From 8e31975f319feb287fe5d03bb722608ec099f46c Mon Sep 17 00:00:00 2001
From: Malte Schokolowski <baw8441@uni-hamburg.de>
Date: Wed, 8 Dec 2021 13:15:59 +0100
Subject: [PATCH] added comments in Processing
---
verarbeitung/Processing.py | 8 ++----
.../__pycache__/Processing.cpython-39.pyc | Bin 3974 -> 3986 bytes
.../__pycache__/json_demo.cpython-39.pyc | Bin 1173 -> 1162 bytes
verarbeitung/import_from_json.py | 27 +++++++++++-------
verarbeitung/json_demo.py | 2 +-
verarbeitung/json_text.json | 1 -
verarbeitung/json_with_citations_v2.json | 1 +
verarbeitung/print_graph_test.py | 14 ++++++---
8 files changed, 31 insertions(+), 22 deletions(-)
delete mode 100644 verarbeitung/json_text.json
create mode 100644 verarbeitung/json_with_citations_v2.json
diff --git a/verarbeitung/Processing.py b/verarbeitung/Processing.py
index d44aa0d..2225a09 100644
--- a/verarbeitung/Processing.py
+++ b/verarbeitung/Processing.py
@@ -43,7 +43,7 @@ def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, t
except ValueError:
continue
except IndexError:
- print(pub_doi)
+ continue
# checks if publication already exists in nodes
@@ -113,7 +113,6 @@ def create_graph_structure_references(pub, search_depth, search_depth_max, test_
continue
# nur aus Testzwecken, da noch was bei Input falsch ist
except IndexError:
- print(reference.doi_url)
continue
reference_pub_obj.group = "depth"
@@ -168,7 +167,6 @@ def create_graph_structure_citations(pub, search_height, search_height_max, test
except ValueError:
continue
except IndexError:
- print(citation.doi_url)
continue
citation_pub_obj.group = "height"
@@ -236,7 +234,6 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False):
# calls a skript to save nodes and edges of graph in .json file
output_to_json(nodes,edges)
- return(nodes,edges)
# only for unit tests
if (test_var == True):
@@ -244,4 +241,5 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False):
for node in nodes:
doi_nodes_list.append(node.doi_url)
return(doi_nodes_list, edges)
-
\ No newline at end of file
+
+ return(nodes,edges)
\ No newline at end of file
diff --git a/verarbeitung/__pycache__/Processing.cpython-39.pyc b/verarbeitung/__pycache__/Processing.cpython-39.pyc
index 29df691cb577fd54163d38a814b22628a3bd296b..da7bd263cdd2ab97aabc416b1431b1463fc2a03e 100644
GIT binary patch
delta 99
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z+XBuS_AIW2jEoG0JvD44%xO%)3?)n;dNUVqC?huu2O|q32O}RN2h-*(J{d*;(tj2j
delta 87
zcmbOv-zLwS$ji&c00aeh*Cz^Z<c;KETr@eIr(UImsf0O=DVQNvpq9OcZ2@NudluJ1
lMn;ChmKrvQObWwhG2T!{ZYB<921W)(7DhhC&1HNti~y)I65#*<
diff --git a/verarbeitung/__pycache__/json_demo.cpython-39.pyc b/verarbeitung/__pycache__/json_demo.cpython-39.pyc
index 7e26222f87d54c667059b60f41230e98859b09d0..d78081e2f26f27652a5db45cae03cdb00034fe8f 100644
GIT binary patch
delta 67
zcmbQr*~Q75$ji&c00c*;Y)Gu$$ji#eeTy?Wvm~)3Ge56*vJ#^&YY`hzdUF+{6(buv
TkX6L7c^8u)BO}M;Gt4IeQJN7>
delta 78
zcmeC;oXW|Y$ji&c00gfutxs&&$jizoP{o&=S&~?inV+YSoL`z(GFg_<m-`kcOt5%!
