code stringlengths 114 1.05M | path stringlengths 3 312 | quality_prob float64 0.5 0.99 | learning_prob float64 0.2 1 | filename stringlengths 3 168 | kind stringclasses 1
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import re
from collections import OrderedDict
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.checkpoint as cp
from .utils import load_state_dict_from_url
__all__ = ["DenseNet", "densenet121", "densenet169", "densenet201", "densenet161"]
model_urls = {
"densenet121": "https... | /rmn-3.1.1-py3-none-any.whl/models/densenet.py | 0.920823 | 0.350032 | densenet.py | pypi |
import os
import requests
import torch
from requests.adapters import HTTPAdapter
from torch import nn
from torch.nn import functional as F
class BasicConv2d(nn.Module):
def __init__(self, in_planes, out_planes, kernel_size, stride, padding=0):
super().__init__()
self.conv = nn.Conv2d(
... | /rmn-3.1.1-py3-none-any.whl/models/inception_resnet_v1.py | 0.942401 | 0.34956 | inception_resnet_v1.py | pypi |
import torch
import torch.nn as nn
from .densenet import densenet121
from .googlenet import googlenet
from .resnet import resnet18
model_urls = {
"resnet18": "https://download.pytorch.org/models/resnet18-5c106cde.pth",
"resnet34": "https://download.pytorch.org/models/resnet34-333f7ec4.pth",
"resnet50": "h... | /rmn-3.1.1-py3-none-any.whl/models/res_dense_gle.py | 0.88573 | 0.349699 | res_dense_gle.py | pypi |
import torch
import torch.nn as nn
from .utils import load_state_dict_from_url
__all__ = [
"ResNet",
"resnet18",
"resnet34",
"resnet50",
"resnet101",
"resnet152",
"resnext50_32x4d",
"resnext101_32x8d",
"wide_resnet50_2",
"wide_resnet101_2",
]
model_urls = {
"resnet18": "h... | /rmn-3.1.1-py3-none-any.whl/models/resnet.py | 0.938251 | 0.442094 | resnet.py | pypi |
import warnings
from collections import namedtuple
import torch
import torch.nn as nn
import torch.nn.functional as F
from .utils import load_state_dict_from_url
__all__ = ["GoogLeNet", "googlenet"]
model_urls = {
# GoogLeNet ported from TensorFlow
"googlenet": "https://download.pytorch.org/models/googlenet... | /rmn-3.1.1-py3-none-any.whl/models/googlenet.py | 0.902143 | 0.333273 | googlenet.py | pypi |
import traceback
import torch
import torch.nn as nn
from .resnet import BasicBlock, Bottleneck, conv1x1
def transpose(in_channels, out_channels, kernel_size=2, stride=2):
return nn.Sequential(
nn.ConvTranspose2d(
in_channels, out_channels, kernel_size=kernel_size, stride=stride
),
... | /rmn-3.1.1-py3-none-any.whl/models/attention.py | 0.908565 | 0.499512 | attention.py | pypi |
import torch
import torch.nn as nn
from .utils import load_state_dict_from_url
__all__ = ["AlexNet", "alexnet"]
model_urls = {
"alexnet": "https://download.pytorch.org/models/alexnet-owt-4df8aa71.pth",
}
class AlexNet(nn.Module):
def __init__(self, in_channels=3, num_classes=1000):
super(AlexNet, ... | /rmn-3.1.1-py3-none-any.whl/models/alexnet.py | 0.884008 | 0.352425 | alexnet.py | pypi |
from pytorchcv.model_provider import get_model as ptcv_get_model
from .alexnet import *
from .brain_humor import *
from .centerloss_resnet import resnet18_centerloss
from .densenet import *
from .fer2013_models import *
from .googlenet import *
from .inception import *
from .inception_resnet_v1 import *
from .masking ... | /rmn-3.1.1-py3-none-any.whl/models/__init__.py | 0.874507 | 0.187021 | __init__.py | pypi |
import torch
import torch.nn as nn
from .utils import load_state_dict_from_url
__all__ = [
"VGG",
"vgg11",
"vgg11_bn",
"vgg13",
"vgg13_bn",
"vgg16",
"vgg16_bn",
"vgg19_bn",
"vgg19",
]
model_urls = {
"vgg11": "https://download.pytorch.org/models/vgg11-bbd30ac9.pth",
"vgg13... | /rmn-3.1.1-py3-none-any.whl/models/vgg.py | 0.928862 | 0.535463 | vgg.py | pypi |
from collections import OrderedDict
from torch import nn
class IntermediateLayerGetter(nn.ModuleDict):
"""
Module wrapper that returns intermediate layers from a model
It has a strong assumption that the modules have been registered
into the model in the same order as they are used.
