Merge pull request #45 from nanovis/q_scores

GPU Q-scores and `dfit` cmd preview and misc

.gitignore

@@ -13,3 +13,5 @@ dev_data/output_old/*
 !dev_data/output/dev_comp_domain_fit_3_domains_10s20q_new_q
 case_study_data
 run
+/dev_data/input/domain_fit_demo_3domains/subunits_cif_test
+*.npz

Reproduce.md

@@ -13,7 +13,9 @@ This guide is to reproduce Fig. 4 of our paper.
 
 1. Download [DiffFit-0.6.2-py3-none-any.whl](https://github.com/nanovis/DiffFit/releases/download/v0.6.2/DiffFit-0.6.2-py3-none-any.whl)
 2. Follow the [installation guide](https://github.com/nanovis/DiffFit?tab=readme-ov-file#install) 
-3. Download the [repository](https://github.com/nanovis/DiffFit/archive/refs/heads/main.zip) and unzip it to Desktop
+3. Download the [repository](https://github.com/nanovis/DiffFit/archive/refs/heads/main.zip) 
+   and unzip it to your working directory 
+   (which is your Desktop if you are on Windows or your home folder if you are on Linux).
 4. Open ChimeraX, launch DiffFit, go to the `Settings` tab, change `Fit atoms:` to `All atoms`. 
 5. Go to the `Disk` tab, set the parameters as below:
    1. Target Volume: `DiffFit-main\dev_data\input\domain_fit_demo_3domains\density2.mrc`

bundle_info.xml

@@ -30,6 +30,7 @@ will be displayed without the ChimeraX- prefix.
   <Dependencies>
     <Dependency name="ChimeraX-Core" version="~=1.1"/>
     <Dependency name="ChimeraX-UI" version="~=1.0"/>
+    <Dependency name="ChimeraX-QScore" version="==1.1"/>
     <Dependency name="torch" version="==2.2.1"/>
     <Dependency name="biopython" version="==1.83"/>
     <Dependency name="mrcfile" version="==1.5.0"/>
@@ -48,6 +49,14 @@ will be displayed without the ChimeraX- prefix.
     <!-- Register a graphical interface tool -->
     <ChimeraXClassifier>ChimeraX :: Tool :: DiffFit ::
       Volume Data :: Differentiable Fit in Map</ChimeraXClassifier>
+
+    <ChimeraXClassifier>ChimeraX :: Command :: dfit :: General ::
+      Fit a single structure into a volume map</ChimeraXClassifier>
+    <ChimeraXClassifier>ChimeraX :: Command :: dfit disk :: General ::
+      Fit a list of structures from disk into a volume map</ChimeraXClassifier>
+    <ChimeraXClassifier>ChimeraX :: Command :: dfit path :: General ::
+      Manipulate the paths in DiffFit results</ChimeraXClassifier>
+
   </Classifiers>
 
 </BundleInfo>