aKBE;Q8yiqh5&P!#OoEJz?2`{Np9BDu)fY?v
diff --git a/verarbeitung/import_from_json.py b/verarbeitung/import_from_json.py
index 7eec532..37c12c5 100644
--- a/verarbeitung/import_from_json.py
+++ b/verarbeitung/import_from_json.py
@@ -1,6 +1,6 @@
# -*- coding: utf-8 -*-
"""
-Functions to read old json files to recreate old grpah structure
+Functions to read old json files to recreate old graph structure
"""
@@ -71,14 +71,20 @@ def add_ref_and_cit_to_pubs(input_dict):
'''
# iterates over the list of edges
- for edge in input_dict["links"]: #iterates over the list of edges
+ for edge in input_dict["links"]:
for node in list_of_nodes_py:
+
+ # adds reference to current node
if (node.doi_url == edge["source"]):
new_reference = Reference(node.doi_url, node.title, node.contributors, node.journal, node.publication_date)
node.references.append(new_reference)
+
+ # adds citation to current node
if (node.doi_url == edge["target"]):
new_citation = Citation(node.doi_url, node.title, node.contributors, node.journal, node.publication_date)
node.citations.append(new_citation)
+
+ # adds edge to list
list_of_edges_py.append([edge["source"],edge["target"]])
@@ -88,21 +94,20 @@ def input_from_json(json_file):
:type json_file: Json File
'''
+ # creates global sets for nodes and edges
global list_of_nodes_py, list_of_edges_py
list_of_nodes_py = []
list_of_edges_py = []
- with open(json_file,'r') as file: #opens the json file with reading permission
- input_dict = json.load(file) #saves the information in a dictionary
- create_pubs_from_json(input_dict)
+ #opens the json file and saves content in dictionary
+ with open(json_file,'r') as file:
+ input_dict = json.load(file)
+ # creates nodes of Class Publication from input Json file
+ create_pubs_from_json(input_dict)
+ # adds references and citations to publications and creates edges
add_ref_and_cit_to_pubs(input_dict)
-
-
-
- # Iteriert über die Liste der Kanten_dictionaries speichert sie als Liste
-
-
+
return(list_of_nodes_py, list_of_edges_py)
diff --git a/verarbeitung/json_demo.py b/verarbeitung/json_demo.py
index 2c9f68d..893945e 100644
--- a/verarbeitung/json_demo.py
+++ b/verarbeitung/json_demo.py
@@ -18,7 +18,7 @@ def format_nodes(V):
new_dict["journal"] = node.journal
new_dict["doi"] = node.doi_url
new_dict["group"] = node.group
- new_dict["citation count"] = len(node.citations)
+ new_dict["citations"] = len(node.citations)
list_of_node_dicts.append(new_dict)
return list_of_node_dicts
diff --git a/verarbeitung/json_text.json b/verarbeitung/json_text.json
deleted file mode 100644
index ad30e34..0000000
--- a/verarbeitung/json_text.json
+++ /dev/null
@@ -1 +0,0 @@
-{"nodes": [{"name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis", "author": ["Emanuel S. R. Ehmki", "Robert Schmidt", "Farina Ohm", "Matthias Rarey"], "year": "May 24, 2019", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.9b00249", "group": "input", "citation count": 5}, {"name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems", "author": ["John A. Keith", "Valentin Vassilev-Galindo", "Bingqing Cheng", "Stefan Chmiela", "Michael Gastegger", "Klaus-Robert M\u00fcller", "Alexandre Tkatchenko"], "year": "July 7, 2021", "journal": "Chem. Rev.", "doi": "https://doi.org/10.1021/acs.chemrev.1c00107", "group": "height", "citation count": 1}, {"name": "Disconnected Maximum Common Substructures under Constraints", "author": ["Robert Schmidt", "Florian Krull", "Anna Lina Heinzke", "Matthias Rarey"], "year": "December 16, 2020", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.0c00741", "group": "height", "citation count": 0}, {"name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design", "author": ["Ansgar Schuffenhauer", "Nadine Schneider", "Samuel Hintermann", "Douglas Auld", "Jutta Blank", "Simona Cotesta", "Caroline Engeloch", "Nikolas Fechner", "Christoph Gaul", "Jerome Giovannoni", "Johanna Jansen", "John Joslin", "Philipp Krastel", "Eugen Lounkine", "John Manchester", "Lauren G. Monovich", "Anna Paola Pelliccioli", "Manuel Schwarze", "Michael D. Shultz", "Nikolaus Stiefl", "Daniel K. Baeschlin"], "year": "November 3, 2020", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "group": "height", "citation count": 8}, {"name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms", "author": ["Robert Schmidt", "Emanuel S. R. Ehmki", "Farina Ohm", "Hans-Christian Ehrlich", "Andriy Mashychev", "Matthias Rarey"], "year": "May 23, 