diff --git a/input_old/README.md b/input_old/README.md
deleted file mode 100644
index 76bd11d5d70daac13e190f4d52269eb381413c69..0000000000000000000000000000000000000000
--- a/input_old/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# Projekt CiS-Projekt 2021/22
-Input-Skripts
-
diff --git a/input_old/__pycache__/input_fj.cpython-39.pyc b/input_old/__pycache__/input_fj.cpython-39.pyc
deleted file mode 100644
index a3e6099f4ab4c56400b2698c812d4b5fc9a9a7aa..0000000000000000000000000000000000000000
Binary files a/input_old/__pycache__/input_fj.cpython-39.pyc and /dev/null differ
diff --git a/input_old/example_urls b/input_old/example_urls
deleted file mode 100644
index 96ac680c65edddcb495312000157edea1ab94884..0000000000000000000000000000000000000000
--- a/input_old/example_urls
+++ /dev/null
@@ -1,2 +0,0 @@
-https://pubs.acs.org/doi/10.1021/acs.jcim.5b00332
-https://pubs.acs.org/doi/10.1021/acs.jcim.6b00709
diff --git a/input_old/input_fj.py b/input_old/input_fj.py
deleted file mode 100644
index ecc8e68fc5a84a446ae3f09dcb5ed56e8d262766..0000000000000000000000000000000000000000
--- a/input_old/input_fj.py
+++ /dev/null
@@ -1,154 +0,0 @@
-#!/usr/bin/env python3
-"""
-Functions for information retrieval of articles from the ACS journal JCIM
-
-"""
-
-__author__ = "Florian Jochens"
-__email__ = "fj@andaco.de"
-__status__ = "Production"
-#__copyright__ = ""
-#__credits__ = ["", "", "", ""]
-#__license__ = ""
-#__version__ = ""
-#__maintainer__ = ""
-
-from bs4 import BeautifulSoup as bs
-import requests as req
-import sys
-from pathlib import Path
-
-class Publication:
- #_registry = []
- _citations = []
- _references = []
-
- def __init__(self, title, publication_date, contributors, doi_url,
- subjects = None, num_citations = None):
- #self._registry.append(self)
- self.title = title
- self.publication_date = publication_date
- self.contributors = contributors
- self.doi_url = doi_url
- self.subjects = subjects
- self.num_citations = num_citations
- #self._citations = []
- #self._references = []
-
-class Citation:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
-class References:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
-def get_article_info(soup):
- header = soup.find('div', class_ = 'article_header-left pull-left')
- article_title = header.find('span', class_ = 'hlFld-Title').text
- publication_date = header.find('span', class_ = 'pub-date-value').text
- for link in header.find('div', class_ = 'article_header-doiurl'):
- doi_url = link.get('href')
- subs = header.find('div', class_ = 'article_header-taxonomy')
- subjects = []
- for sub in subs.find_all('a'):
- subjects.append(sub.get('title'))
- cons = header.find('ul', class_ = 'loa')
- contributors = []
- for con in cons.find_all('span', class_ = 'hlFld-ContribAuthor'):
- contributors.append(con.text)
- numc = header.find('div', class_ = 'articleMetrics_count')
- if not numc.a:
- num_citations = 0
- else:
- num_citations = numc.a.text
-
- pub = Publication(article_title, publication_date, contributors, doi_url,
- subjects, num_citations)
- return pub
-
-def get_download_url():
- export = soup.find('div', class_ = 'cit-download-dropdown_content')
- url = 'https://pubs.acs.org'
- for link in export.find_all('a'):
- if link.get('title') == 'Citation and references':
- url += link.get('href')
- print(url)
- return url
-
-def download(url): # Download citation and references file
- if url.find('='):
- filename = url.rsplit('=', 1)[1]
- path = Path(('./files/' + filename))
- if path.is_file():
- print("File already exists")
- else:
- print("File does not exist")
-
-def get_citation_info(pub, num_citations, soup):
- pub._citations = []
- details = soup.find('ol', class_ = 'cited-content_cbyCitation')
- titles = []
- for title in details.find_all('span',
- class_ = 'cited-content_cbyCitation_article-title'):
- titles.append(title.text.replace('.', ''))
- journal_names = []
- for name in details.find_all('span',
- class_ = 'cited-content_cbyCitation_journal-name'):
- journal_names.append(name.text)
- doi_urls = []
- for url in details.find_all('a'):
- doi_urls.append(url.get('href'))
- contributors = []
- for contrib in details.find_all('span',
- class_ = 'cited-content_cbyCitation_article-contributors'):
- contributors.append(contrib.text)
- for i in range(0, int(num_citations)):
- pub._citations.append(Citation(titles[i], journal_names[i],
- contributors[i], doi_urls[i]))
-def print_pub_info(pub):
- print(f'''Article title: {pub.title}
-Publication date: {pub.publication_date}
-DOI-URL: {pub.doi_url}
-
-Subjects:''')
- print(*(pub.subjects), sep = ", ")
- print('\nContributors:')
- print(*(pub.contributors), sep = ", ")
-
- if int(pub.num_citations) > 0:
- if int(pub.num_citations) == 1:
- print(f'\nThis publication is cited by the following publication:\n')
- else:
- print(f'\nThis publication is cited by the following {pub.num_citations} publications:\n')
- for citation in pub._citations:
- print(f'''
- Title: {citation.title}
- Journal: {citation.journal}
- Contributors: {citation.contributors}
- DOI-URL: {citation.doi_url}
- ''')
- else:
- print('\nThis publication is not cited by any other publication.')
