Recent ProDy updates to Cavi-Finder branch

.github/workflows/main.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["2.7", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2

README.rst

@@ -41,7 +41,7 @@ ProDy has a modular structure with modules inside various subpackages.
 
 The main ones are:
 
-- :mod:`~prody.atomic`` handles all :class:`~prody.atomic.Atomic` objects including :class:`~prody.atomic.AtomGroup` and :class:`.Selection`
+- :mod:`~prody.atomic` handles all :class:`~prody.atomic.Atomic` objects including :class:`~prody.atomic.AtomGroup` and :class:`.Selection`
 
 - :mod:`~prody.database` interfaces with databases such as CATH, DALI, UniProt and Pfam
 

prody/database/dali.py

@@ -515,7 +515,7 @@ def getTitle(self):
 
         return self._title
 
-def daliFilterMultimer(atoms, dali_rec, n_chains=None):
+def daliFilterMultimer(atoms, dali_rec, n_chains=None, reverse=False):
     """
     Filters multimers to only include chains with Dali mappings.
 
@@ -524,6 +524,14 @@ def daliFilterMultimer(atoms, dali_rec, n_chains=None):
 
     :arg dali_rec: the DaliRecord object with which to filter chains
     :type dali_rec: :class:`.DaliRecord`
+
+    :arg n_chains: the number of chains in multimers to keep
+        Default is None, keeping all multimers
+    :arg n_chains: int
+
+    :arg reverse: whether to reverse filtering to exclude by n_chain
+        Default is False
+    :type reverse: bool
     """
     if not isinstance(atoms, Atomic):
         raise TypeError("atoms should be an Atomic object")
@@ -535,6 +543,12 @@ def daliFilterMultimer(atoms, dali_rec, n_chains=None):
     except:
         raise AttributeError("Dali Record does not have any data yet. Please run fetch.")
 
+    if not isinstance(n_chains, (int, type(None))):
+        raise TypeError('n_chains should be None or an integer')
+
+    if not isinstance(reverse, bool):
+        raise TypeError('reverse should be a Boolean')
+
     numChains = 0
     atommap = None
     for i, chain in enumerate(atoms.iterChains()):
@@ -546,17 +560,32 @@ def daliFilterMultimer(atoms, dali_rec, n_chains=None):
             else:
                 atommap += chain
 
-    if n_chains is None or numChains == n_chains:
-        return atommap
-    else:
-        return None
+    if n_chains is None or \
+        not reverse and numChains == n_chains or \
+            reverse and numChains != n_chains:
+        return atommap       
+    return None
 
-def daliFilterMultimers(structures, dali_rec, n_chains=None):
+def daliFilterMultimers(structures, dali_rec, n_chains=None, reverse=False):
     """A wrapper for daliFilterMultimer to apply to multiple structures.
+
+    :arg structures: a list of :class:`.Atomic` objects to be filtered
+    :type structures: list
+
+    :arg dali_rec: the DaliRecord object with which to filter chains
+    :type dali_rec: :class:`.DaliRecord`
+
+    :arg n_chains: the number of chains in multimers to keep
+        Default is None, keeping all multimers
+    :arg n_chains: int
+
+    :arg reverse: whether to reverse filtering to exclude by n_chain
+        Default is False
+    :type reverse: bool
     """
     dali_ags = []
     for entry in structures:
-        result = daliFilterMultimer(entry, dali_rec, n_chains)
+        result = daliFilterMultimer(entry, dali_rec, n_chains, reverse)
         if result is not None:
             dali_ags.append(result)
     return dali_ags

prody/dynamics/__init__.py

@@ -119,6 +119,14 @@
 
   * :class:`.AdaptiveANM` - generate transitions between two conformers using best overlapping modes 
 
+ENM-MD hybrid methods
+===================
+
+The following classes and functions can be used to generate conformers using ENM-MD hybrid methods:
+
+  * :class:`.ClustENM` - generate conformers by exploring combinations of modes and clustering, using minimisation and optionally MD
+  * :function:`.ANMD` - generate conformers by traversing a number of individual modes, applying minimisation to each conformer
+
 Essential Site Scanning Analysis (ESSA)
 ========================================
 
@@ -367,3 +375,7 @@
 from . import logistic
 from .logistic import *
 __all__.extend(logistic.__all__)
+
+from . import anmd
+from .anmd import *
+__all__.extend(anmd.__all__)