2019", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.9b00250", "group": "height", "citation count": 12}, {"name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID", "author": ["Ilaria Proietti Silvestri", "Paul J. J. Colbon"], "year": "July 16, 2021", "journal": "ACS Med. Chem. Lett.", "doi": "https://doi.org/10.1021/acsmedchemlett.1c00251", "group": "height", "citation count": 0}, {"name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies", "author": ["Paul D. Leeson", "A. Patricia Bento", "Anna Gaulton", "Anne Hersey", "Emma J. Manners", "Chris J. Radoux", "Andrew R. Leach"], "year": "May 13, 2021", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.1c00416", "group": "height", "citation count": 0}], "links": [{"source": "https://doi.org/10.1021/acs.chemrev.1c00107", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00741", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00250", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acsmedchemlett.1c00251", "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"source": "https://doi.org/10.1021/acs.jmedchem.1c00416", "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"source": "https://doi.org/10.1021/acs.chemrev.1c00107", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00741", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}]}
\ No newline at end of file
diff --git a/verarbeitung/json_with_citations_v2.json b/verarbeitung/json_with_citations_v2.json
new file mode 100644
index 0000000..60c6160
--- /dev/null
+++ b/verarbeitung/json_with_citations_v2.json
@@ -0,0 +1 @@
+{"nodes": [{"name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis", "author": ["Emanuel S. R. Ehmki", "Robert Schmidt", "Farina Ohm", "Matthias Rarey"], "year": "May 24, 2019", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.9b00249", "group": "input", "citations": 5}, {"name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems", "author": ["John A. Keith", "Valentin Vassilev-Galindo", "Bingqing Cheng", "Stefan Chmiela", "Michael Gastegger", "Klaus-Robert M\u00fcller", "Alexandre Tkatchenko"], "year": "July 7, 2021", "journal": "Chem. Rev.", "doi": "https://doi.org/10.1021/acs.chemrev.1c00107", "group": "height", "citations": 1}, {"name": "Disconnected Maximum Common Substructures under Constraints", "author": ["Robert Schmidt", "Florian Krull", "Anna Lina Heinzke", "Matthias Rarey"], "year": "December 16, 2020", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.0c00741", "group": "height", "citations": 0}, {"name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design", "author": ["Ansgar Schuffenhauer", "Nadine Schneider", "Samuel Hintermann", "Douglas Auld", "Jutta Blank", "Simona Cotesta", "Caroline Engeloch", "Nikolas Fechner", "Christoph Gaul", "Jerome Giovannoni", "Johanna Jansen", "John Joslin", "Philipp Krastel", "Eugen Lounkine", "John Manchester", "Lauren G. Monovich", "Anna Paola Pelliccioli", "Manuel Schwarze", "Michael D. Shultz", "Nikolaus Stiefl", "Daniel K. Baeschlin"], "year": "November 3, 2020", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "group": "height", "citations": 8}, {"name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms", "author": ["Robert Schmidt", "Emanuel S. R. Ehmki", "Farina Ohm", "Hans-Christian Ehrlich", "Andriy Mashychev", "Matthias Rarey"], "year": "May 23, 2019", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.9b00250", "group": "height", "citations": 12}, {"name": "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings", "author": ["Jerome Eberhardt", "Diogo Santos-Martins", "Andreas F. Tillack", "Stefano Forli"], "year": "July 19, 2021", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.1c00203", "group": "input", "citations": 1}, {"name": "Accelerating AutoDock4 with GPUs and Gradient-Based Local Search", "author": ["Diogo Santos-Martins", "Leonardo Solis-Vasquez", "Andreas F Tillack", "Michel F Sanner", "Andreas Koch", "Stefano Forli"], "year": "January 6, 2021", "journal": "Journal of Chemical Theory and Computation", "doi": "https://doi.org/10.1021/acs.jctc.0c01006", "group": "depth", "citations": 14}, {"name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep", "author": ["Yuqi Zhang", "Michel F. Sanner"], "year": "September 11, 2019", "journal": "Journal of Chemical Theory and Computation", "doi": "https://doi.org/10.1021/acs.jctc.9b00557", "group": "depth", "citations": 9}, {"name": "Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise", "author": ["David Ryan Koes", "Matthew P. Baumgartner", "Carlos