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bin folder updated, and conda environment files added
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Juanma committed Dec 1, 2023
1 parent 192bd98 commit c1818cd
Showing 17 changed files with 810 additions and 43 deletions.
2 changes: 1 addition & 1 deletion bin/benchmarking/generate_smiles_from_ed.py
Original file line number Diff line number Diff line change
@@ -10,7 +10,7 @@
# where that 5.0 after std_dev is the standard dev of the random latent vector and
# that 1000 after Nsmiles is the number of smiles to generate
#
# Author: Juanma juanma.parrilla@gcu.ac.uk
# Author: Juanma juanma@chem.gla.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/benchmarking/generate_smiles_from_edesp.py
Original file line number Diff line number Diff line change
@@ -10,7 +10,7 @@
# where that 5.0 after std_dev is the standard dev of the random latent vector and
# that 1000 after Nsmiles is the number of smiles to generate
#
# Author: Juanma juanma.parrilla@gcu.ac.uk
# Author: Juanma juanma@chem.gla.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/optimisers/cage_hg.py
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
# Because the cage is big, this code will alternate cycles of maximising size and
# minimising overlapping. Hopefully this way we get a big molecule.
#
# Author: Juanma juanma.parrilla@gcu.ac.uk
# Author: Juanma juanma@chem.gla.ac.uk
#
##########################################################################################

10 changes: 5 additions & 5 deletions bin/optimisers/cage_hg_esp.py
Original file line number Diff line number Diff line change
@@ -7,7 +7,7 @@
# This code is an extension of the one called "cage_hg.py" but also calculating for
# electron density
#
# Author: Juanma juanma.parrilla@gcu.ac.uk
# Author: Juanma juanma@chem.gla.ac.uk
#
##########################################################################################

@@ -83,26 +83,26 @@

for j in tqdm.tqdm(range(int(10000/factor))):
# try to minimise overlapping ESP
f, grads, output, esps = grad_esp_overlapping(noise_t, vae, ed_to_esp, host_esp)
f, grads, eds, esps = grad_esp_overlapping(noise_t, vae, ed_to_esp, host_esp)
print(np.mean(f.numpy()))
noise_t -= lr * grads[0].numpy() * (1-ed_factor)
# noise_t = np.clip(noise_t, a_min=-5.0, a_max=5.0)

if j % 1000 == 0:
with open(RUN_FOLDER+'cage_esp_optimizedESPED'+slr+'.p', 'wb') as file:
pickle.dump(output, file)
pickle.dump(eds, file)
with open(RUN_FOLDER+'cage_esp_optimizedESP'+slr+'.p', 'wb') as file:
pickle.dump(esps, file)

# try to minimise overlapping ED
f, grads, output = grad_ed_overlapping(noise_t, vae, host_ed)
f, grads, eds = grad_ed_overlapping(noise_t, vae, host_ed)
print(np.mean(f.numpy()))
noise_t -= lr * grads[0].numpy() * ed_factor
# noise_t = np.clip(noise_t, a_min=-5.0, a_max=5.0)

if j % 1000 == 0:
with open(RUN_FOLDER+'cage_esp_optimizedEDED'+slr+'.p', 'wb') as file:
pickle.dump(output, file)
pickle.dump(eds, file)

with open(RUN_FOLDER+'cage_esp_optimized_final.p', 'wb') as file:
pickle.dump(output, file)
2 changes: 1 addition & 1 deletion bin/optimisers/cage_hg_esp_lee.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# Basically, instead of doing two steps each iteration, one for ED and one for ESP,
# we will make a function that combines them into a single step.
#
# Author: Juanma juanma.parrilla@gcu.ac.uk
# Author: Juanma juanma@chem.gla.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/optimisers/cage_hg_split_esp.py
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@
# the guest with both of them, and then merge them together using a factor. This way
# you can give a bigger focus to positive or negative charges.
#
# Author: Juanma juanma.parrilla@gcu.ac.uk
# Author: Juanma juanma@chem.gla.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/optimisers/host_guest_overlapping.py
Original file line number Diff line number Diff line change
@@ -7,7 +7,7 @@
# This code is used with the CB6 host. With the cage host, search the files with cage
# as aprt of the name.
#
# Author: juanma.parrilla@gcu.ac.uk
# Author: juanma@chem.gla.ac.uk
#
##########################################################################################

