Leela S. Dodda leelasd
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leelasd
/ convert_molecules.py
Created
March 2, 2017 01:55
Convert Smiles code to 3D and save to SDF
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| import pandas as pd | |
| from rdkit import Chem | |
| from rdkit.Chem import AllChem | |
| df = pd.read_csv('SMILES.csv') | |
| mols = [Chem.MolFromSmiles(smi) for smi in df.SMILES] | |
| hmols = [Chem.AddHs(m) for m in mols] | |
| for mol in hmols: | |
| AllChem.EmbedMolecule(mol,AllChem.ETKDG()) | |
| print(AllChem.UFFOptimizeMolecule(mol,1000)) | |
| smiles = list(df.SMILES) |
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| # syntax=docker/dockerfile:1 | |
| FROM ubuntu | |
| RUN apt-get update | |
| RUN apt-get install tcsh | |
| RUN mkdir app | |
| COPY boss0520.tar.gz app/boss0520.tar.gz | |
| WORKDIR "/app" | |
| RUN tar xovf boss0520.tar.gz | |
| RUN echo setenv BOSSdir /app/boss > ~/.cshrc | |
| RUN apt-get install wget -y |
leelasd
/ anilin.pdb
Created
February 7, 2016 19:57
PDB file for the MD simulations in OpenMM using OPLS-AA forcefield.
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| REMARK Aniline | |
| REMARK Created by BOSS 4.9 Feb 12 Linux | |
| ATOM 1 C00 UNK 1 0.000 1.400 0.000 | |
| ATOM 2 C01 UNK 1 0.000 0.695 -1.220 | |
| ATOM 3 C02 UNK 1 -0.000 0.694 1.219 | |
| ATOM 4 C03 UNK 1 0.006 -0.713 -1.220 | |
| ATOM 5 C04 UNK 1 0.006 -0.715 1.218 | |
| ATOM 6 C05 UNK 1 0.010 -1.420 -0.002 | |
| ATOM 7 N06 UNK 1 -0.001 2.739 0.001 | |
| ATOM 8 H07 UNK 1 -0.008 1.225 -2.162 |
leelasd
/ cats2d_example.ipynb
Created
February 17, 2022 14:32
— forked from iwatobipen/cats2d_example.ipynb
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leelasd
/ enum_cpds.ipynb
Created
February 17, 2022 14:32
— forked from iwatobipen/enum_cpds.ipynb
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leelasd
/ RG_Decomp_With_map.ipynb
Created
February 17, 2022 14:31
— forked from iwatobipen/RG_Decomp_With_map.ipynb
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leelasd
/ cats2d_example_2.ipynb
Created
February 17, 2022 14:23
— forked from iwatobipen/cats2d_example_2.ipynb
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leelasd
/ parchai_charge_viz.ipynb
Created
February 17, 2022 14:16
— forked from iwatobipen/parchai_charge_viz.ipynb
QM based partial charge calculation and visualization
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leelasd
/ AttentiveFP with color bar.ipynb
Created
February 17, 2022 13:51
— forked from iwatobipen/AttentiveFP with color bar.ipynb
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leelasd
/ rgroup_deconposition_rdkit20200301.ipynb
Created
February 17, 2022 13:48
— forked from iwatobipen/rgroup_deconposition_rdkit20200301.ipynb
rgroup decomposition with pandas tool kit
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