-
-def input(url):
- html_text = req.get(url).text
- soup = bs(html_text, 'html.parser')
-
- pub = get_article_info(soup)
- if int(pub.num_citations) > 0:
- get_citation_info(pub, int(pub.num_citations), soup)
- return pub
-
-#if len(sys.argv) != 2:
-# sys.stderr.write('Usage: {} <url>\n'.format(sys.argv[0]))
-# exit(1)
-#url = sys.argv[1]
-#pub = input(url)
-#print_pub_info(pub)
diff --git a/input_old/pub.py b/input_old/pub.py
deleted file mode 100644
index 13b90e804cd485813b731385b319b3077a017dd2..0000000000000000000000000000000000000000
--- a/input_old/pub.py
+++ /dev/null
@@ -1,32 +0,0 @@
-class Publication:
- #_registry = []
- #_citations = []
- #_references = []
-
- def __init__(self, title, publication_date, contributors, doi_url,
- subjects, num_citations):
- #self._registry.append(self)
- self.title = title
- self.publication_date = publication_date
- self.contributors = contributors
- self.doi_url = doi_url
- self.subjects = subjects
- self.num_citations = num_citations
- self.num_references = num_references
- self._citations = []
- self._references = []
-
-class Citation:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
-class References:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
diff --git a/input_old/test.py b/input_old/test.py
deleted file mode 100755
index dc623ca182691e9e06a6713a4d3d5dcf0bbf23c2..0000000000000000000000000000000000000000
--- a/input_old/test.py
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env python3
-
-from input_fj import input, print_pub_info
-import sys
-
-if len(sys.argv) != 3:
- sys.stderr.write('Usage: {} <url> <url>\n'.format(sys.argv[0]))
- exit(1)
-url = sys.argv[1]
-url2 = sys.argv[2]
-pub = input(url)
-print_pub_info(pub)
-pub2 = input(url2)
-print_pub_info(pub2)
-
diff --git a/input_old/x b/input_old/x
deleted file mode 100644
index c8ade9d56a520a3ac57e5eadce8b81bb3e63c0dd..0000000000000000000000000000000000000000
--- a/input_old/x
+++ /dev/null
@@ -1,234 +0,0 @@
-Article title: Feasibility of Active Machine Learning for Multiclass Compound Classification
-Publication date: January 7, 2016
-DOI-URL: https://doi.org/10.1021/acs.jcim.5b00332
-
-Subjects:
-Algorithms, Molecules, Drug discovery, Screening assays, Receptors
-
-Contributors:
-Tobias Lang, Florian Flachsenberg, Ulrike von Luxburg, Matthias Rarey
-
-This publication is cited by the following 30 publications:
-
-
- Title: Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery
- Journal: Chemical Reviews
- Contributors: Xin Yang, Yifei Wang, Ryan Byrne, Gisbert Schneider, Shengyong Yang.
- DOI-URL: https://doi.org/10.1021/acs.chemrev.8b00728
-
-
- Title: De Novo Molecule Design by Translating from Reduced Graphs to SMILES
- Journal: Journal of Chemical Information and Modeling
- Contributors: Peter Pogány, Navot Arad, Sam Genway, Stephen D. Pickett.
- DOI-URL: https://doi.org/10.1021/acs.jcim.8b00626
-
-
- Title: Designing Algorithms To Aid Discovery by Chemical Robots
- Journal: ACS Central Science
- Contributors: Alon B. Henson, Piotr S. Gromski, Leroy Cronin.
- DOI-URL: https://doi.org/10.1021/acscentsci.8b00176
-
-
- Title: Modeling Kinase Inhibition Using Highly Confident Data Sets
- Journal: Journal of Chemical Information and Modeling
- Contributors: Sorin Avram, Alina Bora, Liliana Halip, Ramona Curpăn.
