Activity for Lina Humbeck
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Lina Humbeck created ticket #111
Option for calculating the Cloud View based on either the scaffolds or the molecules
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Combination of scaffolds and hierarchical clustering
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I tried it a couple of times with the newest version (2.6.3) and everything worked like expected.
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The number of rings was set to two. But after "Export current view" also other scaffolds...
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It is somehow strange. The Minimap changes but only if the layout is updated, e.g.,...
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hang-up during import of multiple sdf files
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We can't just omit the charge in the SMILES. In easier cases it would be possible...
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Give molecule name when reporting „same SMILES already imported“
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Set handling of charges
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It seems that it is fine now. 62967982_4 and 62967982_5 are SMILES that correspond...
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Backslashes in SMILES ignored
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Right that was our intention. This is also helpful if the user doesn't want or isn't...
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To be more flexible it should be view specific. Maybe it is possible to implement...
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I think it would be useful for all views which depict scaffolds. There should be...
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Scaffold Tree export settings
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change node background color in Tree Map and Cloud View
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For example the Tree Map would be clearer if one would be able to restrict the scaffolds...
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I don't know. After clicking "Update" everything was fine. The cloud of a larger...
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cloud view: overlap with inflate and push layout
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plot view: update to adjust to other views
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import: merging: keep highest/lowest value
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color gradient: options for distribution, e.g. logarithmic
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calculate properties: simple operations on imported properties
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plot view: calculate correlation correlation coefficient
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global filter like in the cloud view
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property mappings: modus as accumulation function
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Right, I mean the dendrogram view with an attached table. I would prefer to have...
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Sorry, I forgot to mention that there is a mapping for the edge color. The color...
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Dendrogram depict pseudo-ancestors for molecules
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There is one more use case for an unique molecule id which came up recently. Besides...
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Scaffold Tree, property mapping edge strange color gradient
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Property Mappings: enable copying of color codes
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Heat map and table view: cluster-id as exportable property
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heat map csv export: sort according to view
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A further nice addition would be to set the recent directory to the current working...
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Image export for HeatMap
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I like the solution 2. Two things I miss in the current gradient settings are: configuration...
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dialog for (sub)set reduction before time consuming procedures
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dialog for (sub)set reduction before time consuming procedures
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hide and move columns and rows in table view
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transposing heat map
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progress bar for layout update process
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transfer clustering/sorting to table view
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misleading error message
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The outcome of your observation is the same like in bug #190. Maybe the two possible...
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To increase the "wait_timeout" would be a solution from the user site. What about...
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To increase the "wait_timeout" would be a solution from the user site. What about...
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To increase the "wait_timeout" would be a solution from the user site. What about...
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To increase the "wait_timeout" would be a solution from the user site. What about...
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To increase the "wait_timeout" would be a solution from the user site. What about...
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I used scaffold-hunter-release-2.5.0-29-g60e5b48 which should be basically release...
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Index out of bounds when scrolling in dataset/tree selection
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It seems that the normal MySQL server is not able to handle log files >= 4 GB. This...
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SH closes without error
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I am also unable to delete some of my bigger dataset. At the beginning the import...
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size needed estimation
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I got the following error messages when starting from the terminal: Caused by: java.lang.reflect.InvocationTargetException...
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The SMILES is fine. There is a rule for the electron pair, which implicitly represent...
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How do you create the canonical chiral SMILES? Maybe we can ask the person how created...
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It is a quite puzzling issue. I think the SMILES miss the representation of the electron...
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The molecule shown from CDK 1.4 is not the same like the one from CDK 1.5. But anyway...
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I overlooked that the SMILES for the molecule generated from CDK 1.5 was wrong both...
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Unfortunately, I can't reproduce this. I visualized the scaffold in the original...
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For the molecule SMILES CDK 1.5 consider chirality, but it seems to be unable to...
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additional fingerprint ECFP4
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I tried the new SH version 2.5. a few times and the issue was there once. I will...
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Java Version: 1.8. SH Version: r2931M
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no loading of recently created dataset/tree/session
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invisible newly created dataset
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I guess for most purposes the work-around would be sufficient. Things to keep in...
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Yes, exactly. The scaffold assignment is correct but the arrangement of the scaffold...
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It would be nice to see it directly in SH. Maybe it is possible to write <= before...
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I like your two workarounds, would it be possible to also combine this two. Like...
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session export
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I created the scaffolds by using the default scaffold generation rules. The sdf of...
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unclear interval borders
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status of option "Show Scaffold Molecules" not saved
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changed TreeMap after saved session reopening
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wrong scaffold representation/creation
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Advanced Open file dialog options
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Scrolling in Table View with arrow keys
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Mirroring was only an additional suggestion because I use it sometimes for image...
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Yes, you are right! That is what I mean. I just thought you were writing about the...
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I think we're talk about different things. Your suggestions to alter the change of...
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chiral Scaffold-SMILES
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image without chirality information
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absence of chiral representation
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not intuitive zoom
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Overlapping parts of the molecule in reprensentation
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Extension of supported import file formats
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Image export
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Free rotatability of Scaffold Tree
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Database error during import
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