Support nonstandard residues (#296)

* Can add templates for new residues

* Added documentation on templates

* Bug fixes

Author: peastman

Manual.html

@@ -281,5 +281,34 @@ <h3>Examples</h3>
 <span style="color:grey">fixer.replaceNonstandardResidues()</span>
 </pre></tt>
 
+<h3>Nonstandard Residues</h3>
+
+PDBFixer knows how to build all the standard amino acids and nucleotides.  If you want to apply it to other residues, you need to tell it how.  This is done by defining templates.
+
+A template is a description of a residue: what atoms it contains, how they are bonded to each other, and what conformation they take on.  For residues defined in the PDB Chemical Component Dictionary, you can simply tell PDBFixer to download the definition of whatever residue you need.  For example, if you want to model a protein containing a selenocysteine (PDB code SEC), call
+
+<tt><pre>
+fixer.downloadTemplate('SEC')
+</pre></tt>
+
+Now you can call other methods such as <tt>findMissingAtoms()</tt>, <tt>addMissingAtoms()</tt>, and <tt>addMissingHydrogens()</tt> in the usual way.  PDBFixer will fix problems in the SEC residue exactly as it does for standard ones.
+<p/>
+If your structure contains molecules or residues that are not present in the PDB Chemical Component Dictionary, you can still add templates for them, but you need to define them yourself.  This is done by calling <tt>registerTemplate()</tt>.  It takes two required arguments: an OpenMM Topology object describing the structure of the residue, and a list of positions describing a typical conformation of the residue.  These can be easily obtained from, for example, a PDB or PDBx/mmCIF file containing just the single residue.
+
+<tt><pre>
+pdbx = PDBxFile('MOL.cif')
+fixer.registerTemplate(pdbx.topology, pdbx.positions)
+</pre></tt>
+
+For residues that appear as part of larger molecules rather than in isolation, you need to provide one more piece of information: which atoms should only be present in terminal residues.  For example, a C-terminal amino acid is capped with OXT and HXT atoms, but these atoms are omitted when the residue appears in the middle of a chain and is bonded to another residue.  Likewise, the nitrogen in an N-terminal amino acid has two hydrogens attached to it (H and H2), but when it appears in the middle of a chain and the nitrogen is bonded to another residue, the H2 hydrogen is omitted.  You can pass a third argument containing a list of boolean flags for each atom, specifying which ones should be omitted from non-terminal residues.
+
+<tt><pre>
+pdbx = PDBxFile('RES.cif')
+terminal = [atom.name in ('H2', 'OXT', 'HXT') for atom in pdbx.topology.atoms()]
+fixer.registerTemplate(pdbx.topology, pdbx.positions, terminal)
+</pre></tt>
+
+Strictly speaking, it is the bonds that matter, not the position in the chain.  For example, the sulfur in a CYS residue has a hydrogen that must be omitted when it forms a disulfide bond to another residue.  What matters is whether the sulfur has a bond connecting it to another residue, not the position of the CYS residue in its chain.
+
 </body>
 </html>

pdbfixer/pdbfixer.py

@@ -6,7 +6,7 @@
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2013-2023 Stanford University and the Authors.
+Portions copyright (c) 2013-2024 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -54,6 +54,7 @@
 import os
 import os.path
 import math
+from collections import defaultdict
 
 from pkg_resources import resource_filename
 
@@ -98,6 +99,15 @@ def __init__(self, chainId, number, residueName, standardName):
         self.residueName = residueName
         self.standardName = standardName
 
+class Template:
+    """Template represents a standard residue, or a nonstandard one registered with registerTemplate()."""
+    def __init__(self, topology, positions, terminal=None):
+        self.topology = topology
+        self.positions = positions
+        if terminal is None:
+            terminal = [False]*topology.getNumAtoms()
+        self.terminal = terminal
+
 def _guessFileFormat(file, filename):
     """Guess whether a file is PDB or PDBx/mmCIF based on its filename and contents."""
     filename = filename.lower()
@@ -276,7 +286,7 @@ def __init__(self, filename=None, pdbfile=None, pdbxfile=None, url=None, pdbid=N
         for file in os.listdir(templatesPath):
             templatePdb = app.PDBFile(os.path.join(templatesPath, file))
             name = next(templatePdb.topology.residues()).name
-            self.templates[name] = templatePdb
+            self.templates[name] = Template(templatePdb.topology, templatePdb.positions)
 
     def _initializeFromPDB(self, file):
         """Initialize this object by reading a PDB file."""
@@ -344,6 +354,96 @@ def _initializeFromPDBx(self, file):
                 for row in modData.getRowList():
                     self.modifiedResidues.append(ModifiedResidue(row[asymIdCol], int(row[resNumCol]), row[resNameCol], row[standardResCol]))
 
