Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
P
ProMod3
Manage
Activity
Members
Plan
Jira
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Deploy
Releases
Container registry
Model registry
Analyze
Contributor analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
schwede
ProMod3
Commits
2451a216
Commit
2451a216
authored
9 years ago
by
Gerardo Tauriello
Browse files
Options
Downloads
Patches
Plain Diff
SCHWED-876
: Refactored reconstruct_sidechain to add consider_ligands flag
parent
a76f54cb
No related branches found
No related tags found
No related merge requests found
Changes
2
Expand all
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
sidechain/doc/index.rst
+1
-37
1 addition, 37 deletions
sidechain/doc/index.rst
sidechain/pymod/_reconstruct_sidechains.py
+360
-262
360 additions, 262 deletions
sidechain/pymod/_reconstruct_sidechains.py
with
361 additions
and
299 deletions
sidechain/doc/index.rst
+
1
−
37
View file @
2451a216
...
@@ -20,43 +20,7 @@ function:
...
@@ -20,43 +20,7 @@ function:
.. literalinclude:: ../../../tests/doc/scripts/sidechain_reconstruct.py
.. literalinclude:: ../../../tests/doc/scripts/sidechain_reconstruct.py
.. method:: Reconstruct(prot, keep_sidechains=False, build_disulfids, \
.. autofunction:: Reconstruct
rotamer_model="frm", consider_hbonds=True, \
rotamer_library=None)
The function takes a structure and reconstructs its sidechains given the input
parameters.
:param prot: Structure for sidechain reconstruction. Note, that the
sidechain reconstruction gets directly applied on the
structure itself.
:param keep_sidechains: Flag, whether complete sidechains in *prot* (i.e.
containing all required atoms) should be kept rigid
and directly be added to the frame.
:param build_disulfids: Flag, whether possible disulfid bonds should be
searched. If a disulfid bond is found, the two
participating cysteins are fixed and added to
the frame.
:param rotamer_model: Rotamer model to be used, can either be "frm" or "rrm"
:param consider_hbonds: Flag, whether hbonds should be evaluated in the energy
function. If set to False, no hydrogens will be built
when building rotamers and frame and the **add_polar_hydrogens**
flag won't have any consequences.
:param rotamer_library: A rotamer library to extract the
rotamers from.
:type prot: :class:`ost.mol.EntityHandle`
:type keep_sidechains: :class:`bool`
:type build_disulfids: :class:`bool`
:type rotamer_model: :class:`str`
:type consider_hbonds: :class:`bool`
:type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
Sidechain Module Functionality
Sidechain Module Functionality
...
...
This diff is collapsed.
Click to expand it.
sidechain/pymod/_reconstruct_sidechains.py
+
360
−
262
View file @
2451a216
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment