,2,5],[2,4,2,6],[2,5,2,7],[2,6,2,8],[2,7,2,9],[2,8,2,10],[2,9,2,11],[2,10,2,12],[2,11,2,13],[2,12,2,14],[2,13,2,15],[2,14,2,16],[2,15,2,17],[2,16,2,18],[2,17,1,18],[1,19,2,20],[2,19,2,21],[2,20,2,22],[2,21,2,23],[2,22,2,24],[2,23,2,25],[2,24,2,26],[2,25,2,27],[2,26,2,28],[2,27,2,29],[2,28,2,30],[2,29,2,31],[2,30,2,32],[2,31,3,32],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,2,40],[2,39,2,41],[2,40,-1,-1]],"stap":[[2,1,-1,-1],[2,2,2,0],[2,3,2,1],[2,4,2,2],[2,5,2,3],[2,6,2,4],[2,7,2,5],[2,8,2,6],[2,9,2,7],[2,10,2,8],[2,11,2,9],[2,12,2,10],[2,13,2,11],[2,14,2,12],[2,15,2,13],[2,16,2,14],[2,17,2,15],[2,18,2,16],[2,19,2,17],[2,20,2,18],[2,21,2,19],[2,22,2,20],[2,23,2,21],[2,24,2,22],[2,25,2,23],[2,26,2,24],[2,27,2,25],[2,28,2,26],[2,29,2,27],[2,30,2,28],[2,31,2,29],[2,32,2,30],[2,33,2,31],[2,34,2,32],[-1,-1,2,33],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1]],"loop":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"skip":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"scafLoop":[],"stapLoop":[],"stap_colors":[[34,8947848]]},{"row":13,"col":16,"num":3,"scaf":[[-1,-1,-1,-1],[-1,-1,-1,-1],[3,3,2,2],[3,4,3,2],[3,5,3,3],[3,6,3,4],[3,7,3,5],[3,8,3,6],[3,9,3,7],[3,10,3,8],[3,11,3,9],[3,12,3,10],[3,13,3,11],[3,14,3,12],[3,15,3,13],[4,15,3,14],[3,17,4,16],[3,18,3,16],[3,19,3,17],[3,20,3,18],[3,21,3,19],[3,22,3,20],[3,23,3,21],[3,24,3,22],[3,25,3,23],[3,26,3,24],[3,27,3,25],[3,28,3,26],[3,29,3,27],[3,30,3,28],[3,31,3,29],[3,32,3,30],[2,32,3,31],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[3,38,-1,-1],[3,39,3,37],[3,40,3,38],[3,41,3,39],[-1,-1,3,40]],"stap":[[-1,-1,3,1],[3,0,3,2],[3,1,3,3],[3,2,3,4],[3,3,3,5],[3,4,3,6],[3,5,3,7],[3,6,3,8],[3,7,3,9],[3,8,3,10],[3,9,3,11],[3,10,3,12],[3,11,3,13],[3,12,3,14],[3,13,3,15],[3,14,3,16],[3,15,3,17],[3,16,3,18],[3,17,3,19],[3,18,3,20],[3,19,4,20],[4,21,3,22],[3,21,3,23],[3,22,3,24],[3,23,3,25],[3,24,3,26],[3,25,3,27],[3,26,3,28],[3,27,3,29],[3,28,3,30],[3,29,3,31],[3,30,3,32],[3,31,3,33],[3,32,3,34],[3,33,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1],[-1,-1,-1,-1]],"lo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\ No newline at end of file