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singa
:leaves: SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.
MIT License
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small fixes and dynamic atom name handling
#96
fkaiserbio
closed
1 year ago
0
VoronoiRelaxation
#95
Znbne
opened
3 years ago
2
RCSB CIF file parsing fails
#94
fkaiserbio
closed
4 years ago
4
Feature/mcs
#93
fkaiserbio
closed
4 years ago
0
Ligands parsed by LigandParserService and PDB HETID show wrong connectivity
#92
fkaiserbio
closed
4 years ago
2
Develop/graph visualizer
#91
fkaiserbio
closed
4 years ago
1
implement BioLiP filter
#90
fkaiserbio
opened
5 years ago
0
sifts mapping should use the rest api
#89
cleberecht
opened
5 years ago
1
add support for mmCIF
#88
fkaiserbio
opened
5 years ago
1
InChIKeyProviderTest.fetchWithPubChem() never terminates
#87
fkaiserbio
closed
5 years ago
2
implement canonical SMILES generation from MoleculeGraphs
#86
fkaiserbio
opened
5 years ago
4
SmilesParser fails to parse simple smiles
#85
fkaiserbio
closed
5 years ago
2
implement touching edges for graph nodes
#84
fkaiserbio
closed
5 years ago
3
add support for UniProt variants annotations
#83
fkaiserbio
closed
5 years ago
4
RISubgraphFinder has problems with directed graphs
#82
cleberecht
closed
5 years ago
2
implement sampling of suitable self-similarity value for affinity propagation
#81
fkaiserbio
closed
4 years ago
1
make SiNGA citable via DOI
#80
fkaiserbio
closed
6 years ago
1
Ligands created from LeafSkeletons should be automatically annotated as hetero atom
#79
fkaiserbio
closed
6 years ago
1
implement quaternion superimposition
#78
fkaiserbio
closed
6 years ago
2
add conversion between structure model and MoleculeGraph
#77
fkaiserbio
closed
6 years ago
2
implement fallback strategy for mmtf parsing
#76
cleberecht
opened
6 years ago
0
add support for B-factors
#75
fkaiserbio
closed
4 years ago
1
parsing specific chains in MMTF format is ignored
#74
fkaiserbio
closed
6 years ago
1
alternative positions for MMTF parsing
#73
fkaiserbio
closed
6 years ago
1
MMTF dependencies are not properly exported when module is built
#72
fkaiserbio
closed
6 years ago
1
implement Kuhn-Munkres algorithm to find ideal alignment
#71
fkaiserbio
closed
6 years ago
0
implement rank-biased overlap
#70
fkaiserbio
closed
6 years ago
0
implement PS-score for assessment of binding site similarity
#69
fkaiserbio
closed
7 years ago
1
implement subgraph matching
#68
fkaiserbio
closed
6 years ago
1
retrieval of prototype amino acid structures failes
#67
fkaiserbio
closed
7 years ago
1
parse PDB ligand code based on InChI Key
#66
fkaiserbio
closed
5 years ago
0
Implement RMeSD
#65
fkaiserbio
closed
4 years ago
1
identifiers should be features too
#64
cleberecht
closed
6 years ago
1
batch parsing of local structures is missing the possibility to use a list of PDB identifiers
#63
fkaiserbio
closed
7 years ago
1
implement off-memory caching for consensus alignment
#62
fkaiserbio
closed
4 years ago
1
implement triangular matrix parsing for unlabeled
#61
fkaiserbio
closed
5 years ago
2
integrate parsing of MMTF structures
#60
fkaiserbio
closed
6 years ago
2
add option for PDB parser to skip ligand information retreival
#59
fkaiserbio
closed
7 years ago
1
local PDB parser returns empty structure
#58
fkaiserbio
closed
7 years ago
1
consensus alignment non-functional
#57
fkaiserbio
closed
7 years ago
1
implement ranges / intervall mathmatics
#56
cleberecht
closed
7 years ago
1
parameters need to be handled more elaboratley
#55
cleberecht
closed
7 years ago
1
assignment rules can also be applied to parameters
#54
cleberecht
closed
5 years ago
1
handle assignment rules
#53
cleberecht
closed
7 years ago
1
implement binding-site similarity score for Fit3DS
#52
fkaiserbio
closed
7 years ago
1
infer structure name from file name
#51
cleberecht
closed
7 years ago
1
naming convention for Fit3Ds alignments can be arbitrary
#50
fkaiserbio
closed
7 years ago
1
prevent negative value overflow by benchmarking timestepsize
#49
cleberecht
closed
7 years ago
2
referenced functions in SBML files are not considered
#48
cleberecht
closed
7 years ago
1
implement correct usage of global sbml parameters
#47
cleberecht
closed
7 years ago
1
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