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Commit b2326d85 authored by Malte Schokolowski's avatar Malte Schokolowski
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new branch and finished connect_new_input

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1 merge request!12bug fixes and updates to code
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verarbeitung/construct_new_graph/initialize_graph.py
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...@@ -96,7 +96,7 @@ def complete_inner_edges(): ...@@ -96,7 +96,7 @@ def complete_inner_edges():
edges.append([node.doi_url,reference.doi_url]) edges.append([node.doi_url,reference.doi_url])
def init_graph_construction(doi_input_list, search_depth, search_height, test_var = False): def init_graph_construction(doi_input_list, search_depth, search_height, test_var = False, input_nodes = [], input_edges = []):
''' '''
:param doi_input_list: input list of doi from UI :param doi_input_list: input list of doi from UI
:type doi_input_list: List[String] :type doi_input_list: List[String]
...@@ -128,8 +128,8 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va ...@@ -128,8 +128,8 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va
# creates empty lists to save nodes and edges # creates empty lists to save nodes and edges
global nodes, edges global nodes, edges
nodes = [] nodes = input_nodes
edges = [] edges = input_edges
# initializes nodes/edges from input and gets a list with publication objects for citations and references returned # initializes nodes/edges from input and gets a list with publication objects for citations and references returned
references_obj_list, citations_obj_list = initialize_nodes_list(doi_input_list,search_depth, search_height, test_var) references_obj_list, citations_obj_list = initialize_nodes_list(doi_input_list,search_depth, search_height, test_var)
......
verarbeitung/process_main.py
+ 7
− 7
View file @ b2326d85
...@@ -16,7 +16,7 @@ __status__ = "Production" ...@@ -16,7 +16,7 @@ __status__ = "Production"
import sys import sys
from pathlib import Path from pathlib import Path
from os import error from os import error, path
sys.path.append("../") sys.path.append("../")
...@@ -42,11 +42,11 @@ def Processing(url_list, search_depth, search_height, json_file = 'json_text.jso ...@@ -42,11 +42,11 @@ def Processing(url_list, search_depth, search_height, json_file = 'json_text.jso
''' '''
# updates graph if json file is known in directory otherwise starts new graph construction # updates graph if json file is known in directory otherwise starts new graph construction
try: json_file = Path(json_file)
with open(json_file) as f:
nodes, edges = update_graph(url_list, json_file, search_depth, search_height)
except IOError: if json_file.is_file():
nodes, edges = update_graph(url_list, json_file, search_depth, search_height)
else:
nodes, edges = init_graph_construction(url_list, search_depth, search_height) nodes, edges = init_graph_construction(url_list, search_depth, search_height)
# exports graph to given json file name # exports graph to given json file name
......
verarbeitung/start_script.py
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...@@ -8,4 +8,5 @@ doi_list = [] ...@@ -8,4 +8,5 @@ doi_list = []
doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249') 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://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')
doi_list.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
Processing(doi_list, 2, 2, 'test.json') Processing(doi_list, 2, 2, 'test.json')
\ No newline at end of file
verarbeitung/test.json
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View file @ b2326d85
{"nodes": [{"doi": "https://doi.org/10.1021/acs.jcim.9b00249", "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", "group": "Input", "depth": 0, "citations": 5}, {"doi": "https://doi.org/10.1021/acs.chemrev.1c00107", "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.", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00741", "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", "group": "Citedby", "depth": 1, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "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", "group": "Citedby", "depth": 1, "citations": 8}, {"doi": "https://doi.org/10.1021/acs.jcim.9b00250", "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", "group": "Citedby", "depth": 1, "citations": 12}, {"doi": "https://doi.org/10.1021/acs.jcim.1c00203", "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", "group": "Input", "depth": 0, "citations": 1}, {"doi": "https://doi.org/10.1021/acs.jctc.0c01006", "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", "group": "Reference", "depth": -1, "citations": 14}, {"doi": "https://doi.org/10.1021/acs.jctc.9b00557", "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", "group": "Reference", "depth": -1, "citations": 9}, {"doi": "https://doi.org/10.1021/ci300604z", "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", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/acs.jctc.5b00834", "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", "group": "Reference", "depth": -1, "citations": 48}, {"doi": "https://doi.org/10.1021/ci700036j", "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", "group": "Reference", "depth": -1, "citations": 32}, {"doi": "https://doi.org/10.1021/ci500209e", "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", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/jm2005145", "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", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/ci300399w", "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", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/jp9723574", "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. 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"https://doi.org/10.1021/acs.jcim.9b00778", "target": "https://doi.org/10.1021/acs.jcim.8b00312"}, {"source": "https://doi.org/10.1021/acs.jctc.0c01006", "target": "https://doi.org/10.1021/acs.jcim.9b00778"}, {"source": "https://doi.org/10.1021/acs.jctc.0c01006", "target": "https://doi.org/10.1021/ci049714+"}, {"source": "https://doi.org/10.1021/ci7004498", "target": "https://doi.org/10.1021/jm020155c"}, {"source": "https://doi.org/10.1021/acsmedchemlett.1c00251", "target": "https://doi.org/10.1021/ci025599w"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/ci025599w"}]}
