Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update installation guide in 2023 #172

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Update installation guide in 2023 #172

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0c9f9a6
Update installation steps to work in 2023
sniperyyc Oct 21, 2023
ce20f24
remove extra space; fix #168
sniperyyc Oct 21, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions DeepPurpose/dataset.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -259,7 +259,7 @@ def process_BindingDB(path = None, df = None, y = 'Kd', binary = False, \

df_want = df_want[['BindingDB Reactant_set_id', 'Ligand InChI', 'Ligand SMILES',\
'PubChem CID', 'UniProt (SwissProt) Primary ID of Target Chain',\
'BindingDB Target Chain Sequence'] + idx_str]
'BindingDB Target Chain Sequence'] + idx_str]

for y in idx_str:
df_want[y] = df_want[y].str.replace('>', '')
Expand All @@ -274,7 +274,7 @@ def process_BindingDB(path = None, df = None, y = 'Kd', binary = False, \
'Ligand InChI':'InChI',
'PubChem CID':'PubChem_ID',
'UniProt (SwissProt) Primary ID of Target Chain':'UniProt_ID',
'BindingDB Target Chain Sequence': 'Target Sequence'},
'BindingDB Target Chain Sequence': 'Target Sequence'},
inplace=True)

# have at least uniprot or pubchem ID
Expand Down
7 changes: 3 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,9 +77,8 @@ We recommend to install it locally since Binder needs to be refreshed every time
```bash
conda create -n DeepPurpose python=3.6
conda activate DeepPurpose
conda install -c conda-forge notebook
pip install git+https://github.com/bp-kelley/descriptastorus
pip install DeepPurpose
pip install git+https://github.com/bp-kelley/[email protected]
pip install git+https://github.com/sniperyyc/DeepPurpose
```

### Build from Source
Expand All @@ -88,7 +87,7 @@ First time:
```bash
git clone https://github.com/kexinhuang12345/DeepPurpose.git ## Download code repository
cd DeepPurpose ## Change directory to DeepPurpose
conda env create -f environment.yml ## Build virtual environment with all packages installed using conda
pip install . ## Install DeepPurpose
conda activate DeepPurpose ## Activate conda environment (use "source activate DeepPurpose" for anaconda 4.4 or earlier)
jupyter notebook ## open the jupyter notebook with the conda env

Expand Down
1 change: 1 addition & 0 deletions requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
rdkit-pypi
notebook
numpy
pandas
tqdm
Expand Down