+    def _getTemplate(self, name):
+        """Return the template with a name.  If none has been registered, this will return None."""
+        if name in self.templates:
+            return self.templates[name]
+        return None
+
+    def registerTemplate(self, topology, positions, terminal=None):
+        """Register a template for a nonstandard residue.  This allows PDBFixer to add missing residues of this type,
+        to add missing atoms to existing residues, and to mutate other residues to it.
+        Parameters
+        ----------
+        topology: openmm.app.Topology
+            A Topology containing a single chain with a single residue, describing the nonstandard residue
+            being registered.
+        positions: array of shape (n_atoms, 3)
+            The positions of the atoms in the residue in a typical conformation.  These positions are used
+            when adding missing atoms or residues.
+        terminal: optional list of bool
+            If this is present, it should be a list of length equal to the number of atoms in the residue.
+            If an element is True, that indicates the corresponding atom should only be added to terminal
+            residues.
+        """
+        residues = list(topology.residues())
+        if len(residues) != 1:
+            raise ValueError('The Topology must contain a single residue')
+        if topology.getNumAtoms() != len(positions):
+            raise ValueError('The number of positions does not match the number of atoms in the Topology')
+        if terminal is not None and len(terminal) != topology.getNumAtoms():
+            raise ValueError('The number of terminal flags does not match the number of atoms in the Topology')
+        self.templates[residues[0].name] = Template(topology, positions, terminal)
+
+    def downloadTemplate(self, name):
+        """Attempt to download a residue definition from the PDB and register a template for it.
+
+        Parameters
+        ----------
+        name: str
+            The name of the residue, as specified in the PDB Chemical Component Dictionary.
+
+        Returns
+        -------
+        True if a template was successfully registered, false otherwise.
+        """
+        name = name.upper()
+        try:
+            file = urlopen(f'https://files.rcsb.org/ligands/download/{name}.cif')
+            contents = file.read().decode('utf-8')
+            file.close()
+        except:
+            return False
+
+        # Load the atoms.
+
+        from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
+        reader = PdbxReader(StringIO(contents))
+        data = []
+        reader.read(data)
+        block = data[0]
+        atomData = block.getObj('chem_comp_atom')
+        atomNameCol = atomData.getAttributeIndex('atom_id')
+        symbolCol = atomData.getAttributeIndex('type_symbol')
+        leavingCol = atomData.getAttributeIndex('pdbx_leaving_atom_flag')
+        xCol = atomData.getAttributeIndex('pdbx_model_Cartn_x_ideal')
+        yCol = atomData.getAttributeIndex('pdbx_model_Cartn_y_ideal')
+        zCol = atomData.getAttributeIndex('pdbx_model_Cartn_z_ideal')
+        topology = app.Topology()
+        chain = topology.addChain()
+        residue = topology.addResidue(name, chain)
+        positions = []
+        atomByName = {}
+        terminal = []
+        for row in atomData.getRowList():
+            atomName = row[atomNameCol]
+            atom = topology.addAtom(atomName, app.Element.getBySymbol(row[symbolCol]), residue)
+            atomByName[atomName] = atom
+            terminal.append(row[leavingCol] == 'Y')
+            positions.append(mm.Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol]))*0.1)
+        positions = positions*unit.nanometers
+
+        # Load the bonds.
+
+        bondData = block.getObj('chem_comp_bond')
+        if bondData is not None:
+            atom1Col = bondData.getAttributeIndex('atom_id_1')
+            atom2Col = bondData.getAttributeIndex('atom_id_2')
+            for row in bondData.getRowList():
+                topology.addBond(atomByName[row[atom1Col]], atomByName[row[atom2Col]])
+        self.registerTemplate(topology, positions, terminal)
+        return True
+
     def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
         """Create a new Topology in which missing atoms have been added.
 
