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croningp · Mar 17, 2023 · cf001a7 · cf001a7
1 parent aaaa480
commit cf001a7
Showing 28 changed files with 28 additions and 28 deletions.
diff --git a/bin/benchmarking/generate_smiles_from_ed.py b/bin/benchmarking/generate_smiles_from_ed.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/benchmarking/generate_smiles_from_edesp.py b/bin/benchmarking/generate_smiles_from_edesp.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/cage_hg.py b/bin/optimisers/cage_hg.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/cage_hg_esp.py b/bin/optimisers/cage_hg_esp.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/cage_hg_esp_lee.py b/bin/optimisers/cage_hg_esp_lee.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/cage_hg_split_esp.py b/bin/optimisers/cage_hg_split_esp.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/host_guest_overlapping.py b/bin/optimisers/host_guest_overlapping.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/maximise_hg_esp.py b/bin/optimisers/maximise_hg_esp.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/maximise_hg_polar.py b/bin/optimisers/maximise_hg_polar.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/maximise_polar.py b/bin/optimisers/maximise_polar.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/optimisers/maximise_size.py b/bin/optimisers/maximise_size.py
@@ -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
 #
 ##########################################################################################
 

diff --git a/bin/train/train_ed2esp.py b/bin/train/train_ed2esp.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/bin/train/train_vae.py b/bin/train/train_vae.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/models/ED2ESP.py b/src/models/ED2ESP.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/models/ED2smiles.py b/src/models/ED2smiles.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/models/VAE.py b/src/models/VAE.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/models/VAEattention.py b/src/models/VAEattention.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/models/gpt.py b/src/models/gpt.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/models/layers.py b/src/models/layers.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/utils/TFRecordLoader.py b/src/utils/TFRecordLoader.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/utils/ed_to_smiles.py b/src/utils/ed_to_smiles.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/utils/edesp_to_smiles.py b/src/utils/edesp_to_smiles.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/utils/esp_to_smiles.py b/src/utils/esp_to_smiles.py
@@ -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)
 #
 ##########################################################################################
 

diff --git a/src/utils/optimiser_utils.py b/src/utils/optimiser_utils.py
@@ -2,7 +2,7 @@
 #
 # Some shared functionality for the optimiser scripts.
 #
-# Author: juanma@chem.gla.ac.uk
+# Author: juanma.parrilla@gcu.ac.uk
 #
 ##########################################################################################
 

diff --git a/src/utils/test_accuracy_ed2smiles.py b/src/utils/test_accuracy_ed2smiles.py
@@ -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
 #
 #########################################################################################
 

diff --git a/src/utils/test_accuracy_edesp2smiles.py b/src/utils/test_accuracy_edesp2smiles.py
@@ -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
 #
 #########################################################################################
 

diff --git a/src/utils/test_accuracy_esp2smiles.py b/src/utils/test_accuracy_esp2smiles.py
@@ -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
 #
 #########################################################################################
 

diff --git a/src/utils/view_edm.py b/src/utils/view_edm.py
@@ -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)
 #
 ##########################################################################################