J. Camacho"], "year": "February 4, 2013", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/ci300604z", "group": "depth", "citations": 100}, {"name": "Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking", "author": ["Anita K. Nivedha", "David F. Thieker", "Spandana Makeneni", "Huimin Hu", "Robert J. Woods"], "year": "January 8, 2016", "journal": "Journal of Chemical Theory and Computation", "doi": "https://doi.org/10.1021/acs.jctc.5b00834", "group": "depth", "citations": 48}, {"name": "Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems", "author": ["Stefano Forli", "Maurizio Botta"], "year": "June 22, 2007", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/ci700036j", "group": "depth", "citations": 32}, {"name": "AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins", "author": ["Diogo Santos-Martins", "Stefano Forli", "Maria Jo\u00e3o Ramos", "Arthur J. Olson"], "year": "June 15, 2014", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/ci500209e", "group": "depth", "citations": 100}, {"name": "A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking", "author": ["Stefano Forli", "Arthur J. Olson"], "year": "December 9, 2011", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/jm2005145", "group": "depth", "citations": 100}, {"name": "Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context", "author": ["Douglas R. Houston", "Malcolm D. Walkinshaw"], "year": "January 27, 2013", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/ci300399w", "group": "depth", "citations": 100}, {"name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory", "author": ["Themis Lazaridis"], "year": "April 14, 1998", "journal": "Journal of Physical Chemistry B", "doi": "https://doi.org/10.1021/jp9723574", "group": "depth", "citations": 100}, {"name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids", "author": ["Themis Lazaridis"], "year": "April 14, 1998", "journal": "Journal of Physical Chemistry B", "doi": "https://doi.org/10.1021/jp972358w", "group": "depth", "citations": 100}, {"name": "ZINC20\u2014A Free Ultralarge-Scale Chemical Database for Ligand Discovery", "author": ["John J. Irwin", "Khanh G. Tang", "Jennifer Young", "Chinzorig Dandarchuluun", "Benjamin R. Wong", "Munkhzul Khurelbaatar", "Yurii S. Moroz", "John Mayfield", "Roger A. Sayle"], "year": "October 29, 2020", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.0c00675", "group": "depth", "citations": 25}, {"name": "Structural Biology-Inspired Discovery of Novel KRAS\u2013PDE\u03b4 Inhibitors", "author": ["Yan Jiang", "Chunlin Zhuang", "Long Chen", "Junjie Lu", "Guoqiang Dong", "Zhenyuan Miao", "Wannian Zhang", "Jian Li", "Chunquan Sheng"], "year": "September 20, 2017", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.7b01243", "group": "depth", "citations": 12}, {"name": "Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking", "author": ["Michael M. Mysinger", "Michael Carchia", "John. J. Irwin", "Brian K. Shoichet"], "year": "June 20, 2012", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/jm300687e", "group": "depth", "citations": 100}, {"name": "Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark", "author": ["Thomas Gaillard"], "year": "July 10, 2018", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.8b00312", "group": "depth", "citations": 74}, {"name": "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity", "author": ["Nguyen Thanh Nguyen", "Trung Hai Nguyen", "T. Ngoc Han Pham", "Nguyen Truong Huy", "Mai Van Bay", "Minh Quan Pham", "Pham Cam Nam", "Van V. Vu", "Son Tung Ngo"], "year": "December 30, 2019", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.9b00778", "group": "depth", "citations": 65}, {"name": "Glide:\u2009 A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy", "author": ["Richard A. Friesner", "Jay L. Banks", "Robert B. Murphy", "Thomas A. Halgren", "Jasna J. Klicic", "Daniel T. Mainz", "Matthew P. Repasky", "Eric H. Knoll", "Mee Shelley", "Jason K. Perry", "David E. Shaw", "Perry Francis", "Peter S. Shenkin"], "year": "February 27, 2004", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/jm0306430", "group": "depth", "citations": 97}, {"name": "Surflex:\u2009 Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine", "author": ["Ajay N. Jain"], "year": "January 21, 2003", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/jm020406h", "group": "depth", "citations": 100}, {"name": "ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein\u2013Ligand