@@ -375,7 +475,7 @@ def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
         addedOXT = []
         residueCenters = [self._computeResidueCenter(res).value_in_unit(unit.nanometers) for res in self.topology.residues()]*unit.nanometers
         for chain in self.topology.chains():
-            if omitUnknownMolecules and not any(residue.name in self.templates for residue in chain.residues()):
+            if omitUnknownMolecules and all(self._getTemplate(residue.name) is None for residue in chain.residues()):
                 continue
             chainResidues = list(chain.residues())
             newChain = newTopology.addChain(chain.id)
@@ -413,7 +513,7 @@ def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
 
                     # Find corresponding atoms in the residue and the template.
 
-                    template = self.templates[residue.name]
+                    template = self._getTemplate(residue.name)
                     atomPositions = dict((atom.name, self.positions[atom.index]) for atom in residue.atoms())
                     points1 = []
                     points2 = []
@@ -508,7 +608,7 @@ def _addMissingResiduesToChain(self, chain, residueNames, startPosition, endPosi
         # Add the residues.
 
         for i, residueName in enumerate(residueNames):
-            template = self.templates[residueName]
+            template = self._getTemplate(residueName)
 
             # Find a translation that best matches the adjacent residue.
 
@@ -703,7 +803,7 @@ def findNonstandardResidues(self):
                     replacement = modres[key]
                     if replacement == 'DU':
                         replacement = 'DT'
-                    if replacement in self.templates:
+                    if self._getTemplate(replacement) != None:
                         nonstandard[residue] = replacement
         self.nonstandardResidues = [(r, nonstandard[r]) for r in sorted(nonstandard, key=lambda r: r.index)]
 
@@ -731,7 +831,7 @@ def replaceNonstandardResidues(self):
 
             for residue, replaceWith in self.nonstandardResidues:
                 residue.name = replaceWith
-                template = self.templates[replaceWith]
+                template = self._getTemplate(replaceWith)
                 standardAtoms = set(atom.name for atom in template.topology.atoms())
                 for atom in residue.atoms():
                     if atom.element in (None, hydrogen) or atom.name not in standardAtoms:
@@ -760,6 +860,10 @@ def applyMutations(self, mutations, chain_id):
         Notes
         -----
 
+        If a target residue is not a standard amino acid, and if no template
+        has been registered for it with registerTemplate(), this function
+        attempts to look it up from the PDB and create a new template for it.
+
         We require three letter codes to avoid possible ambiguitities.
         We can't guarantee that the resulting model is a good one; for
         significant changes in sequence, you should probably be using
@@ -800,10 +904,11 @@ def applyMutations(self, mutations, chain_id):
             if residue.name != old_name:
                 raise(ValueError("You asked to mutate chain %s residue %d name %s, but that residue is actually %s!" % (chain_id, resSeq, old_name, residue.name)))
 
-            try:
-                template = self.templates[new_name]
-            except KeyError:
-                raise(KeyError("Cannot find residue %s in template library!" % new_name))
+            if self._getTemplate(new_name) is None:
+                # Try to download a template from the PDB.
+                self.downloadTemplate(new_name)
+                if self._getTemplate(new_name) is None:
+                    raise(KeyError("Cannot find residue %s in template library!" % new_name))
 
             # Store mutation
             residue_map[residue] = new_name
@@ -816,7 +921,7 @@ def applyMutations(self, mutations, chain_id):
             for residue in residue_map.keys():
                 replaceWith = residue_map[residue]
                 residue.name = replaceWith
-                template = self.templates[replaceWith]
+                template = self._getTemplate(replaceWith)
                 standardAtoms = set(atom.name for atom in template.topology.atoms())
                 for atom in residue.atoms():
                     if atom.element in (None, hydrogen) or atom.name not in standardAtoms:
@@ -858,23 +963,60 @@ def findMissingAtoms(self):
         missingAtoms = {}
         missingTerminals = {}
 