\ No newline at end of file \ No newline at end of file
verarbeitung/update_graph/connect_new_input.py
+ 111
− 42
View file @ b2326d85
...@@ -16,69 +16,138 @@ __status__ = "Production" ...@@ -16,69 +16,138 @@ __status__ = "Production"
import sys import sys
from pathlib import Path from pathlib import Path
from os import error from os import error
sys.path.append("../") sys.path.append("../")
from .import_from_json import input_from_json from .import_from_json import input_from_json
from verarbeitung.construct_new_graph.initialize_graph import initialize_nodes_list, complete_inner_edges from verarbeitung.construct_new_graph.initialize_graph import init_graph_construction
from verarbeitung.construct_new_graph.add_citations_rec import add_citations from verarbeitung.construct_new_graph.add_citations_rec import add_citations, get_cit_type_list, create_global_lists_cit
from verarbeitung.construct_new_graph.export_to_json import output_to_json
def find_furthermost_citations(node, old_search_depth, cit_type):
'''
:param node: node which is known but not from input group
:type node: Publication
def connect_old_and_new_input(json_file, new_doi_list, search_depth, search_height, test_var = False): :param old_search_depth: depth to search for references from old construction call
:type old_search_depth: int
:param cit_type: determines whether the function call is for a reference or citation
:type cit_type: String
function to find the furthermost citation/reference for given node which is from the same group
'''
citations_saved = get_cit_type_list(node, cit_type)
# group of node and old search depth/height determines how often the loop needs to be repeated
for depth in range(old_search_depth - abs(node.group)):
new_citations = []
for citation in citations_saved:
for cit_node in nodes:
if citation.doi_url == cit_node.doi_url:
for new_cit in get_cit_type_list(cit_node, cit_type):
for new_cit_node in nodes:
if new_cit.doi_url == new_cit_node.doi_url:
new_citations.append(node)
citations_saved = new_citations
# returns the references/citations which needs to be processed to complete contruction
return(citations_saved)
def complete_changed_group_nodes(inserted_nodes, old_search_depth, old_search_height, new_search_depth, new_search_height, test_var):
''' '''
:param json_file: json file with old graph :param inserted_nodes: list of nodes which are inserted to new input array
:type json_file: json file :type inserted_nodes: List[String]
:param new_doi_list: additional dois which has to be connected to the old graph :param old_search_depth: depth to search for references from old construction call
:type new_doi_list: list of strings :type old_search_depth: int
:param search_depth: depth to search for references :param old_search_height: height to search for citations from old construction call
:type search_depth: int :type old_search_height: int
:param search_height: height to search for citations :param new_search_depth: depth to search for references from new construction call
:type search_height: int :type new_search_depth: int
:param new_search_height: height to search for citations from new construction call
:type new_search_height: int
:param test_var: variable to differenciate between test and url call :param test_var: variable to differenciate between test and url call
:type test_var: boolean :type test_var: boolean
connetcs the old graph and the new input dois to a complete new graph completes the references and citations for nodes which were known in non input group
''' '''
global nodes, edges #changed_group_node_citations = []
nodes = [] #changed_group_node_references = []
edges = []
nodes, edges = input_from_json(json_file) # saves which nodes were handled because they were known before
handled_inserted_nodes = []
for node in nodes:
complete_changed_group_nodes(new_doi_list, search_depth, search_height, test_var) # moves known reference node to input and completes citations and references for this node
if (node.group < 0) and (node.doi_url in inserted_nodes):
node_citations = create_global_lists_cit(nodes, edges, node, 1, new_search_height, "Citation", test_var)
add_citations(nodes, edges, node_citations, 1, new_search_height, "Citation", test_var)
old_max_references = find_furthermost_citations(node, old_search_depth, "Reference")
add_citations(nodes, edges, old_max_references, old_search_depth, new_search_depth, "Reference", test_var)
node.group = 0
handled_inserted_nodes.append(node)
# initializes nodes/edges from input and gets a list with publication objects for citations and references returned # moves known citation node to input and completes citations and references for this node
references_obj_list, citations_obj_list = initialize_nodes_list(new_doi_list,search_depth, search_height, test_var) elif (node.group > 0) and (node.doi_url in inserted_nodes):
node_references = create_global_lists_cit(nodes, edges, node, 1, new_search_depth, "Reference", test_var)
add_citations(nodes, edges, node_references, 1, new_search_depth, "Reference", test_var)
old_max_citations = find_furthermost_citations(node, old_search_height, "Citation")
add_citations(nodes, edges, old_max_citations, old_search_height, new_search_height, "Citation", test_var)
# function calls to begin recursive processing up to max depth/height node.group = 0
add_citations(nodes, edges, citations_obj_list, 1, search_height, "Citation", test_var) handled_inserted_nodes.append(node)
add_citations(nodes, edges, references_obj_list, 1, search_depth, "Reference", test_var)
# adds edges between reference group and citation group of known publications return(handled_inserted_nodes)
complete_inner_edges(test_var)
# calls a skript to save nodes and edges of graph in .json file
output_to_json(nodes,edges, test_var)
return(nodes, edges) def connect_old_and_new_input(input_nodes_list, input_edges_list, inserted_nodes, old_search_depth, old_search_height, new_search_depth, new_search_height, test_var = False):
'''
:param input_nodes_list: list of nodes which are processed for new construction call
:type input_nodes_list: List[Publication]
:param input_edges_list: list of links between nodes from input_nodes_list.