This means t... | /rmn-3.1.1-py3-none-any.whl/models/_utils.py | 0.952673 | 0.761561 | _utils.py | pypi |
import traceback
import torch
import torch.nn as nn
from .resnet import BasicBlock, Bottleneck, conv1x1
def up_pooling(in_channels, out_channels, kernel_size=2, stride=2):
return nn.Sequential(
nn.ConvTranspose2d(
in_channels, out_channels, kernel_size=kernel_size, stride=stride
),
... | /rmn-3.1.1-py3-none-any.whl/models/masking.py | 0.926003 | 0.630486 | masking.py | pypi |
import torch
import torch.nn as nn
def block(in_channels, out_channels, kernel_size=3, stride=1, padding=1):
return nn.Sequential(
nn.Conv2d(
in_channels,
out_channels,
kernel_size=kernel_size,
stride=stride,
padding=padding,
),
n... | /rmn-3.1.1-py3-none-any.whl/models/segmentation/unet_basic.py | 0.940871 | 0.453322 | unet_basic.py | pypi |
import torch
from torch import nn
from torch.nn import functional as F
from ._utils import _SimpleSegmentationModel
__all__ = ["DeepLabV3"]
class DeepLabV3(_SimpleSegmentationModel):
"""
Implements DeepLabV3 model from
`"Rethinking Atrous Convolution for Semantic Image Segmentation"
<https://arxiv.o... | /rmn-3.1.1-py3-none-any.whl/models/segmentation/deeplabv3.py | 0.953134 | 0.545346 | deeplabv3.py | pypi |
from .. import resnet
from .._utils import IntermediateLayerGetter
from ..utils import load_state_dict_from_url
from .deeplabv3 import DeepLabHead, DeepLabV3
from .fcn import FCN, FCNHead
__all__ = ["fcn_resnet50", "fcn_resnet101", "deeplabv3_resnet50", "deeplabv3_resnet101"]
model_urls = {
"fcn_resnet50_coco": ... | /rmn-3.1.1-py3-none-any.whl/models/segmentation/segmentation.py | 0.791257 | 0.33273 | segmentation.py | pypi |
import os
import cv2
import numpy as np
import pandas as pd
from torch.utils.data import Dataset
from torchvision.transforms import transforms
from utils.augmenters.augment import seg
EMOTION_DICT = {
0: "angry",
1: "disgust",
2: "fear",
3: "happy",
4: "sad",
5: "surprise",
6: "neutral",
... | /rmn-3.1.1-py3-none-any.whl/utils/datasets/fer2013dataset.py | 0.581897 | 0.325574 | fer2013dataset.py | pypi |
import torch
EPS = 1e-10
def nanmean(x):
return torch.mean(x[x == x])
def _fast_hist(true, pred, num_classes):
mask = (true >= 0) & (true < num_classes)
hist = (
torch.bincount(
num_classes * true[mask] + pred[mask],
minlength=num_classes**2,
)
.reshape(n... | /rmn-3.1.1-py3-none-any.whl/utils/metrics/segment_metrics.py | 0.929216 | 0.811452 | segment_metrics.py | pypi |
from . import DATA_DIR
import csv
REMIND_TO_ECOINVENT_EMISSION_FILEPATH = (DATA_DIR / "ecoinvent_to_gains_emission_mappping.csv")
class InventorySet:
"""
Hosts different filter sets to for ecoinvent activities and exchanges.
It stores:
* material_filters: filters for activities related to materials.... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/activity_maps.py | 0.69987 | 0.569015 | activity_maps.py | pypi |
from . import DATA_DIR
from wurst import searching as ws
import csv
import pprint
import wurst
import bw2io
from bw2data.database import DatabaseChooser
FILEPATH_FIX_NAMES = (DATA_DIR / "fix_names.csv")
FILEPATH_BIOSPHERE_FLOWS = (DATA_DIR / "dict_biosphere.txt")
class DatabaseCleaner:
"""
Class that cleans... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/clean_datasets.py | 0.696887 | 0.345519 | clean_datasets.py | pypi |
from wurst.geo import geomatcher
from rmnd_lca import DATA_DIR
REGION_MAPPING_FILEPATH = (DATA_DIR / "regionmappingH12.csv")
class Geomap:
"""
Map ecoinvent locations to REMIND regions and vice-versa.
"""
def __init__(self):
self.geo = self.get_REMIND_geomatcher()
@staticmethod
def... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/geomap.py | 0.579638 | 0.411584 | geomap.py | pypi |
import os
from . import DATA_DIR
import csv
FILEPATH_BIOSPHERE_FLOWS = (DATA_DIR / "flows_biosphere.csv")
class Export:
"""
Class that exports the transformed data into matrices:
* A matrix: contains products exchanges
* B matrix: contains exchanges activities and the biosphere
The A and B matri... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/export.py | 0.560974 | 0.561335 | export.py | pypi |
from . import DATA_DIR
import pandas as pd
import xarray as xr
from pathlib import Path
import csv
import numpy as np
REMIND_ELEC_MARKETS = (DATA_DIR / "electricity" / "remind_electricity_markets.csv")
REMIND_ELEC_EFFICIENCIES = (DATA_DIR / "electricity" / "remind_electricity_efficiencies.csv")
REMIND_ELEC_EMISSIONS =... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/data_collection.py | 0.596316 | 0.317439 | data_collection.py | pypi |
from . import DATA_DIR
import csv
import pandas as pd
CO2_FUELS = DATA_DIR / "fuel_co2_emission_factor.txt"
LHV_FUELS = DATA_DIR / "fuels_lower_heating_value.txt"
CLINKER_RATIO_ECOINVENT_36 = DATA_DIR / "cement" / "clinker_ratio_ecoinvent_36.csv"
CLINKER_RATIO_ECOINVENT_35 = DATA_DIR / "cement" / "clinker_ratio_ecoin... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/utils.py | 0.589953 | 0.244397 | utils.py | pypi |
import wurst
from wurst import searching as ws
import itertools
from .geomap import Geomap
from .activity_maps import InventorySet
from .utils import *
import uuid
import copy
class Steel:
"""
Class that modifies steel markets in ecoinvent based on REMIND output data.