+        # Determine which atoms have an external bond to another residue.
+
+        hasExternal = defaultdict(bool)
+        for atom1, atom2 in self.topology.bonds():
+            if atom1.residue != atom2.residue:
+                hasExternal[(atom1.residue, atom1.name)] = True
+                hasExternal[(atom2.residue, atom2.name)] = True
+        for chain in self.topology.chains():
+            chainResidues = list(chain.residues())
+            for residue in chain.residues():
+                atomNames = [atom.name for atom in residue.atoms()]
+                if all(name in atomNames for name in ['C', 'O', 'CA']):
+                    # We'll be adding peptide bonds.
+                    if residue != chainResidues[0]:
+                        hasExternal[(residue, 'N')] = True
+                    if residue != chainResidues[-1]:
+                        hasExternal[(residue, 'C')] = True
+
         # Loop over residues.
 
         for chain in self.topology.chains():
+            nucleic = any(res.name in dnaResidues or res.name in rnaResidues for res in chain.residues())
             chainResidues = list(chain.residues())
             for residue in chain.residues():
-                if residue.name in self.templates:
-                    template = self.templates[residue.name]
+                template = self._getTemplate(residue.name)
+                if template is not None:
+                    # If an atom is marked as terminal only, and if it is bonded to any atom that has an external bond
+                    # to another residue, we need to omit that atom and any other terminal-only atom bonded to it.
+
+                    bondedTo = defaultdict(set)
+                    for atom1, atom2 in template.topology.bonds():
+                        bondedTo[atom1].add(atom2)
+                        bondedTo[atom2].add(atom1)
+                    skip = set()
+                    for atom, terminal in zip(template.topology.atoms(), template.terminal):
+                        if terminal:
+                            for atom2 in bondedTo[atom]:
+                                if hasExternal[(residue, atom2.name)]:
+                                    skip.add(atom)
+                    for atom, terminal in zip(template.topology.atoms(), template.terminal):
+                        if terminal:
+                            for atom2 in bondedTo[atom]:
+                                if atom2 in skip:
+                                    skip.add(atom)
                     atomNames = set(atom.name for atom in residue.atoms())
-                    templateAtoms = list(template.topology.atoms())
-                    if residue == chainResidues[0] and (chain.index, 0) not in self.missingResidues:
+                    templateAtoms = [atom for atom in template.topology.atoms() if atom not in skip]
+                    if nucleic and residue == chainResidues[0] and (chain.index, 0) not in self.missingResidues:
                         templateAtoms = [atom for atom in templateAtoms if atom.name not in ('P', 'OP1', 'OP2')]
 
                     # Add atoms from the template that are missing.
 
                     missing = []
                     for atom in templateAtoms:
-                        if atom.name not in atomNames:
+                        if atom.name not in atomNames and atom.element != app.element.hydrogen:
                             missing.append(atom)
                     if len(missing) > 0:
                         missingAtoms[residue] = missing
@@ -1118,9 +1260,22 @@ def _downloadNonstandardDefinitions(self):
 
     def _describeVariant(self, residue, definitions):
         """Build the variant description to pass to addHydrogens() for a residue."""
-        if residue.name not in definitions:
+        if residue.name not in app.PDBFile._standardResidues and self._getTemplate(residue.name) is not None:
+            # The user has registered a template for this residue.  Use the hydrogens from it.
+            template = self._getTemplate(residue.name)
+            atoms = [(atom.name, atom.element.symbol.upper(), terminal) for atom, terminal in zip(template.topology.atoms(), template.terminal)]
+            resAtoms = dict((atom.name, atom) for atom in residue.atoms())
+            bonds = []
+            for atom1, atom2 in template.topology.bonds():
+                if atom1.element == app.element.hydrogen and atom2.name in resAtoms:
+                    bonds.append((atom1.name, atom2.name))
+                elif atom2.element == app.element.hydrogen and atom1.name in resAtoms:
+                    bonds.append((atom2.name, atom1.name))
+        elif residue.name in definitions:
+            # We downloaded a definition.
+            atoms, bonds = definitions[residue.name]
+        else:
             return None
-        atoms, bonds = definitions[residue.name]
 
         # See if the heavy atoms are identical.