8 changes: 4 additions & 4 deletions bin/optimisers/maximise_hg_esp.py
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@
# the molecules with different signs nearby.
# In the comments and code, ED means electron density, ESP means electrostatic potential
#
# Author: juanma.parrilla@gcu.ac.uk
# Author: juanma@chem.gla.ac.uk
#
##########################################################################################

@@ -72,19 +72,19 @@

for j in tqdm.tqdm(range(int(5000/factor))):
# try to minimise overlapping ESP
f, grads, output, esps = grad_esp_overlapping(noise_t, vae, ed_to_esp, host_esp)
f, grads, eds, esps = grad_esp_overlapping(noise_t, vae, ed_to_esp, host_esp)
print(np.mean(f.numpy()))
noise_t -= lr * grads[0].numpy() * (1-ed_factor)
noise_t = np.clip(noise_t, a_min=-5.0, a_max=5.0)

if j % 1000 == 0:
with open(RUN_FOLDER+'cb6_esp_optimisedESPED'+slr+'.p', 'wb') as file:
pickle.dump(output, file)
pickle.dump(eds, file)
with open(RUN_FOLDER+'cb6_esp_optimisedESPESP'+slr+'.p', 'wb') as file:
pickle.dump(esps, file)

# try to minimise overlapping ED
f, grads, output = grad_ed_overlapping(noise_t, vae, host_ed)
f, grads, eds = grad_ed_overlapping(noise_t, vae, host_ed)
print(np.mean(f.numpy()))
noise_t -= lr * grads[0].numpy() * ed_factor
noise_t = np.clip(noise_t, a_min=-5.0, a_max=5.0)
2 changes: 1 addition & 1 deletion bin/optimisers/maximise_hg_polar.py
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
# "host_guest_overlapping.py" and "maximise_polar.py". This script is like those two
# together.
#
# Author: juanma.parrilla@gcu.ac.uk
# Author: juanma@chem.gla.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/optimisers/maximise_polar.py
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
# hosts and guests via gradient descent. Main difference is that he was using the GAN to
# generate the guests, while I will use the trained VAE.
#
# Author: juanma.parrilla@gcu.ac.uk
# Author: juanma@chem.gla.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/optimisers/maximise_size.py
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
# hosts and guests via gradient descent. Main difference is that he was using the GAN to
# generate the guests, while I will use the trained VAE.
#
# Author: juanma.parrilla@gcu.ac.uk
# Author: juanma@chem.gla.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/train/train_ed2esp.py
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
# This script is a sort of main file for ED2ESP (FCN) model. This script will aim to
# show to train it, and also to save and load the model.
#
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion bin/train/train_vae.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# variants. This script will aim to show to train it, and also to save and load the model.
# This file is modified to train in Dragonsoop
#
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
#
##########################################################################################

23 changes: 0 additions & 23 deletions environment.yml

This file was deleted.