:ivar scenario: name of a Remind sce... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/steel.py | 0.571767 | 0.308659 | steel.py | pypi |
from . import DATA_DIR
import wurst
from prettytable import PrettyTable
from wurst import searching as ws
from bw2io import ExcelImporter, Migration
from bw2io.importers.base_lci import LCIImporter
from carculator import (
CarInputParameters,
fill_xarray_from_input_parameters,
CarModel,
InventoryCalcu... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/inventory_imports.py | 0.698329 | 0.305069 | inventory_imports.py | pypi |
import copy
import uuid
import numpy as np
import wurst
from wurst import searching as ws
from .activity_maps import InventorySet
from .geomap import Geomap
from .utils import *
class Cement:
"""
Class that modifies clinker and cement production datasets in ecoinvent based on REMIND and WBCSD's GNR data.
:... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/cement.py | 0.587943 | 0.305807 | cement.py | pypi |
from .geomap import Geomap
import wurst
import wurst.searching as ws
import pandas as pd
import uuid
import copy
from .geomap import REGION_MAPPING_FILEPATH
class Cars():
"""
Class that modifies carculator inventories in ecoinvent
based on REMIND output data.
:ivar db: ecoinvent database in list-of... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/cars.py | 0.496094 | 0.253203 | cars.py | pypi |
import os
from . import DATA_DIR
from .activity_maps import InventorySet
from .geomap import Geomap
from wurst import searching as ws
from wurst.ecoinvent import filters
import csv
import numpy as np
import uuid
import wurst
from datetime import date
PRODUCTION_PER_TECH = (
DATA_DIR / "electricity" / "electricity_... | /rmnd_lca-0.1.6-py3-none-any.whl/rmnd_lca/electricity.py | 0.790085 | 0.378517 | electricity.py | pypi |
<a href="https://ascl.net/2204.008"><img src="https://img.shields.io/badge/ascl-2204.008-blue.svg?colorB=262255" alt="ascl:2204.008" /></a>
[](https://pypi.python.org/pypi/rmnest)
[](http... | /rmnest-0.2.0.tar.gz/rmnest-0.2.0/README.md | 0.669637 | 0.986031 | README.md | pypi |
import pytoml as toml
from pathlib import Path
from .utils import slugify
ASSIGNMENT = 'assignment'
READING = 'reading'
class BaseTrackObject(object):
def __str__(self):
return "({}) - {} - {}".format(
self.__class__.__name__, self.name, self.uuid
)
def _slugify_with_order(self,... | /rmotr_curriculum_tools-0.3.1.tar.gz/rmotr_curriculum_tools-0.3.1/rmotr_curriculum_tools/models.py | 0.691289 | 0.2083 | models.py | pypi |
from __future__ import unicode_literals
from pathlib import Path
import pytoml as toml
from .models import *
from . import utils
from . import exceptions
UNIT_GLOB = 'unit-*'
LESSON_GLOB = 'lesson-*'
DOT_RMOTR_FILE_NAME = '.rmotr'
README_FILE_NAME = 'README.md'
MAIN_PY_NAME = 'main.py'
TESTS_DIR_NAME = 'tests'
SOLUT... | /rmotr_curriculum_tools-0.3.1.tar.gz/rmotr_curriculum_tools-0.3.1/rmotr_curriculum_tools/io.py | 0.530723 | 0.158142 | io.py | pypi |
# Risk Management Python (rmpy) Package
The `rmpy` package is a comprehensive and powerful tool designed for risk management and quantitative finance in Python. It provides a suite of functionalities to perform essential risk assessments, calculations, and analyses on financial assets and portfolios. This package stre... | /rmpy-1.1.8.tar.gz/rmpy-1.1.8/README.md | 0.465145 | 0.98829 | README.md | pypi |
import argparse
import json
import sys
import requests
def dict_list_key(item):
"""Provide the value to sort the dictionary item on.
:param dict item: The item to sort
:rtype: mixed
"""
if 'vhost' in item and 'name' in item:
return item['vhost'], item['name']
elif 'user' in item and... | /rmq-definitions-1.1.0.tar.gz/rmq-definitions-1.1.0/rmq_definitions.py | 0.41253 | 0.171651 | rmq_definitions.py | pypi |
from websocketdatamanager.rmq_engine import RMQEngine
from tasktools.taskloop import TaskLoop
import asyncio
class ReadMQBroker:
"""
This class pretends to create a knut in what receive data from RMQ queues and send directly to the objects form dj-collector on the database
"""
def __init__(self, queu... | /rmq_engine-0.0.5.tar.gz/rmq_engine-0.0.5/rmq_engine/rabbitmq.py | 0.534855 | 0.251191 | rabbitmq.py | pypi |
import pika
import pika.spec
import traceback
import sys
def consumer_function(function):
"""
:param function: Message processing function to wrap. Should take only body and properties parameters.
