Merge pull request #106 from peastman/structure

Removed the remaining internal dependence on PdbStructure

pdbfixer/pdbfixer.py

@@ -73,6 +73,20 @@ proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR'
 rnaResidues = ['A', 'G', 'C', 'U', 'I']
 rnaResidues = ['A', 'G', 'C', 'U', 'I']
 dnaResidues = ['DA', 'DG', 'DC', 'DT', 'DI']
 dnaResidues = ['DA', 'DG', 'DC', 'DT', 'DI']
 
 
+class Sequence(object):
+    """Sequence holds the sequence of a chain, as specified by SEQRES records."""
+    def __init__(self, chainId, residues):
+        self.chainId = chainId
+        self.residues = residues
+
+class ModifiedResidue(object):
+    """ModifiedResidue holds information about a modified residue, as specified by a MODRES record."""
+    def __init__(self, chainId, number, residueName, standardName):
+        self.chainId = chainId
+        self.number = number
+        self.residueName = residueName
+        self.standardName = standardName
+
 def _overlayPoints(points1, points2):
 def _overlayPoints(points1, points2):
     """Given two sets of points, determine the translation and rotation that matches them as closely as possible.
     """Given two sets of points, determine the translation and rotation that matches them as closely as possible.
 
 
@@ -214,10 +228,11 @@ class PDBFixer(object):
         if len(atoms)==0:
         if len(atoms)==0:
             raise Exception("Structure contains no atoms.")
             raise Exception("Structure contains no atoms.")
             
             
-        self.structure = structure
-        self.pdb = app.PDBFile(structure)
-        self.topology = self.pdb.topology
-        self.positions = self.pdb.positions
+        pdb = app.PDBFile(structure)
+        self.topology = pdb.topology
+        self.positions = pdb.positions
+        self.sequences = [Sequence(s.chain_id, s.residues) for s in structure.sequences]
+        self.modifiedResidues = [ModifiedResidue(r.chain_id, r.number, r.residue_name, r.standard_name) for r in structure.modified_residues]
         
         
         # Load the templates.
         # Load the templates.
         
         
@@ -369,7 +384,7 @@ class PDBFixer(object):
     
     
     def _computeResidueCenter(self, residue):
     def _computeResidueCenter(self, residue):
         """Compute the centroid of a residue."""
         """Compute the centroid of a residue."""
-        return unit.sum([self.pdb.positions[atom.index] for atom in residue.atoms()])/len(list(residue.atoms()))
+        return unit.sum([self.positions[atom.index] for atom in residue.atoms()])/len(list(residue.atoms()))
     
     
     def _addMissingResiduesToChain(self, chain, residueNames, startPosition, endPosition, loopDirection, orientTo, newAtoms, newPositions, firstIndex):
     def _addMissingResiduesToChain(self, chain, residueNames, startPosition, endPosition, loopDirection, orientTo, newAtoms, newPositions, firstIndex):
         """Add a series of residues to a chain."""
         """Add a series of residues to a chain."""
@@ -446,9 +461,8 @@ class PDBFixer(object):
             chainIndices = list()
             chainIndices = list()
         if chainIds != None:
         if chainIds != None:
             # Add all chains that match the selection to the list.
             # Add all chains that match the selection to the list.
-            chain_id_list = [c.chain_id for c in self.structure.models[0].chains]
-            for (chainNumber, chainId) in enumerate(chain_id_list):
-                if chainId in chainIds:
+            for (chainNumber, chain) in enumerate(allChains):
+                if chain.id in chainIds:
                     chainIndices.append(chainNumber)
                     chainIndices.append(chainNumber)
             # Ensure only unique entries remain.
             # Ensure only unique entries remain.
             chainIndices = list(set(chainIndices))
             chainIndices = list(set(chainIndices))
@@ -495,9 +509,9 @@ class PDBFixer(object):
         
         
         chainSequence = {}
         chainSequence = {}
         chainOffset = {}
         chainOffset = {}
-        for sequence in self.structure.sequences:
+        for sequence in self.sequences:
             for chain in chains:
             for chain in chains:
-                if chain.id != sequence.chain_id:
+                if chain.id != sequence.chainId:
                     continue
                     continue
                 if chain in chainSequence:
                 if chain in chainSequence:
                     continue
                     continue
@@ -553,7 +567,7 @@ class PDBFixer(object):
         
         
         # Now add ones based on MODRES records.
         # Now add ones based on MODRES records.
         
         
-        modres = dict(((m.chain_id, str(m.number), m.residue_name), m.standard_name) for m in self.structure.modified_residues)
+        modres = dict(((m.chainId, str(m.number), m.residueName), m.standardName) for m in self.modifiedResidues)
         for chain in self.topology.chains():
         for chain in self.topology.chains():
             for residue in chain.residues():
             for residue in chain.residues():
                 key = (chain.id, residue.id, residue.name)
                 key = (chain.id, residue.id, residue.name)
@@ -603,7 +617,7 @@ class PDBFixer(object):
             self.positions = modeller.positions
             self.positions = modeller.positions
 
 
 
 
-    def applyMutations(self, mutations, chain_id, which_model=0):
+    def applyMutations(self, mutations, chain_id):
         """Apply a list of amino acid substitutions to make a mutant protein.
         """Apply a list of amino acid substitutions to make a mutant protein.
 
 
         Parameters
         Parameters
@@ -614,8 +628,6 @@ class PDBFixer(object):
             alanine 133 to glycine.  
             alanine 133 to glycine.  
         chain_id : str
         chain_id : str
             String based chain ID of the single chain you wish to mutate.
             String based chain ID of the single chain you wish to mutate.
-        which_model : int, default = 0
-            Which model to use in the pdb structure.
 
 
         Notes
         Notes
         -----
         -----
@@ -644,10 +656,11 @@ class PDBFixer(object):
         index_to_old_name = dict((r.index, r.name) for r in self.topology.residues())
         index_to_old_name = dict((r.index, r.name) for r in self.topology.residues())
         index_to_new_residues = {}
         index_to_new_residues = {}
         
         
-        chain_id_to_chain_number = dict((c.chain_id, k) for k, c in enumerate(self.structure.models[which_model].chains))
+        chain_id_to_chain_number = dict((c.id, k) for k, c in enumerate(self.topology.chains()))
         chain_number = chain_id_to_chain_number[chain_id]
         chain_number = chain_id_to_chain_number[chain_id]
+        chain = list(self.topology.chains())[chain_number]
         
         
-        resSeq_to_index = dict((r.number, k) for k, r in enumerate(self.structure.models[which_model].chains[chain_number]))
+        resSeq_to_index = dict((int(r.id), k) for k, r in enumerate(chain.residues()))
         
         
         for mut_str in mutations:
         for mut_str in mutations:
             old_name, resSeq, new_name = mut_str.split("-")
             old_name, resSeq, new_name = mut_str.split("-")