Interactions", "author": ["Guo-Bo Li", "Ling-Ling Yang", "Wen-Jing Wang", "Lin-Li Li", "Sheng-Yong Yang"], "year": "February 9, 2013", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/ci300493w", "group": "depth", "citations": 99}, {"name": "A Knowledge-Based Energy Function for Protein\u2212Ligand, Protein\u2212Protein, and Protein\u2212DNA Complexes", "author": ["Chi Zhang", "Song Liu", "Qianqian Zhu", "Yaoqi Zhou"], "year": "February 16, 2005", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/jm049314d", "group": "depth", "citations": 100}, {"name": "Novel Anti-Hepatitis B Virus Activity of Euphorbia schimperi and Its Quercetin and Kaempferol Derivatives", "author": ["Mohammad K. Parvez", "Sarfaraz Ahmed", "Mohammed S. Al-Dosari", "Mazin A. S. Abdelwahid", "Ahmed H. Arbab", "Adnan J. Al-Rehaily", "Mai M. Al-Oqail"], "year": "October 21, 2021", "journal": "ACS Omega", "doi": "https://doi.org/10.1021/acsomega.1c04320", "group": "height", "citations": 0}, {"name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID", "author": ["Ilaria Proietti Silvestri", "Paul J. J. Colbon"], "year": "July 16, 2021", "journal": "ACS Med. Chem. Lett.", "doi": "https://doi.org/10.1021/acsmedchemlett.1c00251", "group": "height", "citations": 0}, {"name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies", "author": ["Paul D. Leeson", "A. Patricia Bento", "Anna Gaulton", "Anne Hersey", "Emma J. Manners", "Chris J. Radoux", "Andrew R. Leach"], "year": "May 13, 2021", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.1c00416", "group": "height", "citations": 0}, {"name": "Topological Characterization and Graph Entropies of Tessellations of Kekulene Structures: Existence of Isentropic Structures and Applications to Thermochemistry, Nuclear Magnetic Resonance, and Electron Spin Resonance", "author": ["S. Ruth Julie Kavitha", "Jessie Abraham", "Micheal Arockiaraj", "Joseph Jency", "Krishnan Balasubramanian"], "year": "September 1, 2021", "journal": "J. Phys. Chem. A", "doi": "https://doi.org/10.1021/acs.jpca.1c06264", "group": "height", "citations": 0}, {"name": "Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase", "author": ["Stefano Bonciarelli", "Jenny Desantis", "Laura Goracci", "Lydia Siragusa", "Ismael Zamora", "Elisabeth Ortega-Carrasco"], "year": "June 1, 2021", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.1c00226", "group": "height", "citations": 0}, {"name": "Computational Approaches to Identify Structural Alerts and Their Applications in Environmental Toxicology and Drug Discovery", "author": ["Hongbin Yang", "Chaofeng Lou", "Weihua Li", "Guixia Liu", "Yun Tang"], "year": "February 24, 2020", "journal": "Chem. Res. 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\ No newline at end of file
diff --git a/verarbeitung/print_graph_test.py b/verarbeitung/print_graph_test.py
index 274e81e..579fab0 100644
--- a/verarbeitung/print_graph_test.py
+++ b/verarbeitung/print_graph_test.py
@@ -15,11 +15,13 @@ __status__ = "Production"
import sys
+
#sys.path.insert(1, 'C:\Users\Malte\Git\CiS-Projekt\ci-s-projekt-verarbeitung\input')
sys.path.append(".")
from input.interface import InputInterface as Input
#import input
from Processing import process_main
+from import_from_json import input_from_json
# a function to print nodes and edges from a graph
def print_graph(nodes, edges):
@@ -33,12 +35,12 @@ def print_graph(nodes, edges):
print(len(edges))
-# program test, because there is no connection to UI yet.
+# program test with some random dois
def try_known_publications():
doi_list = []
doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
#doi_list.append('https://doi.org/10.1021/acs.jcim.9b00249')
- #doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203')
+ doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203')
#arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
doi_list.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
#arr.append('https://doi.org/10.1021/acs.jcim.0c00741')
@@ -51,8 +53,12 @@ def try_known_publications():
#arr.append[url]
- nodes, edges = process_main(doi_list,1,1)
+ nodes, edges = process_main(doi_list,2,2)
print_graph(nodes, edges)
-try_known_publications()
\ No newline at end of file
+ return(nodes, edges)
+
+nodes, edges = try_known_publications()
+#nodes_new, edges_new = input_from_json("json_text.json")
+#print_graph(nodes_new, edges_new)
\ No newline at end of file
--
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