- DOI-URL: https://doi.org/10.1021/acs.jcim.7b00729
-
-
- Title: Predictive Models for Fast and Effective Profiling of Kinase Inhibitors
- Journal: Journal of Chemical Information and Modeling
- Contributors: Alina Bora, Sorin Avram, Ionel Ciucanu, Marius Raica, and Stefana Avram .
- DOI-URL: https://doi.org/10.1021/acs.jcim.5b00646
-
-
- Title: Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery
- Journal: Bioinformatics
- Contributors: Huangqingbo Sun, Robert F Murphy, .
- DOI-URL: https://doi.org/10.1093/bioinformatics/btab322
-
-
- Title: An Artificial Intelligence Approach Based on Hybrid CNN-XGB Model to Achieve High Prediction Accuracy through Feature Extraction, Classification and Regression for Enhancing Drug Discovery in Biomedicine
- Journal: International Journal of Biology and Biomedical Engineering
- Contributors: Mukesh Madanan, Biju T. Sayed, Nurul Akhmal Mohd Zulkefli, Nitha C. Velayudhan.
- DOI-URL: https://doi.org/10.46300/91011.2021.15.22
-
-
- Title: Artificial Intelligence in Medicinal Chemistry
- Journal:
- Contributors: Edward Griffen, Alexander Dossetter, Andrew Leach, Shane Montague.
- DOI-URL: https://doi.org/10.1002/0471266949.bmc267
-
-
- Title: Practical Chemogenomic Modeling and Molecule Discovery Strategies Unveiled by Active Learning
- Journal:
- Contributors: J.B. Brown.
- DOI-URL: https://doi.org/10.1016/B978-0-12-801238-3.11533-8
-
-
- Title: Machine learning phases and criticalities without using real data for training
- Journal: Physical Review B
- Contributors: D.-R. Tan, F.-J. Jiang.
- DOI-URL: https://doi.org/10.1103/PhysRevB.102.224434
-
-
- Title: Active learning effectively identifies a minimal set of maximally informative and asymptotically performant cytotoxic structure–activity patterns in NCI-60 cell lines
- Journal: RSC Medicinal Chemistry
- Contributors: Takumi Nakano, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.1039/D0MD00110D
-
-
- Title: Active learning efficiently converges on rational limits of toxicity prediction and identifies patterns for molecule design
- Journal: Computational Toxicology
- Contributors: Ahsan Habib Polash, Takumi Nakano, Christin Rakers, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.1016/j.comtox.2020.100129
-
-
- Title: Practical considerations for active machine learning in drug discovery
- Journal: Drug Discovery Today: Technologies
- Contributors: Daniel Reker.
- DOI-URL: https://doi.org/10.1016/j.ddtec.2020.06.001
-
-
- Title: Designing compact training sets for data-driven molecular property prediction through optimal exploitation and exploration
- Journal: Molecular Systems Design & Engineering
- Contributors: Bowen Li, Srinivas Rangarajan.
- DOI-URL: https://doi.org/10.1039/C9ME00078J
-
-
- Title: Applicability Domain of Active Learning in Chemical Probe Identification: Convergence in Learning from Non-Specific Compounds and Decision Rule Clarification
- Journal: Molecules
- Contributors: Ahsan Habib Polash, Takumi Nakano, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.3390/molecules24152716
-
-
- Title: Capturing and applying knowledge to guide compound optimisation
- Journal: Drug Discovery Today
- Contributors: Matthew Segall, Tamsin Mansley, Peter Hunt, Edmund Champness.
- DOI-URL: https://doi.org/10.1016/j.drudis.2019.02.004
-
-
- Title: A novel graph kernel on chemical compound classification
- Journal: Journal of Bioinformatics and Computational Biology
- Contributors: Qiangrong Jiang, Jiajia Ma.
- DOI-URL: https://doi.org/10.1142/S0219720018500269
-
-
- Title: Accelerating Drug Discovery Using Convolution Neural Network Based Active Learning
- Journal:
- Contributors: Pengfei Liu, Kwong-Sak Leung.
- DOI-URL: https://doi.org/10.1109/TENCON.2018.8650298
-
-
- Title: An Adaptive Lightweight Security Framework Suited for IoT
- Journal:
- Contributors: Menachem Domb.
- DOI-URL: https://doi.org/10.5772/intechopen.73712
-
-
- Title: Adaptive mining and model building of medicinal chemistry data with a multi-metric perspective
- Journal: Future Medicinal Chemistry
- Contributors: JB Brown.