"""
def process(channel, method, header, body):
properties = header
result = function(... | /rmq_interface-1.1-py3-none-any.whl/rmq_interface/rmq_interface.py | 0.608012 | 0.178401 | rmq_interface.py | pypi |
# Rectangular Micro QR Code (rMQR Code) Generator
The rMQR Code is a rectangular two-dimensional barcode. This is easy to print in narrow space compared to conventional QR Code. This package can generate... | /rmqrcode-0.3.0.tar.gz/rmqrcode-0.3.0/README.md | 0.650134 | 0.864768 | README.md | pypi |
import warnings
from django.contrib.postgres import fields
from django.db import models
class DateRangeField(fields.DateRangeField):
def __init__(self, *args, **kwargs):
warnings.warn(
'DateRangeField is deprecated and will be removed in '
'rmr-django 2.0, use '
'djan... | /rmr-django-1.1.5.tar.gz/rmr-django-1.1.5/rmr/models/fields/range.py | 0.677581 | 0.249556 | range.py | pypi |
def read_command_line(objectstring='requested'):
from argparse import ArgumentParser as AP
parser = AP()
parser.add_argument('files', nargs="*",
help="optional list of directories containing rmt\
calculations",
default=["."])
parser... | /rmt_utilities-1.0-py3-none-any.whl/rmt_utilities/dipole_cli.py | 0.750553 | 0.218024 | dipole_cli.py | pypi |
from rmt_utilities.dataobjects import DataFile
from rmt_utilities.atomicunits import eV, c
from pathlib import Path
from itertools import zip_longest
import numpy as np
class RMTCalc:
"""
Primary data structure: holds all metadata for a given rmt calculation
and provides methods ``.HHG()`` and ``.ATAS()``... | /rmt_utilities-1.0-py3-none-any.whl/rmt_utilities/rmtutil.py | 0.804444 | 0.486636 | rmtutil.py | pypi |
def read_command_line(objectstring='requested distribution'):
from argparse import ArgumentParser as AP
from argparse import FileType
parser = AP(description=f"Plot the {objectstring} from the RMT-\
produced files. Note that if an input.conf file cannot be found in either the default \
directory (../) or t... | /rmt_utilities-1.0-py3-none-any.whl/rmt_utilities/reform_cli.py | 0.782288 | 0.187188 | reform_cli.py | pypi |
from rmt_utilities.rmtutil import RMTCalc
from pathlib import Path
class regress_report:
"""report on the agreement between two rmt calculations file by file"""
def __init__(self, failList=[], passList=[], location=None):
"""
Parameters
----------
failList : list of tuples
... | /rmt_utilities-1.0-py3-none-any.whl/rmt_utilities/regress.py | 0.807499 | 0.516656 | regress.py | pypi |
from typing import Sequence, Tuple, Union
import miniball as mnbl
import numpy as nmpy
from scipy.spatial.distance import pdist as PairwiseDistances
array_t = nmpy.ndarray
def Simplex(
dimension: int,
/,
*,
centered: bool = False,
around: array_t = None,
with_a_margin: float = None,
wi... | /rn_simplex-2021.5-py3-none-any.whl/rn_simplex/simplex.py | 0.931907 | 0.479991 | simplex.py | pypi |
from functools import partial
from multiprocessing import Pool
from pathlib import Path
from typing import Iterator, Tuple, Callable, List, Any
import numpy as np
from pysam import AlignmentFile
from .utils import echo
def chop_contig(size: int, chunksize: int) -> Iterator[Tuple[int, int]]:
"""
For a contig... | /rna_cd-0.2.0-py3-none-any.whl/rna_cd/bam_process.py | 0.759582 | 0.442034 | bam_process.py | pypi |
import datetime
from pathlib import Path
from typing import List, Any
import joblib
import click
import io
import base64
import json
import pkg_resources
def echo(msg: str):
"""Wrapper around click.secho to include datetime"""
fmt = "[ {0} ] {1}".format(str(datetime.datetime.utcnow()), msg)
click.secho(... | /rna_cd-0.2.0-py3-none-any.whl/rna_cd/utils.py | 0.631594 | 0.253309 | utils.py | pypi |
import enum
from pathlib import Path
from typing import List, Optional, Tuple
import numpy as np
import matplotlib.pyplot as plt
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline
from sklearn.svm import SVC
from sklearn.decomposition import PCA
from sklearn.model_selection import G... | /rna_cd-0.2.0-py3-none-any.whl/rna_cd/models.py | 0.932039 | 0.562447 | models.py | pypi |
import argparse # Argument parsing
import logging # Logging behaviour
import pandas # Handle large datasets
import pytest
import yaml # Handle Yaml IO
import os.path as op # Path and file system manipulation
import pandas # Deal with TSV files (design)
from itertools import chain # Chain iterators
from pathlib... | /rna_count_salmon-1.9-py3-none-any.whl/scripts/common_script_rna_count_salmon.py | 0.762513 | 0.487612 | common_script_rna_count_salmon.py | pypi |
import argparse # Parse command line
import logging # Traces and loggings
import os # OS related activities
import pandas as pd # Parse TSV files
import pytest # Unit testing
import shlex # Lexical analysis
import sys # System related methods
from pathlib import Path # Paths related methods
from snakemake.util... | /rna_count_salmon-1.9-py3-none-any.whl/scripts/prepare_design.py | 0.660829 | 0.381508 | prepare_design.py | pypi |
import argparse # Parse command line
import logging # Traces and loggings
import os # OS related activities
import pytest # Unit testing
import shlex # Lexical analysis
import sys # System related methods
import yaml # Parse Yaml files
from pathlib import Path # Paths related methods
from snakemake.utils impor... | /rna_count_salmon-1.9-py3-none-any.whl/scripts/prepare_config.py | 0.61451 | 0.17858 | prepare_config.py | pypi |
# RNA-FM
This repository contains codes and pre-trained models for **RNA foundation model (RNA-FM)**.
