I have 100 polymers and I want to compare their solubility by their fingerprint.
By using rdkit I reach a list of bits for each polymer like as [39, 80, 152, 233, 234, 265, 310, 314, 321, 356, 360, 406, 547, 650, 662, 726, 730, 801, 819, 849, 935]', but I faced with this error: " it could not convert string to float: "
my first question is how can I reach to just one bit for each polymer?
and how can I define each bit as a single feature in rdkit?
Based on your problem, I believe you use Morgan Fingerprint with radius=2 and fpSize=1024. However, count fingerprint results in a list of hashed value.
If you want to deal with comparison, I suggested you should use rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect in here #1.
If you want to use count fingerprint, see here #2 and search this query: The types of atom pairs and torsions are normal (default), hashed and bit vector (bv). The types of the Morgan fingerprint are bit vector (bv, default) and count vector (count).
If you want to get the result as np.array, you can run bv = GetMorganFingerprintAsBitVect(mol, radius=your_radius, nBits=1024, *args, **kwargs).ToBitString(), then run np.frombuffer(bv.encode(), dtype=np.uint8) - 48
However, I cannot provide explicit description and solution without the code so please provide it for further support. Thank you.
#1: https://www.rdkit.org/docs/source/rdkit.Chem.rdMolDescriptors.html?highlight=getmorganfingerprintasbitvect#rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect
#2: https://www.rdkit.org/docs/GettingStartedInPython.html
Related
I am trying to train a yolov5 model, but I'm getting an exception error when I try to execute the training module. The error occurs after the model is loaded and when it tries to read the training images. Below is my code and an excerpt of the error. Any help would be appreciated.
!python train.py --img 640 --batch 16 --epochs 150 --data pollen_data.yaml --weights yolov5x.pt
Model summary: 567 layers, 86217814 parameters, 86217814 gradients, 204.2 GFLOPs
Transferred 739/745 items from yolov5x.pt
Scaled weight_decay = 0.0005
optimizer: SGD with parameter groups 123 weight (no decay), 126 weight, 126 bias
albumentations: version 1.0.3 required by YOLOv5, but version 0.1.12 is currently installed
Traceback (most recent call last):
File "/content/yolov5/utils/datasets.py", line 405, in __init__
t = t.read().strip().splitlines()
File "/usr/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "train.py", line 643, in <module>
main(opt)
File "train.py", line 539, in main
train(opt.hyp, opt, device, callbacks)
File "train.py", line 227, in train
prefix=colorstr('train: '), shuffle=True)
File "/content/yolov5/utils/datasets.py", line 110, in create_dataloader
prefix=prefix)
File "/content/yolov5/utils/datasets.py", line 415, in __init__
raise Exception(f'{prefix}Error loading data from {path}: {e}\nSee {HELP_URL}')
Exception: train: Error loading data from /content/datasets/images/training/im0.jpg: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte
The training images I have (im0.jpg and im1.jpg) are two large files. The first has dimensions of 9058 x 11185, and the second file is 13385 x 12832. I realize they are not square but I'm assuming that the train.py module will make them square, so it's okay. Is that right?
Or could the non-square dimensions be causing the choke?
Also, what is the meaning of the exception "error loading data from /content/datasets/images/training/im0.jpg: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte"?
Thank you.
I've been using yolov5 for the past 1 month.I must say your error is wierd.
And also, you cant train your model with image size as 12000. By default it should be 640.In your case it might change based on your dataset but i'm quite sure that it wont be 12000.
There is a mistake in your data directory also.
--data /content/datasets/annotations/dataset.yaml.txt
The data file wont have '.txt' extension. It should be a '.yaml' file. SO change that to
--data /content/datasets/annotations/dataset.yaml
It should start training after these changes. If not, close this question and please provide additional information and ask another question.
the error
'utf-8' codec can't decode byte 0xff in position 0: invalid start byte
is raised when you use a image of format which is not mentioned by default.
IMG_FORMATS = 'bmp', 'dng', 'jpeg', 'jpg', 'mpo', 'png', 'tif', 'tiff', 'webp' # include image suffixes
But you have mentioned that it is an jpg. I'm confused now. And also if it helps, pls try this solution provided in this issue. link
I just started using GNU Radio, I must say I am quite a noob but I have some background on RF related stuff.
Here's the thing:
I recorded a file that I now want to repeat through my HackRF and GNU Radio.
This is the exact settings for the filter:
The settings you see are casual (since I cannot get it working I started testing with random values).
