Nucleic Acid builder and general improvements (#354)

Fixes #102 #351 Migrating support from Incentive for the following: - Nucleic Acid builder in the Builder panel (Jarrett Johnson @JarrettSJohnson) - `fnab` command to build nucleic acid chains by sequence (Jarrett Johnson @JarrettSJohnson) - Improvements to nucleic acid building from native structures (Thomas Stewart @TstewDev) - highlight attachment points for improved usability (Thomas Holder @speleo3) Co-authored-by: Jarrett Johnson <jarrett.johnson@schrodinger.com> Co-authored-by: Thomas Stewart <thomas.stewart@schrodinger.com> Co-authored-by: Thomas Holder <thomas@thomas-holder.de>
schrodinger · Apr 8, 2024 · 246e0a4 · 246e0a4
1 parent c33c916
commit 246e0a4
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Showing 23 changed files with 971 additions and 54 deletions.
diff --git a/data/chempy/fragments/atpA.pkl b/data/chempy/fragments/atpA.pkl
diff --git a/data/chempy/fragments/atpB.pkl b/data/chempy/fragments/atpB.pkl
diff --git a/data/chempy/fragments/atp_ttpA.pkl b/data/chempy/fragments/atp_ttpA.pkl
diff --git a/data/chempy/fragments/atp_ttpB.pkl b/data/chempy/fragments/atp_ttpB.pkl
diff --git a/data/chempy/fragments/ctpA.pkl b/data/chempy/fragments/ctpA.pkl
diff --git a/data/chempy/fragments/ctpB.pkl b/data/chempy/fragments/ctpB.pkl
diff --git a/data/chempy/fragments/ctp_gtpA.pkl b/data/chempy/fragments/ctp_gtpA.pkl
diff --git a/data/chempy/fragments/ctp_gtpB.pkl b/data/chempy/fragments/ctp_gtpB.pkl
diff --git a/data/chempy/fragments/gtpA.pkl b/data/chempy/fragments/gtpA.pkl
diff --git a/data/chempy/fragments/gtpB.pkl b/data/chempy/fragments/gtpB.pkl
diff --git a/data/chempy/fragments/gtp_ctpA.pkl b/data/chempy/fragments/gtp_ctpA.pkl
diff --git a/data/chempy/fragments/gtp_ctpB.pkl b/data/chempy/fragments/gtp_ctpB.pkl
diff --git a/data/chempy/fragments/ttpA.pkl b/data/chempy/fragments/ttpA.pkl
diff --git a/data/chempy/fragments/ttpB.pkl b/data/chempy/fragments/ttpB.pkl
diff --git a/data/chempy/fragments/ttp_atpA.pkl b/data/chempy/fragments/ttp_atpA.pkl
diff --git a/data/chempy/fragments/ttp_atpB.pkl b/data/chempy/fragments/ttp_atpB.pkl
diff --git a/data/chempy/fragments/utpA.pkl b/data/chempy/fragments/utpA.pkl
diff --git a/modules/pmg_qt/builder.py b/modules/pmg_qt/builder.py
diff --git a/modules/pmg_tk/skins/normal/builder.py b/modules/pmg_tk/skins/normal/builder.py
@@ -345,7 +345,7 @@ def combine(self):
     def get_panel(self):
         if self.getRepeating():
             return [
-                [ 1, 'Attaching Multiple Fragmnts',''],
+                [ 1, 'Attaching Multiple Fragments',''],
                 [ 2, 'Create As New Object','cmd.get_wizard().create_new()'],                
                 [ 2, 'Combine w/ Existing Object','cmd.get_wizard().combine()'],                
                 [ 2, 'Done','cmd.set_wizard()'],

diff --git a/modules/pymol/api.py b/modules/pymol/api.py
@@ -259,7 +259,8 @@
       vdw_fit
 
 from .editor import \
-      fab
+      fab,                \
+      fnab
 
 from .computing import \
       clean

diff --git a/modules/pymol/editor.py b/modules/pymol/editor.py
diff --git a/modules/pymol/keywords.py b/modules/pymol/keywords.py
@@ -83,6 +83,7 @@ def get_command_keywords(self_cmd=cmd):
         'extract'       : [ self_cmd.extract           , 0 , 0 , ''  , parsing.STRICT ],
         'exec'          : [ self_cmd.python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'fab'           : [ self_cmd.fab               , 0 , 0 , ''  , parsing.STRICT ],
+        'fnab'          : [ self_cmd.fnab              , 0 , 0 , ''  , parsing.STRICT ],
         'feedback'      : [ self_cmd.feedback          , 0,  0 , ''  , parsing.STRICT ],
         'fetch'         : [ self_cmd.fetch             , 0,  0 , ''  , parsing.STRICT ],
         'fit'           : [ self_cmd.fit               , 0 , 0 , ''  , parsing.STRICT ],

diff --git a/testing/tests/api/build.py b/testing/tests/api/build.py
@@ -3,7 +3,6 @@
 """
 from pymol import cmd, testing
 
-@testing.requires('incentive')
 @testing.requires_version('2.3')
 class TestNucBuilder(testing.PyMOLTestCase):
     def testCanInit(self):
-Original file line number
+Diff line change
@@ Expand Up / @@ -259,7 +259,8 @@ @@
           vdw_fit
     from .editor import \
-          fab
+          fab,                \
+          fnab
     from .computing import \
           clean
@@ Expand Down @@