**RNA-FM outperforms all tested single-sequence RNA language models across a variety of structure prediction tasks as well as several function-related tasks.**
You can find more details about **RNA-FM** in our paper, [... | /rna-fm-0.1.2.tar.gz/rna-fm-0.1.2/README.md | 0.71423 | 0.974043 | README.md | pypi |
import os
from typing import Sequence, Tuple, List, Union
import pickle
import re
import shutil
import torch
from pathlib import Path
from .constants import proteinseq_toks, rnaseq_toks
RawMSA = Sequence[Tuple[str, str]]
class FastaBatchedDataset(object):
def __init__(self, sequence_labels, sequence_strs):
... | /rna-fm-0.1.2.tar.gz/rna-fm-0.1.2/fm/data.py | 0.720762 | 0.253405 | data.py | pypi |
import fm
import torch
from argparse import Namespace
import warnings
import urllib
from pathlib import Path
import os
def load_model_and_alphabet(model_name):
if model_name.endswith(".pt"): # treat as filepath
return load_model_and_alphabet_local(model_name)
else:
return load_model_and_alpha... | /rna-fm-0.1.2.tar.gz/rna-fm-0.1.2/fm/pretrained.py | 0.521227 | 0.282413 | pretrained.py | pypi |
import math
from typing import Optional
import torch
import torch.nn as nn
import torch.nn.functional as F
from .multihead_attention import MultiheadAttention # noqa
from .axial_attention import ColumnSelfAttention, RowSelfAttention
def gelu(x):
"""Implementation of the gelu activation function.
For infor... | /rna-fm-0.1.2.tar.gz/rna-fm-0.1.2/fm/modules.py | 0.935715 | 0.536556 | modules.py | pypi |
from torch import nn
import torch
from functools import wraps
class DownStreamModule(nn.Module):
"""
base contact predictor for msa
"""
def __init__(self, backbone_args, backbone_alphabet, depth_reduction="none",
need_token=False, need_attention=[], need_embedding=[12], need_extrafe... | /rna-fm-0.1.2.tar.gz/rna-fm-0.1.2/fm/downstream/downstream_module.py | 0.80784 | 0.294564 | downstream_module.py | pypi |
from typing import Union
from numpy import arange, argmax, delete, einsum, log2, ndarray, std, sum, unique
from pandas import DataFrame, Series
def _m_numpy(gene_expression: ndarray) -> ndarray:
"""Internal control gene-stability measure `M`.
Computes Eq. (4) in Ref. [1].
[1]: Vandesompele, Jo, et al. ... | /rna_genorm-0.1.0-py3-none-any.whl/genorm/algorithms.py | 0.957108 | 0.730386 | algorithms.py | pypi |
import yaml
import json
import jsonschema
from jsonschema import Draft4Validator, validators
from pathlib import Path
from dataclasses import dataclass
from rna_map import settings, logger
from rna_map.settings import get_py_path
log = logger.get_logger("PARAMETERS")
@dataclass(frozen=True, order=True)
class Input... | /rna_map-0.3.0-py3-none-any.whl/rna_map/parameters.py | 0.539711 | 0.198783 | parameters.py | pypi |
import yaml
import cloup
from cloup import option_group, option
from rna_map.logger import get_logger
log = get_logger('CLI_OPTS')
def main_options():
return option_group(
"Main arguments",
"These are the main arguments for the command line interface",
option(
"-fa",
... | /rna_map-0.3.0-py3-none-any.whl/rna_map/cli_opts.py | 0.510008 | 0.216136 | cli_opts.py | pypi |
import os
import shutil
import subprocess
from typing import Optional
from pathlib import Path
from dataclasses import dataclass
import pandas as pd
from rna_map.settings import get_py_path
from rna_map.logger import get_logger
from rna_map.exception import DREEMInputException, DREEMExternalProgramException
log = get... | /rna_map-0.3.0-py3-none-any.whl/rna_map/external_cmd.py | 0.639736 | 0.181771 | external_cmd.py | pypi |
def tpm(counts, lengths):
"""
Performs TPM normalization on a pandas DataFrame of count data
Args:
counts (pandas.DataFrame): DataFrame containing raw count data for each gene in each sample
lengths (pandas.Series): Series containing gene lengths
Returns:
pandas.DataFrame: DataFrame contai... | /rna_seq_normalization-0.3.0-py3-none-any.whl/rna_seq_normalization/Normalization.py | 0.958895 | 0.931275 | Normalization.py | pypi |
import pandas as pd
import numpy as np
import editdistance
import vienna
from seq_tools import sequence, extinction_coeff
def add(df: pd.DataFrame, p5_seq: str, p3_seq: str) -> pd.DataFrame:
"""
adds a 5' and 3' sequence to the sequences in the dataframe
:param df: dataframe
:param p5_seq: 5' sequenc... | /rna_seq_tools-0.7.1.tar.gz/rna_seq_tools-0.7.1/seq_tools/dataframe.py | 0.760562 | 0.563498 | dataframe.py | pypi |
from seq_tools import dot_bracket, sequence
def get_extinction_coeff(seq, ntype, double_stranded=False, structure=None):
"""
get the extinction coefficient for a sequence
:param seq: sequence
:param ntype: DNA or RNA
:param double_stranded: is double stranded?
