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Commit 47aef9dc authored by pinyili2's avatar pinyili2
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mrdna/readers/__init__.py
+ 3
− 1
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......@@ -11,6 +11,9 @@ 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_scadnano(sc_file, **model_parameters):
from .segmentmodel_from_scadnano import mrdna_model_from_scadnano
return mrdna_model_from_scadnano(sc_file, **model_parameters)
def read_vhelix(maya_file, **model_parameters):
from .polygon_mesh import parse_maya_file, convert_maya_bases_to_segment_model
......@@ -44,6 +47,5 @@ def read_atomic_pdb(pdb_file, **model_parameters):
return SegmentModelFromPdb(pdb_file)
def read_oxdna(coordinate_file, topology_file, virt2nuc=None, **model_parameters):
""" Idealized coordinate file: coordinates for detecting stacks and base pairs, defaults to coordinate_file """
from .segmentmodel_from_oxdna_pinyi import mrdna_model_from_oxdna
return mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc, **model_parameters)
mrdna/readers/segmentmodel_from_cadnano.py
+ 1
− 1
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......@@ -171,7 +171,7 @@ def gen_prop_table(part):
id_series=id_series+gen_id_series(i,part)
nt_prop=pd.DataFrame(id_series)
nt_prop.reset_index(names=list(range(len(nt_prop.index))),inplace=True)
nt_prop.reset_index(inplace=True)
nt_prop["seq"]=-1
ind_tuple=list(zip(nt_prop["vh"],nt_prop["zid"],nt_prop["fwd"]))
stacks=[]
......
mrdna/readers/segmentmodel_from_lists.py
+ 0
− 4
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......@@ -471,13 +471,9 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
model._reader_list_hmap = hmap
model._reader_list_fwd = fwd
model._reader_list_hrank = hrank
df=pd.DataFrame({"r":coordinate,"bp":basepair,"stack":stack,"threeprime":three_prime,"seq":sequence,"orientation":orientation,"fwd":fwd,"hmap":hmap,"hrank":hrank,})
if sequence is None:
for s in model.segments:
s.randomize_unset_sequence()
model._dataframe=df
return model
def model_from_pandas(df,coordinate_col="r",bp_col="bp",stack_col="stack",three_prime_col="threeprime",
......
mrdna/readers/segmentmodel_from_oxdna_pinyi.py
+ 8
− 8
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......@@ -3,8 +3,8 @@ from .segmentmodel_from_lists import model_from_basepair_stack_3prime
from ..arbdmodel.coords import rotationAboutAxis
import pickle
import pandas as pd
from oxlibs import *
import sys
import mrdna.readers.libs as libs
import numpy as np
from scipy.spatial import distance_matrix
pd.options.mode.chained_assignment = None # default='warn'
......@@ -89,10 +89,12 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
L.append(pd.Series({"index":index,"vh":vh,"zid":z,"strand":strand,"is_scaf":bool(is_scaf)}))
return L
def get_virt2nuc(virt2nuc,top_data):
vh_vb,pattern=pd.read_pickle(virt2nuc)
sys.modules["libs"]=libs
virt_pickle=open(virt2nuc,"rb")
vh_vb,pattern=pickle.load(virt_pickle)
L1=_find_vh_vb_table(vh_vb._scaf,1)
L2=_find_vh_vb_table(vh_vb._stap,0)
nt_prop=pd.DataFrame(L1+L2)
nt_prop=pd.DataFrame(L1+L2,dtype=object)
nt_prop.set_index("index",inplace=True)
nt_prop.sort_index(inplace=True)
nt_prop["threeprime"]=top_data[2]
......@@ -126,9 +128,8 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
bp=nt_prop["bp"]
stack=nt_prop["stack"]
three_prime=nt_prop["threeprime"]
nt_prop["r"]=r
nt_prop["orientation"]=orientation
nt_prop["r"]=list(r)
except:
## Reverse direction so indices run 5'-to-3'
top_data = [a[::-1] for a in top_data]
......@@ -149,7 +150,7 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
five_prime = len(r) - top_data[3] -1
three_prime[three_prime >= len(r)] = -1
five_prime[five_prime >= len(r)] = -1
nt_prop=pd.DataFrame({"r":r,"bp":bp,"stack":stack,"threeprime":three_prime, "seq":seq,"orientation":orientation})
nt_prop=pd.DataFrame({"r":list(r),"bp":list(bp),"stack":list(stack),"threeprime":list(three_prime), "seq":list(seq),"orientation":list(orientation)})
def _debug_write_bonds():
from ..arbdmodel import ParticleType, PointParticle, ArbdModel, Group
......@@ -186,7 +187,6 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
logger.info(f'mrdna_model_from_oxdna: num_bp, num_ss_nt, num_stacked: {np.sum(bp>=0)//2} {np.sum(bp<0)} {np.sum(stack >= 0)}')
model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
"""
......
mrdna/readers/test.ipynb
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mrdna/readers/test/libs deleted 120000 → 0
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../libs
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mrdna/readers/test/test.json deleted 100644 → 0
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14 G 413 -1
mrdna/readers/test/test_insert.json
+ 1
− 1
View file @ 47aef9dc
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