304 changes: 304 additions & 0 deletions environmentTF10.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,304 @@
name: edtf10
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- aiohttp=3.8.5=py39hd1e30aa_0
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- alsa-lib=1.2.8=h166bdaf_0
- aom=3.5.0=h27087fc_0
- apptools=5.1.0=pyh44b312d_0
- argh=0.29.3=pyhd8ed1ab_0
- asttokens=2.2.1=pyhd8ed1ab_0
- async-timeout=4.0.3=pyhd8ed1ab_0
- attr=2.5.1=h166bdaf_1
- attrs=23.1.0=pyh71513ae_1
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=pyhd8ed1ab_3
- backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0
- blosc=1.21.5=h0f2a231_0
- boost=1.78.0=py39h7c9e3ff_4
- boost-cpp=1.78.0=h6582d0a_3
- brotli=1.1.0=hd590300_0
- brotli-bin=1.1.0=hd590300_0
- brotli-python=1.1.0=py39h3d6467e_0
- bzip2=1.0.8=h7f98852_4
- c-ares=1.19.1=hd590300_0
- ca-certificates=2023.7.22=hbcca054_0
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- configobj=5.0.8=pyhd8ed1ab_0
- contourpy=1.1.0=py39h7633fee_0
- cudatoolkit=11.2.2=hc23eb0c_12
- cudnn=8.1.0.77=h90431f1_0
- cycler=0.11.0=pyhd8ed1ab_0
- dav1d=1.2.1=hd590300_0
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- double-conversion=3.3.0=h59595ed_0
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- exceptiongroup=1.1.3=pyhd8ed1ab_0
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- expat=2.5.0=hcb278e6_1
- ffmpeg=6.0.0=gpl_h14e97fc_104
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- fontconfig=2.14.2=h14ed4e7_0
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- freetype=2.12.1=hca18f0e_1
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- glew=2.1.0=h9c3ff4c_2
- glib=2.76.4=hfc55251_0
- glib-tools=2.76.4=hfc55251_0
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- pip:
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- google-auth-oauthlib==0.4.6
- google-pasta==0.2.0
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- h5py==3.9.0
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- keras-preprocessing==1.1.2
- libclang==16.0.6
- markdown==3.4.4
- markupsafe==2.1.3
- oauthlib==3.2.2
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- pyasn1==0.5.0
- pyasn1-modules==0.3.0
- requests-oauthlib==1.3.1
- rsa==4.9
- tensorboard==2.10.1
- tensorboard-data-server==0.6.1
- tensorboard-plugin-wit==1.8.1
- tensorflow==2.10.1
- tensorflow-estimator==2.10.0
- tensorflow-io-gcs-filesystem==0.33.0
- termcolor==2.3.0
- urllib3==1.26.16
- werkzeug==2.3.7
- wrapt==1.15.0
prefix: /home/juanma/miniconda3/envs/edtf10
303 changes: 303 additions & 0 deletions environmentTF13.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,303 @@
name: ed_tf13
channels:
- conda-forge
- defaults
dependencies:
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- _openmp_mutex=4.5=2_gnu
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- pip:
- absl-py==1.4.0
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- gast==0.4.0
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- google-auth-oauthlib==1.0.0
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- grpcio==1.57.0
- h5py==3.9.0
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- libclang==16.0.6
- markdown==3.4.4
- markupsafe==2.1.3
- numpy==1.24.3
- nvidia-cublas-cu11==11.11.3.6
- nvidia-cudnn-cu11==8.6.0.163
- oauthlib==3.2.2
- opt-einsum==3.3.0