:param structure: structure of th... | /rna_seq_tools-0.7.1.tar.gz/rna_seq_tools-0.7.1/seq_tools/extinction_coeff.py | 0.841435 | 0.523238 | extinction_coeff.py | pypi |
import re
import itertools
from dataclasses import dataclass
@dataclass(frozen=True, order=True)
class SequenceStructure:
"""
A class to hold the parameters for a structure
"""
sequence: str
structure: str
def __post_init__(self):
"""
check that the sequence and structure are... | /rna_seq_tools-0.7.1.tar.gz/rna_seq_tools-0.7.1/seq_tools/structure.py | 0.765593 | 0.666619 | structure.py | pypi |
def get_max_stretch(seq) -> float:
"""
computes max stretch of the same letter in string
"""
max_stretch = 0
current_stretch = 0
for i, nuc in enumerate(seq):
if i == 0:
current_stretch += 1
else:
if nuc == seq[i - 1]:
current_stretch += 1
... | /rna_seq_tools-0.7.1.tar.gz/rna_seq_tools-0.7.1/seq_tools/sequence.py | 0.769297 | 0.488039 | sequence.py | pypi |
import os
import click
import tabulate
import pandas as pd
from seq_tools import sequence, dataframe
from seq_tools.logger import setup_applevel_logger, get_logger
pd.set_option("display.max_colwidth", None)
def validate_dataframe(df) -> None:
"""
validates a dataframe to have a column named `sequence` and ... | /rna_seq_tools-0.7.1.tar.gz/rna_seq_tools-0.7.1/seq_tools/cli.py | 0.675015 | 0.472318 | cli.py | pypi |
"""Secondary structure analysis"""
import os
import tempfile
import shutil
import subprocess
from rna_tools.rna_tools_config import VARNA_JAR_NAME, VARNA_PATH
class ExceptionOpenPairsProblem(Exception):
pass
def draw_ss(title, seq, ss, img_out, resolution=4, verbose=False):
"""Draw Secondary Structure usi... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/SecondaryStructure.py | 0.546738 | 0.350588 | SecondaryStructure.py | pypi |
r"""rna_rosetta_run.py - prepare & run ROSETTA simulations
Based on C. Y. Cheng, F. C. Chou, and R. Das, Modeling complex RNA tertiary folds with Rosetta, 1st ed., vol. 553. Elsevier Inc., 2015.
http: // www.sciencedirect.com / science / article / pii / S0076687914000524
The script makes(1) a folder for you job, with... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/rna_rosetta/rna_rosetta_run.py | 0.547222 | 0.426979 | rna_rosetta_run.py | pypi |
from __future__ import print_function
import logging
from rna_tools.rna_tools_logging import logger
from rna_tools.tools.rna_calc_rmsd.lib.rmsd.calculate_rmsd import get_coordinates
from rna_tools.tools.extra_functions.select_fragment import select_pdb_fragment_pymol_style, select_pdb_fragment
from rna_tools.tools.simr... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/rna_filter/rna_get_dists.py | 0.674265 | 0.358943 | rna_get_dists.py | pypi |
# RNA_DCA (DeCoupling Analysis)
https://marks.hms.harvard.edu/ev_rna/
A set of scripts to perform DCA analysis, authors Marcin Magnus & Gokhan Gokturk (under supervision of MM).
> Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional in... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/rna_filter/README.md | 0.751101 | 0.832373 | README.md | pypi |
class Renumerator(object):
"""
Generic renumerator class. Provides methods for changing the ID numbering
in all ModernaStructure-based objects.
"""
def __init__(self, struct):
"""
:Arguments:
* struct - the structure to be renumbered (descendant of ModernaStructure)
"... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/Renumerator_new.py | 0.540439 | 0.337094 | Renumerator_new.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
import re,os
from Bio.PDB.Atom import Atom
from ... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/CheckPdb.py | 0.692746 | 0.322299 | CheckPdb.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
from Bio.PDB import Superimposer
from rna_tools.... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/ModernaSuperimposer.py | 0.497559 | 0.24809 | ModernaSuperimposer.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
from rna_tools.tools.mini_moderna3.moderna.Moderna... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/Helix.py | 0.82559 | 0.227523 | Helix.py | pypi |
import re
from Bio.PDB.Residue import Residue
from Bio.PDB.Atom import Atom
from numpy import array
from rna_tools.tools.mini_moderna3.moderna.sequence.ModernaAlphabet import alphabet
from rna_tools.tools.mini_moderna3.moderna.analyze.BaseRecognizer import BaseRecognizer, BaseRecognitionError
from rna_tools.tools.mini_... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/RNAResidue.py | 0.654674 | 0.223261 | RNAResidue.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
from rna_tools.tools.mini_moderna3.moderna.util.E... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/Renumerator.py | 0.479991 | 0.182772 | Renumerator.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
from rna_tools.tools.mini_moderna3.moderna.Moderna... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/fragment_library/StructureLibrary.py | 0.684264 | 0.238151 | StructureLibrary.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
import sys, re, os, os.path
from rna_tools.tools... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/fragment_library/LIRdb.py | 0.438785 | 0.209187 | LIRdb.py | pypi |