This is the error I get:
Executing: /usr/bin/python3 -u /home/scare/LAB/RadioFrequencies/GNU Radio/reply_433.py
gr-osmosdr 0.2.0.0 (0.2.0) gnuradio 3.8.2.0
built-in sink types: uhd hackrf bladerf soapy redpitaya file
[INFO] [UHD] linux; GNU C++ version 11.1.0; Boost_107600; UHD_4.0.0.0-0-unknown
Using HackRF One with firmware 2017.02.1
Traceback (most recent call last):
File "/home/scare/LAB/RadioFrequencies/GNU Radio/reply_433.py", line 211, in <module>
main()
File "/home/scare/LAB/RadioFrequencies/GNU Radio/reply_433.py", line 187, in main
tb = top_block_cls()
File "/home/scare/LAB/RadioFrequencies/GNU Radio/reply_433.py", line 137, in __init__
firdes.high_pass(
File "/usr/lib/python3.9/site-packages/gnuradio/filter/filter_swig.py", line 124, in high_pass
return _filter_swig.firdes_high_pass(*args, **kwargs)
RuntimeError: firdes check failed: 0 < fa <= sampling_freq / 2
Done (return code 1)
Where obviously the interesting part is the RuntimeError: firdes check failed: 0 < fa <= sampling_freq / 2
Unfortunately, I don't get what that 'fa' stands for.
Any idea?
Cheers
I just got done solving this same error. The error is caused by a filter's Cut-off and transition parameters being set incorrectly (in my case far too large). GNU radio handles the variable 'samp_rate' differently for each block and filters seem to interpret it was a point to center the filter on (that's my take on it so don't quote me).
I also looked in the source code and can't find anything helpful on 'fa'
So try adjusting your cutoff to be something below samp_rate and make your transition width something to the tune of 250e3. I used GUI sliders to set the filter how I liked and I will make these permanent in the final version.
Screen Cap of Settings Here
Slider Settings For Both Sliders
Mike Ossmann's "SDR with HackRF One, Lesson 10 - Filters helped" me out here. Also just a great SDR lecture series for GNU radio if you haven't come across them yet. (just make sure to use the QT GUI).
I hope this helped. I am pretty new to GNU so sorry if the explanation is a little half-baked.
fa is the cutoff_frequency in the function that is throwing the error message. The cutoff frequency has to be greater than 0 and no more than the Nyquist limit. There are some functions called sanity_check_xxx (xxx being whether one cutoff or 2, i.e. bandpass, and optionally c for complex) around line 750 in gr_filter/lib/firdes.cc in the GNU Radio repository on GitHub.
In the question the samp_rate would need to be at least 800MHz to support a high pass cutoff of 400Mhz. As far as I can tell sample rate is used the same way in these filter functions as anywhere else in GNU Radio.
I ran into the same error message because I used 'firdes.band_passinstead offirdes.complex_band_pass` and the low cutoff was negative, which it should be for the complex band pass filter.
I'm trying to convert a csv file of incident codes with their descriptions to a json file. with the following code.
require 'csv'
require 'json'
csv = File.open('incidentCodes.json').read
CSV.parse(csv).to_json
File.open("incidentCodes.json", "w") do |f|
f.write(csv)
end
Every time I run the code though it says "CSV::MalformedCSVError(Illegal quoting in line 1) "
This is the first few lines of my CSV
111, "Building fire. Excludes confined fires."
112, "Fire in structure, other than in a building. Included are fires on or in piers, quays, or pilings: tunnels or under-
ground connecting structures; bridges, trestles, or overhead elevated structures; transformers, power or utility
vaults or equipment; fences; and tents."
113, "Cooking fire involving the contents of a cooking vessel without fire extension beyond the vessel"
114, "Chimney or flue fire originating in and confined to a chimney or flue. Excludes fires that extend beyond the
chimney."
I tried bypassing using CSV.parse with other methods I saw but it was then only writing "[['incidentCodes.csv']]" to the json file.
Im very new to ruby so any help is a big help.
You have an extra space after the comma.
> CSV.parse '111, "Building fire. Excludes confined fires."'
=> CSV::MalformedCSVError: Illegal quoting in line 1.
> CSV.parse '111,"Building fire. Excludes confined fires."'
=> [["111", "Building fire. Excludes confined fires."]]
I've been working on writing some mkdocs documentation which includes mermaid diagrams that I'd like to keep in the markdown files instead of turning into images and embedding them
I came across this great solution here: https://github.com/squidfunk/mkdocs-material/issues/693#issuecomment-411885426
Which uses the super-fences feature of the pymdown-extensions plugin to create a custom code block which renders the mermaid diagrams inside the code block.