- DOI-URL: https://doi.org/10.4155/fmc-2018-0188
-
-
- Title: Chemogenomic Active Learning's Domain of Applicability on Small, Sparse qHTS Matrices: A Study Using Cytochrome P450 and Nuclear Hormone Receptor Families
- Journal: ChemMedChem
- Contributors: Christin Rakers, Rifat Ara Najnin, Ahsan Habib Polash, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.1002/cmdc.201700677
-
-
- Title: Automating drug discovery
- Journal: Nature Reviews Drug Discovery
- Contributors: Gisbert Schneider.
- DOI-URL: https://doi.org/10.1038/nrd.2017.232
-
-
- Title: Classifiers and their Metrics Quantified
- Journal: Molecular Informatics
- Contributors: J. B. Brown.
- DOI-URL: https://doi.org/10.1002/minf.201700127
-
-
- Title: Active Search for Computer-aided Drug Design
- Journal: Molecular Informatics
- Contributors: Dino Oglic, Steven A. Oatley, Simon J. F. Macdonald, Thomas Mcinally, Roman Garnett, Jonathan D. Hirst, Thomas Gärtner.
- DOI-URL: https://doi.org/10.1002/minf.201700130
-
-
- Title: Selection of Informative Examples in Chemogenomic Datasets
- Journal:
- Contributors: Daniel Reker, J. B. Brown.
- DOI-URL: https://doi.org/10.1007/978-1-4939-8639-2_13
-
-
- Title: The value of prior knowledge in machine learning of complex network systems
- Journal: Bioinformatics
- Contributors: Dana Ferranti, David Krane, David Craft, .
- DOI-URL: https://doi.org/10.1093/bioinformatics/btx438
-
-
- Title: Lightweight adaptive Random-Forest for IoT rule generation and execution
- Journal: Journal of Information Security and Applications
- Contributors: Menachem Domb, Elisheva Bonchek-Dokow, Guy Leshem.
- DOI-URL: https://doi.org/10.1016/j.jisa.2017.03.001
-
-
- Title: Active learning for computational chemogenomics
- Journal: Future Medicinal Chemistry
- Contributors: Daniel Reker, Petra Schneider, Gisbert Schneider, JB Brown.
- DOI-URL: https://doi.org/10.4155/fmc-2016-0197
-
-
- Title: Small Random Forest Models for Effective Chemogenomic Active Learning
- Journal: Journal of Computer Aided Chemistry
- Contributors: Christin Rakers, Daniel Reker, J.B. Brown.
- DOI-URL: https://doi.org/10.2751/jcac.18.124
-
-
- Title: Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
- Journal: PLOS Computational Biology
- Contributors: Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng, Lei Xie, .
- DOI-URL: https://doi.org/10.1371/journal.pcbi.1005135
-
-Article title: Matched Molecular Series: Measuring SAR Similarity
-Publication date: May 1, 2017
-DOI-URL: https://doi.org/10.1021/acs.jcim.6b00709
-
-Subjects:
-Substituents, Mathematical methods, Structure activity relationship, Biological databases
-
-Contributors:
-Emanuel S. R. Ehmki, Christian Kramer
-
-This publication is cited by the following 5 publications:
-
-
- Title: Matched Molecular Series Analysis for ADME Property Prediction
- Journal: Journal of Chemical Information and Modeling
- Contributors: Mahendra Awale, Sereina Riniker, Christian Kramer.
- DOI-URL: https://doi.org/10.1021/acs.jcim.0c00269
-
-
- Title: Approaches using AI in medicinal chemistry
- Journal:
- Contributors: Christian Tyrchan, Eva Nittinger, Dea Gogishvili, Atanas Patronov, Thierry Kogej.
- DOI-URL: https://doi.org/10.1016/B978-0-12-822249-2.00002-5
-
-
- Title: Bioactivity Prediction Based on Matched Molecular Pair and Matched Molecular Series Methods
- Journal: Current Pharmaceutical Design
- Contributors: Xiaoyu Ding, Chen Cui, Dingyan Wang, Jihui Zhao, Mingyue Zheng, Xiaomin Luo, Hualiang Jiang, Kaixian Chen.
- DOI-URL: https://doi.org/10.2174/1381612826666200427111309
-
-
- Title: BRADSHAW: a system for automated molecular design
- Journal: Journal of Computer-Aided Molecular Design
- Contributors: Darren V. S. Green, Stephen Pickett, Chris Luscombe, Stefan Senger, David Marcus, Jamel Meslamani, David Brett, Adam Powell, Jonathan Masson.
- DOI-URL: https://doi.org/10.1007/s10822-019-00234-8
-
-
- Title: The use of matched molecular series networks for cross target structure activity relationship translation and potency prediction
- Journal: MedChemComm
- Contributors: Christopher E. Keefer, George Chang.
- DOI-URL: https://doi.org/10.1039/C7MD00465F
-