From df296ad8886748cece22fcb6d20f87576329e87f Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Tue, 20 Aug 2024 19:40:43 -0500
Subject: [PATCH] add
---
mrdna/readers/__init__.py | 4 +--
mrdna/readers/segmentmodel_from_lists.py | 36 +++++++++++-------------
2 files changed, 18 insertions(+), 22 deletions(-)
diff --git a/mrdna/readers/__init__.py b/mrdna/readers/__init__.py
index 8c0b352..955f236 100644
--- a/mrdna/readers/__init__.py
+++ b/mrdna/readers/__init__.py
@@ -37,10 +37,10 @@ def read_list(infile,**model_parameters):
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):
+ seq_col="seq",orientation_col="orientation"):
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),
+ seq_col,orientation_col)
def read_atomic_pdb(pdb_file, **model_parameters):
from .segmentmodel_from_pdb import SegmentModelFromPdb
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index c257108..2a1a8dd 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -477,45 +477,39 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
return model
def model_from_pandas(df,coordinate_col="r",bp_col="bp",stack_col="stack",three_prime_col="threeprime",
- seq_col=None,orientation_col=None,
+ seq_col="seq",orientation_col="orientation",
max_basepairs_per_bead = 5,
max_nucleotides_per_bead = 5,
local_twist = False,
dimensions=(5000,5000,5000)
,**model_parameters):
try:
- c=df[coordinate_col]
+ c=np.array(list(df[coordinate_col]))
except:
print("cannot locate coordinate")
try:
- bp=df[bp_col]
+ bp=np.array(df[bp_col])
except:
print("cannot locate bp")
try:
- stack=df[stack_col]
+ stack=np.array(df[stack_col])
except:
print("cannot find stack")
try:
- tprime=df[three_prime_col]
+ tprime=np.array(df[three_prime_col])
except:
print("cannot locate 3's")
- if seq_col is not None:
- try:
- seq=df[seq_col]
- except:
- print("no sequence inputted")
- seq=None
- else:
+ try:
+ seq=np.array(df[seq_col])
+ except:
+ print("no sequence inputted")
seq=None
- if orientation_col is not None:
- try:
- orient=df[orientation_col]
- except:
- print("no orientation inputted")
- orient=None
- else:
- orient=None
+ try:
+ orient=np.array(list(df[orientation_col]))
+ except:
+ print("no orientation inputted")
+ orient=None
try:
model=model_from_basepair_stack_3prime(c, bp, stack, tprime,
@@ -525,6 +519,8 @@ 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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