:type input_edges_list: List[List[String,String]]
def complete_changed_group_nodes(new_doi_list, search_depth_max, search_height_max, test_var): :param inserted_nodes: list of nodes which are inserted to new input array
''' :type inserted_nodes: List[String]
work in progress
:param old_search_depth: depth to search for references from old construction call
:type old_search_depth: int
:param old_search_height: height to search for citations from old construction call
:type old_search_height: int
:param new_search_depth: depth to search for references from new construction call
:type new_search_depth: int
:param new_search_height: height to search for citations from new construction call
:type new_search_height: int
:param test_var: variable to differenciate between test and url call
:type test_var: boolean
completes the references and citations for nodes which were known in non input group
''' '''
changed_group_node_citations = [] global nodes, edges
changed_group_node_references = [] nodes = input_nodes_list
edges = input_edges_list
for node in nodes: handled_inserted_nodes = complete_changed_group_nodes(inserted_nodes, old_search_depth, old_search_height, new_search_depth, new_search_height, test_var)
if (node.group < 0) and (node.doi in new_doi_list):
node.group = "input"
# copy all nodes from inserted_nodes to new node, if node is not in handled_inserted_nodes
not_handled_inserted_nodes = [node for node in inserted_nodes if node not in handled_inserted_nodes]
elif (node.group > 0) and (node.doi in new_doi_list): # initializes nodes/edges from input and gets a list with publication objects for citations and references returned
node.group = "input" #references_obj_list, citations_obj_list = initialize_nodes_list(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var)
# function calls to begin recursive processing up to max depth/height
#add_citations(nodes, edges, citations_obj_list, 1, new_search_height, "Citation", test_var)
#add_citations(nodes, edges, references_obj_list, 1, new_search_depth, "Reference", test_var)
init_graph_construction(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var = test_var, input_nodes = nodes, input_edges = edges)
verarbeitung/update_graph/update_depth.py
+ 2
− 0
View file @ b2326d85
...@@ -133,6 +133,8 @@ def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var): ...@@ -133,6 +133,8 @@ def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
# adds edges between reference group and citation group of known publications # adds edges between reference group and citation group of known publications
complete_inner_edges() complete_inner_edges()
return(old_depth, old_height)
verarbeitung/update_graph/update_graph.py
+ 4
− 4
View file @ b2326d85
# -*- coding: utf-8 -*- 1# -*- coding: utf-8 -*-
""" """
Functions to update a graph representing citations between multiple ACS/Nature journals Functions to update a graph representing citations between multiple ACS/Nature journals
...@@ -20,6 +20,7 @@ sys.path.append("../../") ...@@ -20,6 +20,7 @@ sys.path.append("../../")
from input.publication import Publication from input.publication import Publication
from verarbeitung.get_pub_from_input import get_pub from verarbeitung.get_pub_from_input import get_pub
from verarbeitung.construct_new_graph.initialize_graph import init_graph_construction
from .Knoten_Vergleich import doi_listen_vergleichen from .Knoten_Vergleich import doi_listen_vergleichen
from .delete_nodes_edges import delete_nodes_and_edges from .delete_nodes_edges import delete_nodes_and_edges
from .connect_new_input import connect_old_and_new_input from .connect_new_input import connect_old_and_new_input
...@@ -85,7 +86,6 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes ...@@ -85,7 +86,6 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
# gets information from previous cunstruction call # gets information from previous cunstruction call
old_obj_input_list , old_edges_list = input_from_json(json_file) old_obj_input_list , old_edges_list = input_from_json(json_file)
print(type(old_edges_list[1]))
# one global list to save the process of removing unneeded publications and one to save valid edges # one global list to save the process of removing unneeded publications and one to save valid edges
global processed_list, valid_edges global processed_list, valid_edges
...@@ -104,9 +104,9 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes ...@@ -104,9 +104,9 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
if (len(deleted_nodes) > 0): if (len(deleted_nodes) > 0):
processed_list, valid_edges = delete_nodes_and_edges(processed_list, common_nodes, old_edges_list) processed_list, valid_edges = delete_nodes_and_edges(processed_list, common_nodes, old_edges_list)
update_depth(processed_list, valid_edges, search_depth, search_height, test_var) old_search_depth, old_search_height = update_depth(processed_list, valid_edges, search_depth, search_height, test_var)
if (len(inserted_nodes) > 0): if (len(inserted_nodes) > 0):
connect_old_and_new_input(json_file, inserted_nodes, search_depth, search_height, test_var) connect_old_and_new_input(processed_list, valid_edges, inserted_nodes, old_search_depth, old_search_height, search_depth, search_height, test_var)
return(processed_list, valid_edges) return(processed_list, valid_edges)
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