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Minor changes to README #2

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82e948f
Case sensitive when cd
hwpang Jun 15, 2024
3a9dc89
The environment file extension in the repo is .yaml, not .yml
hwpang Jun 15, 2024
cf7f6b9
Update README.md
hwpang Jun 15, 2024
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12 changes: 6 additions & 6 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -30,12 +30,12 @@ We recommend using [conda](https://docs.conda.io/en/latest/) to install QupKake.
Clone the repository:
```bash
git clone https://github.com/Shualdon/QupKake.git
cd qupkake
cd QupKake
```

Create a conda environment from the environment.yml file:
Create a conda environment from the environment.yaml file:
```bash
conda env create -f environment.yml
conda env create -f environment.yaml
conda activate qupkake
```
This will create a conda environment with all the dependencies installed.
Expand All @@ -56,7 +56,7 @@ conda activate qupkake
Clone the repository and install using pip:
```bash
git clone https://github.com/Shualdon/QupKake.git
cd qupkake
cd QupKake
pip install .
```
This will install the package and all the rest of the dependencies.
Expand Down Expand Up @@ -108,9 +108,9 @@ $ qupkake file <filename>

Specific flags for this input type are:
```bash
-s, --smiles_col: column name for SMILES strings. Default: smiles
-s, --smiles-col: column name for SMILES strings. Default: smiles

-n, --name_col: column name for molecule names. Default: name
-n, --name-col: column name for molecule names. Default: name

-o, --output: output file name (SDF with pKa predictions). Default: qupkake_output.sdf
```
Expand Down