From ffbe85f0901d0aa25010f2a54e95b45413909190 Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Sat, 17 Aug 2024 11:21:34 -0500
Subject: [PATCH] update init
---
mrdna/readers/__init__.py | 11 ++++++++---
mrdna/readers/segmentmodel_from_cadnano.py | 1 -
mrdna/readers/segmentmodel_from_lists.py | 7 ++++---
3 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/mrdna/readers/__init__.py b/mrdna/readers/__init__.py
index 33b2a79..1b61d77 100644
--- a/mrdna/readers/__init__.py
+++ b/mrdna/readers/__init__.py
@@ -33,12 +33,17 @@ def read_list(infile,**model_parameters):
from .segmentmodel_from_lists import model_from_basepair_stack_3prime
return model_from_basepair_stack_3prime(coords, bp, stack, three_prime)
+def read_pandas(df,coordinate_col="r",bp_col="bp",stack_col="stack",three_prime_col="threeprime",
+ seq_col=None,orientation_col=None):
+ from .segmentmodel_from_lists import model_from_pandas
+ return model_from_pandas(df,coordinate_col,bp_col,stack_col,three_prime_col,
+ seq_col,orientation_col),
def read_atomic_pdb(pdb_file, **model_parameters):
from .segmentmodel_from_pdb import SegmentModelFromPdb
return SegmentModelFromPdb(pdb_file)
-def read_oxdna(coordinate_file, topology_file, idealized_coordinate_file=None, **model_parameters):
+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 import mrdna_model_from_oxdna
- return mrdna_model_from_oxdna(coordinate_file, topology_file, idealized_coordinate_file, **model_parameters)
+ from .segmentmodel_from_oxdna_pinyi import mrdna_model_from_oxdna
+ return mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc, **model_parameters)
diff --git a/mrdna/readers/segmentmodel_from_cadnano.py b/mrdna/readers/segmentmodel_from_cadnano.py
index 7021722..f8127e7 100644
--- a/mrdna/readers/segmentmodel_from_cadnano.py
+++ b/mrdna/readers/segmentmodel_from_cadnano.py
@@ -222,5 +222,4 @@ def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
stack=np.array((list(nt_prop["stack"])))
orientation=np.array(list(nt_prop["orientation"]))
model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
- model._dataframe=nt_prop
return model
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index 922b3d2..3f96df7 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -230,7 +230,7 @@ def set_splines(seg, coordinate, hid, hmap, hrank, fwd, basepair, orientation=No
def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
- sequence=None, orientation=None,
+ sequence=None, orientation=None,
max_basepairs_per_bead = 5,
max_nucleotides_per_bead = 5,
local_twist = False,
@@ -471,10 +471,12 @@ 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
@@ -527,7 +529,6 @@ def model_from_pandas(df,coordinate_col="r",bp_col="bp",stack_col="stack",three_
local_twist = local_twist,
dimensions=dimensions
**model_parameters)
- model._dataframe=df
return model
except:
print("cannot phrase DataFrame, aborted")
--
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