__author__ = "Kristian Rother, Magdalena Rother, Tomasz Puton"
__copyright__ = "Copyright 2008, The Moderna Project"
__license__ = "GPL"
__credits__ = ["Janusz Bujnicki"]
__maintainer__ = "Kristian Rother"
__email__ = "krother@rubor.de"
__status__ = "Production"
from math import sqrt
from numpy import array, dot, zer... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/builder/FCCDLoopCloser.py | 0.865409 | 0.391493 | FCCDLoopCloser.py | pypi |
__author__ = "Pawel Skiba, Magdalena Rother, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__version__ = "0.1.0"
__maintainer__ = "Pawel Skiba"
__email__ = "pw.skiba@gmail.com"
__status__ = "Prototype"
from rna_tools.tools.mini_moderna3.mo... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/isosteric/IsostericityMatrices.py | 0.50415 | 0.224247 | IsostericityMatrices.py | pypi |
__author__ = "Magdalena Musielak, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Musielak"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
COMMAND_EXAMPLES = {
'add_modification':... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/examples/usage_examples.py | 0.429908 | 0.243474 | usage_examples.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
"""
A procedure for calculating stacking of RNA nu... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/StackingCalculator.py | 0.767908 | 0.521349 | StackingCalculator.py | pypi |
__author__ = "Kristian Rother"
__copyright__ = "Copyright 2008, Kristian Rother"
__credits__ = ["Sabrina Hofmann"]
__license__ = "GPL"
__maintainer__ = "Kristian Rother"
__email__ = "krother@rubor.de"
__status__ = "Production"
from .MolParameters import *
import re
class Bond:
"""Something connecting two ato... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/MolGraphParser.py | 0.602529 | 0.219306 | MolGraphParser.py | pypi |
__author__ = "Kristian Rother"
__copyright__ = "Copyright 2008, Genesilico"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Kristian Rother"
__email__ = "krother@rubor.de"
__status__ = "beta"
class GeometryStandards:
"""Defines allowed and disallowed geometry values."""
bonds = {
... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/GeometryParameters.py | 0.518059 | 0.46217 | GeometryParameters.py | pypi |
__author__ = "Tomasz Osinski"
__copyright__ = "Genesilico 2008"
__credits__ = ["Kristian Rother", "Raphael Bauer", "Marcin Domagalski", \
"Magdalena Rother", "Janusz Bujnicki", "Marie Curie"]
__license__ = "GPL"
__status__ = "Production"
from Bio.PDB.Vector import calc_dihedral
from math import pi, sin, at... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/PuckerCalculator.py | 0.816516 | 0.232125 | PuckerCalculator.py | pypi |
from rna_tools.tools.mini_moderna3.moderna.analyze.GeometryParameters import BACKBONE_DIST_MATRIX, \
PHOSPHATE_DIST_MATRIX, O3_P_DIST_HI
from rna_tools.tools.mini_moderna3.moderna.Constants import BACKBONE_ATOMS, \
BACKBONE_RIBOSE_ATOMS_WITHOUT_O2
DIST_TOLERANCE = 1.05
# distance for intra-residue backbone ... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/ChainConnectivity.py | 0.759582 | 0.358325 | ChainConnectivity.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
# Suite angles from Richardson to use as fragments... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/RNASuites.py | 0.409457 | 0.162746 | RNASuites.py | pypi |
__author__ = "Kristian Rother, Raphael Bauer"
__credits__ = ["Marcin Domagalski","Magdalena Musielak", "Janusz Bujnicki", "Marie Curie"]
__license__ = "GPL"
__version__ = "1.0.1"
__maintainer__ = "Kristian Rother"
__email__ = "krother@rubor.de"
__status__ = "Production"
from PDB.PDBParser import PDBParser
from math ... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/suites/suite2.py | 0.796292 | 0.292867 | suite2.py | pypi |
__author__ = "Kristian Rother, Raphael Bauer"
__credits__ = ["Raphael Bauer","Markus Weber","Marcin Domagalski","Magdalena Musielak", "Janusz Bujnicki", "Marie Curie"]
__license__ = "GPL"
__version__ = "1.0.1"
__maintainer__ = "Kristian Rother"
__email__ = "krother@rubor.de"
__status__ = "Production"
from math impor... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/suites/suite_clusters.py | 0.753104 | 0.20199 | suite_clusters.py | pypi |
__author__ = "Kristian Rother, Raphael Bauer"
__credits__ = ["Marcin Domagalski","Magdalena Musielak", "Janusz Bujnicki", "Marie Curie"]
__license__ = "GPL"
__version__ = "1.0.1"
__maintainer__ = "Kristian Rother"
__email__ = "krother@rubor.de"
__status__ = "Production"
from rna_tools.tools.mini_moderna3.moderna.PDB... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/analyze/suites/suite.py | 0.698021 | 0.187114 | suite.py | pypi |
from rna_tools.tools.mini_moderna3.moderna.modifications.ResidueEditor import ResidueEditor
from rna_tools.tools.mini_moderna3.moderna.util.Errors import RemoveModificationError
from rna_tools.tools.mini_moderna3.moderna.util.LogFile import log
from rna_tools.tools.mini_moderna3.moderna.Constants import BASE_PATH, BACK... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/modifications/ModificationRemover.py | 0.470737 | 0.168994 | ModificationRemover.py | pypi |
from rna_tools.tools.mini_moderna3.moderna.modifications.ResidueEditor import ResidueEditor
from rna_tools.tools.mini_moderna3.moderna.modifications.BaseExchanger import BaseExchanger
