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Hi Lucidrains
First of all thanks for the contribution. You are doing an awesome job here.
I'm trying to implement the Seq2Seq model using DeepSpeed since I will have 32k seq_len as input. This is…
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in GDB-17 smiles is CN=C1C=CNN=N1
in B3LYP smiles is C[N]c1cc[nH]nn1
here is a simple script
mol = Chem.MolFromSmiles('C[N]c1cc[nH]nn1')
fp = AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=51…
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I've started to use AccurateMassSearch to identify small molecules following a PeakPickerHiRes -> FeatureFinderMetabo -> FeatureLinkerUnlabeledQT workflow (in KNIME). This seems like a promising appro…
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The current data preprocessing pipeline uses the following steps:
1. Converts each variant peptide string into its canonical SMILES format (in a linear fashion)
2. Embeds/optimizesthe 3D coordinates…
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Request by @jschrier to ensure that the smiles string representations in the chemicals dataframe are correctly (consistently) implemented.
*Why:* We're calculating large swaths of descriptors wron…
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Spectra are referenced incorrectly for index is incompatible with ms_run id_format.
id_format is defined as "scan number only nativeID format"
https://github.com/HUPO-PSI/mzTab/blob/master/exam…
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When I run sparse_molecular_dataset.py ,I get the error -- 'Explicit valence for atom # 7 C, 5, is greater than permitted ERROR: Could not sanitize molecule ending on line 5729584' and 'numpy.core._in…
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* My operating system: Windows 10
* My JDK: jdk-13.0.1
* My JRE: jre-1.8.0_231
I am attempting to build and run MZmine 3 (current git) using Eclipse for the first time. I followed the instructi…
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[Errno 2] No such file or directory: './datasets/fine-tune.smi'
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In the same way we have an [Activities Browser](https://www.ebi.ac.uk/chembl/beta/g/#browse/activities), a [Compounds Browser](https://www.ebi.ac.uk/chembl/beta/g/#browse/compounds), etc. This replace…