Skip to content

Commit

Permalink
updated contact email
Browse files Browse the repository at this point in the history
Juanma committed Mar 17, 2023
1 parent aaaa480 commit cf001a7
Showing 28 changed files with 28 additions and 28 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@chem.gla.ac.uk
# Author: Juanma juanma.parrilla@gcu.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@chem.gla.ac.uk
# Author: Juanma juanma.parrilla@gcu.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@chem.gla.ac.uk
# Author: Juanma juanma.parrilla@gcu.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion 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@chem.gla.ac.uk
# Author: Juanma juanma.parrilla@gcu.ac.uk
#
##########################################################################################

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@chem.gla.ac.uk
# Author: Juanma juanma.parrilla@gcu.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@chem.gla.ac.uk
# Author: Juanma juanma.parrilla@gcu.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@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion 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@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.ac.uk
#
##########################################################################################

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@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.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@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.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@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.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@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.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@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/models/ED2ESP.py
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
# This code is very similar to VAEresnet, but instead of trying to reconstruct its input
# as a VAE does, it tries to convert electron densities to electro static potentials.
#
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/models/ED2smiles.py
Original file line number Diff line number Diff line change
@@ -7,7 +7,7 @@
# I am not adding comments to most of the stuff that is directly copy-pasted. Check the
# tutorials above and then you will easily understand it.
#
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/models/VAE.py
Original file line number Diff line number Diff line change
@@ -8,7 +8,7 @@
# from that repo. I suggest you get the book and check chapter 3, because the
# code is very well explained there.
#
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/models/VAEattention.py
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@
# do was reducing the dimensionality from 4D to 2D, because that's the shape of the
# self-attention that the smiles decoder will need.
#
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/models/gpt.py
Original file line number Diff line number Diff line change
@@ -8,7 +8,7 @@
# I am not adding comments to most of the stuff that is directly copy-pasted. Check the
# tutorials above and then you will easily understand it.
#
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/models/layers.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# - identity_block and conv_block are copied from keras resnet50, using conv3d instead.
# - attention is adapted from taki0112 SAGAN implementation
#
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/utils/TFRecordLoader.py
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@
# This code is a mixture of https://keras.io/examples/keras_recipes/tfrecord/
# and how Jarek did it on the branch "developer" (develop/input/tfrecords.py)
#
# Author: Juan Manuel Parrilla Gutierrez (juanma@chem.gla.ac.uk)
# Author: Juan Manuel Parrilla Gutierrez (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/utils/ed_to_smiles.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# generate the smiles, save them as a pickle file, and then it will use rdkit to generate
# molecule visualisations.
#
# @author: Juan Manuel Parrilla (juanma@chem.gla.ac.uk)
# @author: Juan Manuel Parrilla (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/utils/edesp_to_smiles.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# generate the smiles, save them as a pickle file, and then it will use rdkit to generate
# molecule visualisations.
#
# @author: Juan Manuel Parrilla (juanma@chem.gla.ac.uk)
# @author: Juan Manuel Parrilla (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/utils/esp_to_smiles.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# generate the smiles, save them as a pickle file, and then it will use rdkit to generate
# molecule visualisations.
#
# @author: Juan Manuel Parrilla (juanma@chem.gla.ac.uk)
# @author: Juan Manuel Parrilla (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/utils/optimiser_utils.py
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@
#
# Some shared functionality for the optimiser scripts.
#
# Author: juanma@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.ac.uk
#
##########################################################################################

2 changes: 1 addition & 1 deletion src/utils/test_accuracy_ed2smiles.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# For it to match, all the tokens (from start to first stop) need to match perfectly.
# Given a folder with weights, it will load them into the model, and test the accuracy
# against the test set.
# Author: juanma@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.ac.uk
#
#########################################################################################

2 changes: 1 addition & 1 deletion src/utils/test_accuracy_edesp2smiles.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# For it to match, all the tokens (from start to first stop) need to match perfectly.
# Given a folder with weights, it will load them into the model, and test the accuracy
# against the test set.
# Author: juanma@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.ac.uk
#
#########################################################################################

2 changes: 1 addition & 1 deletion src/utils/test_accuracy_esp2smiles.py
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
# For it to match, all the tokens (from start to first stop) need to match perfectly.
# Given a folder with weights, it will load them into the model, and test the accuracy
# against the test set.
# Author: juanma@chem.gla.ac.uk
# Author: juanma.parrilla@gcu.ac.uk
#
#########################################################################################

2 changes: 1 addition & 1 deletion src/utils/view_edm.py
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@
# Created on Thu Apr 9 11:29:39 2020. Displays the electron density using orbkit
# and mayavi.
#
# @author: jmg. Adapted now by Juan Manuel Parrilla (juanma@chem.gla.ac.uk)
# @author: jmg. Adapted now by Juan Manuel Parrilla (juanma.parrilla@gcu.ac.uk)
#
##########################################################################################

0 comments on commit cf001a7

Please sign in to comment.