- protobuf==4.24.2
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- pyasn1-modules==0.3.0
- requests-oauthlib==1.3.1
- rsa==4.9
- tensorboard==2.13.0
- tensorboard-data-server==0.7.1
- tensorflow==2.13.0
- tensorflow-estimator==2.13.0
- tensorflow-io-gcs-filesystem==0.33.0
- termcolor==2.3.0
- typing-extensions==4.5.0
- urllib3==1.26.16
- werkzeug==2.3.7
- wrapt==1.15.0
prefix: /home/juanma/.conda/envs/ed_tf13
183 changes: 183 additions & 0 deletions environmentTF7.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,183 @@
name: electrondensity
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
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- boost=1.74.0=py39h5472131_4
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- ncurses=6.2=h58526e2_4
- nspr=4.32=h9c3ff4c_1
- nss=3.71=hb5efdd6_0
- olefile=0.46=pyh9f0ad1d_1
- openjpeg=2.4.0=hb52868f_1
- openssl=1.1.1l=h7f98852_0
- pandas=1.3.4=py39hde0f152_1
- parso=0.8.2=pyhd8ed1ab_0
- pcre=8.45=h9c3ff4c_0
- pexpect=4.8.0=pyh9f0ad1d_2
- pickleshare=0.7.5=py_1003
- pillow=8.3.2=py39ha612740_0
- pip=21.3.1=pyhd8ed1ab_0
- pixman=0.40.0=h36c2ea0_0
- prompt-toolkit=3.0.22=pyha770c72_0
- pthread-stubs=0.4=h36c2ea0_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pycairo=1.20.1=py39hedcb9fc_1
- pycparser=2.21=pyhd8ed1ab_0
- pygments=2.10.0=pyhd8ed1ab_0
- pyopenssl=21.0.0=pyhd8ed1ab_0
- pyparsing=3.0.5=pyhd8ed1ab_0
- pyqt=5.12.3=py39hf3d152e_7
- pyqt-impl=5.12.3=py39h0fcd23e_7
- pyqt5-sip=4.19.18=py39he80948d_7
- pyqtchart=5.12=py39h0fcd23e_7
- pyqtwebengine=5.12.1=py39h0fcd23e_7
- pysocks=1.7.1=py39hf3d152e_4
- python=3.9.7=hb7a2778_3_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python_abi=3.9=2_cp39
- pytz=2021.3=pyhd8ed1ab_0
- qt=5.12.9=hda022c4_4
- rdkit=2021.09.2=py39hccf6a74_0
- readline=8.1=h46c0cb4_0
- reportlab=3.5.68=py39he59360d_0
- requests=2.26.0=pyhd8ed1ab_0
- scipy=1.7.2=py39hee8e79c_0
- selfies=2.1.1=pyhd8ed1ab_0
- setuptools=58.5.3=py39hf3d152e_0
- sqlalchemy=1.4.26=py39h3811e60_1
- sqlite=3.36.0=h9cd32fc_2
- tk=8.6.11=h27826a3_1
- tornado=6.1=py39h3811e60_2
- tqdm=4.62.3=pyhd8ed1ab_0
- traitlets=5.1.1=pyhd8ed1ab_0
- tzdata=2021e=he74cb21_0
- urllib3=1.26.7=pyhd8ed1ab_0
- wcwidth=0.2.5=pyh9f0ad1d_2
- wheel=0.37.0=pyhd8ed1ab_1
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.2=h7f98852_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xtb=6.4.1=hf06ca72_1
- xz=5.2.5=h516909a_1
- zlib=1.2.11=h36c2ea0_1013
- zstd=1.5.0=ha95c52a_0
- pip:
- absl-py==0.15.0
- astunparse==1.6.3
- cachetools==4.2.4
- flatbuffers==1.12
- gast==0.4.0
- google-auth==2.3.3
- google-auth-oauthlib==0.4.6
- google-pasta==0.2.0
- grpcio==1.34.1
- h5py==3.1.0
- keras==2.7.0
- keras-nightly==2.5.0.dev2021032900
- keras-preprocessing==1.1.2
- libclang==12.0.0
- markdown==3.3.4
- numpy==1.19.5
- oauthlib==3.1.1
- opt-einsum==3.3.0
- protobuf==3.19.1
- pyasn1==0.4.8
- pyasn1-modules==0.2.8
- requests-oauthlib==1.3.0
- rsa==4.7.2
- six==1.15.0
- tensorboard==2.7.0
- tensorboard-data-server==0.6.1
- tensorboard-plugin-wit==1.8.0
- tensorflow==2.7.0
- tensorflow-estimator==2.7.0
- tensorflow-io-gcs-filesystem==0.21.0
- termcolor==1.1.0
- typing-extensions==3.7.4.3
- werkzeug==2.0.2
- wrapt==1.12.1
prefix: /home/juanma/miniconda3/envs/electrondensity

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