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Change dependencies order when installing to fix when running in different CUDA versions. #16

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Change dependencies order when installing to fix when running in different CUDA versions. #16

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f47a245
Create install.sh
mainguyenanhvu Apr 21, 2023
ae2cd52
Update install.sh
mainguyenanhvu Apr 21, 2023
871211c
Change import pybel to from openbabel import pybel
mainguyenanhvu Apr 22, 2023
80adfbb
Change import pybel to from openbabel import pybel
mainguyenanhvu Apr 22, 2023
b55c482
Remove adundant dependencies and fix order install
mainguyenanhvu Apr 22, 2023
25e6bbf
Update README.md
mainguyenanhvu Apr 22, 2023
2d4d6ac
Change heavyprevalence to heavydegree, hetero too
mainguyenanhvu Apr 22, 2023
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11 changes: 11 additions & 0 deletions README.md
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Expand Up @@ -44,12 +44,23 @@ sudo make install
cd ..
```

Or easily setup by using install.sh:
```
chmod +x install.sh
./install.sh
```

Usage example
---------------

```
python predict.py -p protein.pdb -mp model_path -o output_path
```

Ex:
```
python predict.py -p protein.pdb -mp models/ -o output
```

For more input options, check 'predict.py'. All other molecules (waters, ions, ligands) should be removed from the structure. If the input protein has not been protonated, add --protonate to the execution command.\
The provided models have been trained on a subset of scPDB (training_subset_of_scpdb.proteins)
31 changes: 31 additions & 0 deletions install.sh
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@@ -0,0 +1,31 @@
conda create -n deepsurf python=3.6.9
conda activate deepsurf
sudo apt update
sudo apt install -y p7zip
sudo apt install -y libopenbabel-dev
sudo apt install -y g++
sudo apt install -y swig
conda install pytorch==1.2.0 torchvision==0.4.0 cudatoolkit=10.0 -c pytorch
conda install -c conda-forge openbabel
pip install tensorflow-gpu==1.13.1
pip install scikit-learn==0.20.3

git clone https://github.com/stemylonas/DeepSurf
cd DeepSurf

cd lds
chmod a+x compile.sh
./compile.sh
cd ..

pip install gdown --ignore-installed certifi
gdown 1nIBoD3_5nuMqgRGx4G1OHZwLsiUjb7JG
p7zip -d models.7z

wget www.cgl.ucsf.edu/Overview/ftp/dms.zip
unzip dms.zip
rm dms.zip
cd dms
chmod 777 -R .
sudo make install
cd ..
2 changes: 1 addition & 1 deletion protein.py
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Expand Up @@ -7,7 +7,7 @@
"""

import os, numpy as np
import pybel
from openbabel import pybel
from utils import simplify_dms


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6 changes: 3 additions & 3 deletions tfbio_data.py
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Expand Up @@ -7,7 +7,7 @@

import numpy as np

import pybel
from openbabel import pybel
from math import ceil, sin, cos, sqrt, pi
from itertools import combinations
import collections
Expand Down Expand Up @@ -62,7 +62,7 @@ def __init__(self, atom_codes=None, atom_labels=None,
specified this argument is ignored.
named_properties: list of strings, optional
Names of atomic properties to retrieve from pybel.Atom object. If
not specified ['hyb', 'heavyvalence', 'heterovalence',
not specified ['hyb', 'heavydegree', 'heterodegree',
'partialcharge'] is used.
save_molecule_codes: bool, optional (default True)
If set to True, there will be an additional feature to save
Expand Down Expand Up @@ -151,7 +151,7 @@ def __init__(self, atom_codes=None, atom_labels=None,
self.NAMED_PROPS = named_properties
else:
# pybel.Atom properties to save
self.NAMED_PROPS = ['hyb', 'heavyvalence', 'heterovalence',
self.NAMED_PROPS = ['hyb', 'heavydegree', 'heterodegree',
'partialcharge']
self.FEATURE_NAMES += self.NAMED_PROPS

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