from rna_tools.tools.mini_moderna3.moderna.modifications.ModificationRemover import ModificationRemover
from rna_tools.tools.mini_modern... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/modifications/ModificationAdder.py | 0.511717 | 0.198181 | ModificationAdder.py | pypi |
from rna_tools.tools.mini_moderna3.moderna.modifications.ResidueEditor import ResidueEditor
from rna_tools.tools.mini_moderna3.moderna.modifications.ModificationRemover import remove_modification
from rna_tools.tools.mini_moderna3.moderna.util.Errors import ExchangeBaseError
from rna_tools.tools.mini_moderna3. moderna.... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/modifications/BaseExchanger.py | 0.542621 | 0.179064 | BaseExchanger.py | pypi |
from rna_tools.tools.mini_moderna3.moderna.util.decorators import toplevel_function
from rna_tools.tools.mini_moderna3.moderna.util.validators import validate_alignment, validate_seq, \
validate_filename, validate_path, \
validate_alphabet, validate_alphabet_list
from rna_tools.tools.mini_moderna3.moderna.lpha... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/sequence/commands.py | 0.866118 | 0.596933 | commands.py | pypi |
__author__ = "Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Kristian Rother"
__email__ = "krother@genesilico.pl"
__status__ = "Production"
from rna_tools.tools.mini_moderna3.moderna.sequence.ModernaSequence import Sequenc... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/sequence/AlignmentMatcher.py | 0.782122 | 0.262357 | AlignmentMatcher.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
import re
from rna_tools.tools.mini_moderna3.moder... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/sequence/ModernaSequence.py | 0.832373 | 0.197773 | ModernaSequence.py | pypi |
__author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother"
__copyright__ = "Copyright 2008, The Moderna Project"
__credits__ = ["Janusz Bujnicki"]
__license__ = "GPL"
__maintainer__ = "Magdalena Rother"
__email__ = "mmusiel@genesilico.pl"
__status__ = "Production"
"""
The exception model of Moderna contains
one se... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/mini_moderna3/moderna/util/Errors.py | 0.61173 | 0.176352 | Errors.py | pypi |
import sys, re, html.entities, getopt, io, codecs, datetime
from functools import reduce
try:
from simplediff import diff, string_diff
except ImportError:
sys.stderr.write("info: simplediff module not found, only linediff is available\n")
sys.stderr.write("info: it can be downloaded at https://github.com/p... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/diffpdb/lib/diff2html.py | 0.42477 | 0.223314 | diff2html.py | pypi |
from pymol import cmd, stored
import re
try:
from collections import OrderedDict
_orderedDict = True
except ImportError:
_orderedDict = False
# PyMOL 1.7.4 introduces support for multi-letter chains, so we can afford to
# use a smaller alphabet. In earlier versions, use lower-case letters if needed
# (requ... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/PyMOL4RNA/external_flatten_object.py | 0.783368 | 0.253425 | external_flatten_object.py | pypi |
import logging
import argparse
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.PDB import PDBParser
from Bio.PDB import PDBIO
from Bio.PDB.Atom import PDBConstructionWarning
import warnings
warnings.simplefilter('ignore', PDBConstructionWarning)
# logger
logger = logging.getLogger()
handler = loggin... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/renum_pdb_to_aln/renum_pdb_to_aln.py | 0.62223 | 0.210401 | renum_pdb_to_aln.py | pypi |
from rna_tools.tools.pdb_formatix.SingleLineUtils import get_res_code, get_res_num, get_atom_code, \
set_atom_code, set_line_bfactor
import re
class PDBFile(object):
"""Class for holding data from a PDB file and modifying it.
"""
# find 'ATOM' lines in a PDB file
ATOM_LINE_PATTERN = re.compile('^... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/pdb_formatix/PDBFile.py | 0.617167 | 0.342957 | PDBFile.py | pypi |
import math
def draw_circle(x, y, z, r=8.0, cr=1.0, cg=0.4, cb=0.8, w=2.0):
"""
Create a CGO circle
PARAMS
x, y, z
X, Y and Z coordinates of the origin
r
Radius of the circle
cr, cg, cb
Color triplet, [r,g,b] where r,g,b are all [0.0,1.0... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/pymol_drawing/pymol_drawing.py | 0.52902 | 0.487307 | pymol_drawing.py | pypi |
r"""rna_plot_density.py - generate a density plot
Don't open Excel, Jupyter. Simple plot a density of one column and save it to a file.
Example::
# file
fn rmsd_all
0 19_Bujnicki_Human_4_rpr_n0-000001.pdb-000001_A... 14.73
1 19_Bujnicki_Human_4... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/plotting/rna_plot_boxplotlike.py | 0.681621 | 0.332907 | rna_plot_boxplotlike.py | pypi |
from __future__ import print_function
__docformat__ = 'reStructuredText'
import os
import Bio.PDB.PDBParser
import Bio.PDB.Superimposer
from Bio.PDB.PDBIO import Select
from Bio.PDB import PDBIO
from Bio.SVDSuperimposer import SVDSuperimposer
from numpy import sqrt, array, asarray
class RNAmodel:
"""RNAmodel
... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools/tools/rna_calc_evo_rmsd/RNAmodel.py | 0.500977 | 0.270565 | RNAmodel.py | pypi |
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