It works in mkdocs running locally, but when I submit the configuration file to readthedocs it fails the yaml validation
Your mkdocs.yml could not be loaded, possibly due to a syntax error (line 18, column 19)
Line 18 in the mkdocs.yml config file is the section which calls the superfences python class
format: !!python/name:pymdownx.superfences.fence_div_format
Looking in the yaml specification https://yaml.org/spec/1.2/spec.html Shows that !! is for an explicit tag and it seems to have been part of the spec for quite some time ( back to version 1). I've tried making the value a string but this then causes issue with python reading it as a string
Does anyone know if readthedocs supports this or have you been able to get this working some other way?
ReadTheDocs is parsing the mkdocs.yaml file using pyyaml and it seems that it does not recognize !!.
For example:
>>> import yaml
>>> document = """
a: 1
b:
c: 3
d: !!4
"""
>>> print(yaml.dump(yaml.load(document)))
<stdin>:1: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.8/site-packages/yaml/__init__.py", line 114, in load
return loader.get_single_data()
File "/usr/lib/python3.8/site-packages/yaml/constructor.py", line 51, in get_single_data
return self.construct_document(node)
File "/usr/lib/python3.8/site-packages/yaml/constructor.py", line 60, in construct_document
for dummy in generator:
File "/usr/lib/python3.8/site-packages/yaml/constructor.py", line 413, in construct_yaml_map
value = self.construct_mapping(node)
File "/usr/lib/python3.8/site-packages/yaml/constructor.py", line 218, in construct_mapping
return super().construct_mapping(node, deep=deep)
File "/usr/lib/python3.8/site-packages/yaml/constructor.py", line 143, in construct_mapping
value = self.construct_object(value_node, deep=deep)
File "/usr/lib/python3.8/site-packages/yaml/constructor.py", line 100, in construct_object
data = constructor(self, node)
File "/usr/lib/python3.8/site-packages/yaml/constructor.py", line 427, in construct_undefined
raise ConstructorError(None, None,
yaml.constructor.ConstructorError: could not determine a constructor for the tag 'tag:yaml.org,2002:4'
in "<unicode string>", line 5, column 8:
d: !!4
^
>>>
See: https://github.com/readthedocs/readthedocs.org/issues/6889
This problem began as the commonly-seen “incompatible character encodings: ASCII-8BIT and UTF-8” problem, but that is not what I'm asking. Rather, I discovered that this problem was happening because certain fields of my database are being tagged as ASCII-8BIT when they're retrieved, while most are correctly shown as UTF-8.
For example, in a table with columns country and nationality, where both columns in row 16 have identical values (copied-and-pasted), I get
irb(main):003:0> c = Country.find(16)
irb(main):004:0> puts "#{c.name}, #{c.name.encoding}, #{c.name.bytes.to_a}"
�land Islands, UTF-8, [195, 133, 108, 97, 110, 100, 32, 73, 115, 108, 97, 110, 100, 115]
irb(main):005:0> puts "#{c.nationality}, #{c.nationality.encoding}, #{c.nationality.bytes.to_a}"
�land Islands, ASCII-8BIT, [195, 133, 108, 97, 110, 100, 32, 73, 115, 108, 97, 110, 100, 115]
Likewise, a simple puts name gives �land Islands while for nationality it gives "\xC3\x85land Islands" -- same bytes, different presentation.
The encoding for a given column appears to be constant regardless of whether the string has non-ascii characters, so it is not simply a problem with the string. That is, all the values in nationality are interpreted as ascii and all those in name as UTF-8.
The problem is not limited to a single table, and I have not found any pattern to which columns are mis-recognized.
Here are the settings and environment:
Rails 3.0.0 on Windows 7 64-bit
Database adapter: mysql2 and mysql both show same behavior
Database.yml includes encoding: utf8
application.rb includes config.encoding = "utf-8"
MySQL database, table, and both columns are defined as utf8
Both columns in MySQL are varchar, 255, allow null
I can reproduce the problem with a fresh installation of Rails and nothing except the Country model defined, to access the database. I have not yet tried with a fresh, one-line database.
Anyone know what's going on here?
Same problem here! mysql2 gem, Rails 3.0.3 and "incompatible character encodings" errors
I found the solution, use ruby-mysql gem instead mysql or mysql2 gems.
I think I'm living a similar problem.
When I retrivied datas from MySQL DB rails convert a string to float:
Columns "Complemento" and "estado" are string in DB although action "show" says
Complemento: 0.0 -> at DB is "apto 191"
Escola was successfully created.
Nome: Silva Braga
Endereco: Rua Dr Arnaldo
Numero: 99
Complemento: 0.0 -> DB is "apto 191"
Cidade: São Paulo
Estado: 0.0 -> DB is "MG"
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