Python Topology.addAtom方法代码示例

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def __init__(self, file):
        """Load a prmtop file."""
        top = Topology()
        ## The Topology read from the prmtop file
        self.topology = top

        # Load the prmtop file

        prmtop = amber_file_parser.PrmtopLoader(file)
        self._prmtop = prmtop

        # Add atoms to the topology

        PDBFile._loadNameReplacementTables()
        lastResidue = None
        c = top.addChain()
        for index in range(prmtop.getNumAtoms()):
            resNumber = prmtop.getResidueNumber(index)
            if resNumber != lastResidue:
                lastResidue = resNumber
                resName = prmtop.getResidueLabel(iAtom=index).strip()
                if resName in PDBFile._residueNameReplacements:
                    resName = PDBFile._residueNameReplacements[resName]
                r = top.addResidue(resName, c)
                if resName in PDBFile._atomNameReplacements:
                    atomReplacements = PDBFile._atomNameReplacements[resName]
                else:
                    atomReplacements = {}
            atomName = prmtop.getAtomName(index).strip()
            if atomName in atomReplacements:
                atomName = atomReplacements[atomName]

            # Try to guess the element.

            upper = atomName.upper()
            if upper.startswith('CL'):
                element = elem.chlorine
            elif upper.startswith('NA'):
                element = elem.sodium
            elif upper.startswith('MG'):
                element = elem.magnesium
            else:
                try:
                    element = elem.get_by_symbol(atomName[0])
                except KeyError:
                    element = None
            top.addAtom(atomName, element, r)

        # Add bonds to the topology

        atoms = list(top.atoms())
        for bond in prmtop.getBondsWithH():
            top.addBond(atoms[bond[0]], atoms[bond[1]])
        for bond in prmtop.getBondsNoH():
            top.addBond(atoms[bond[0]], atoms[bond[1]])

        # Set the periodic box size.

        if prmtop.getIfBox():
            top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
def generateTopologyFromOEMol(molecule):
    """
    Generate an OpenMM Topology object from an OEMol molecule.

    Parameters
    ----------
    molecule : openeye.oechem.OEMol
        The molecule from which a Topology object is to be generated.

    Returns
    -------
    topology : simtk.openmm.app.Topology
        The Topology object generated from `molecule`.

    """
    # Create a Topology object with one Chain and one Residue.
    from simtk.openmm.app import Topology
    topology = Topology()
    chain = topology.addChain()
    resname = molecule.GetTitle()
    residue = topology.addResidue(resname, chain)

    # Create atoms in the residue.
    for atom in molecule.GetAtoms():
        name = atom.GetName()
        element = Element.getByAtomicNumber(atom.GetAtomicNum())
        atom = topology.addAtom(name, element, residue)

    # Create bonds.
    atoms = { atom.name : atom for atom in topology.atoms() }
    for bond in molecule.GetBonds():
        topology.addBond(atoms[bond.GetBgn().GetName()], atoms[bond.GetEnd().GetName()])

    return topology

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def add(self, addTopology, addPositions):
        """Add chains, residues, atoms, and bonds to the model.

        Specify what to add by providing a new Topology object and the corresponding atomic positions.
        All chains, residues, atoms, and bonds contained in the Topology are added to the model.

        Parameters:
         - addTopoology (Topology) a Topology whose contents should be added to the model
         - addPositions (list) the positions of the atoms to add
        """
        # Copy over the existing model.

        newTopology = Topology()
        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
        newAtoms = {}
        newPositions = []*nanometer
        for chain in self.topology.chains():
            newChain = newTopology.addChain()
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain)
                for atom in residue.atoms():
                    newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
                    newAtoms[atom] = newAtom
                    newPositions.append(deepcopy(self.positions[atom.index]))
        for bond in self.topology.bonds():
            newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])

        # Add the new model

        newAtoms = {}
        for chain in addTopology.chains():
            newChain = newTopology.addChain()
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain)
                for atom in residue.atoms():
                    newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
                    newAtoms[atom] = newAtom
                    newPositions.append(deepcopy(addPositions[atom.index]))
        for bond in addTopology.bonds():
            newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
        self.topology = newTopology
        self.positions = newPositions

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def _createTopology(self):
        """Build the topology of the system
        """
        top = Topology()
        positions = []
        velocities = []

        boxVectors = []
        for x, y, z in self._conn.execute('SELECT x, y, z FROM global_cell'):
            boxVectors.append(mm.Vec3(x, y, z))
        unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
        top.setUnitCellDimensions(unitCellDimensions*angstrom)

        atoms = {}
        lastChain = None
        lastResId = None
        c = top.addChain()
        q = """SELECT id, name, anum, resname, resid, chain, x, y, z, vx, vy, vz
        FROM particle ORDER BY id"""
        for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z, vx, vy, vz) in self._conn.execute(q):
            newChain = False
            if chain != lastChain:
                lastChain = chain
                c = top.addChain()
                newChain = True
            if resId != lastResId or newChain:
                lastResId = resId
                if resName in PDBFile._residueNameReplacements:
                    resName = PDBFile._residueNameReplacements[resName]
                r = top.addResidue(resName, c)
                if resName in PDBFile._atomNameReplacements:
                    atomReplacements = PDBFile._atomNameReplacements[resName]
                else:
                    atomReplacements = {}

            if atomNumber == 0 and atomName.startswith('Vrt'):
                elem = None
            else:
                elem = Element.getByAtomicNumber(atomNumber)
            
            if atomName in atomReplacements:
                atomName = atomReplacements[atomName]

            atoms[atomId] = top.addAtom(atomName, elem, r)
            positions.append(mm.Vec3(x, y, z))

            velocities.append(mm.Vec3(vx, vy, vz))
    
        for p0, p1 in self._conn.execute('SELECT p0, p1 FROM bond'):
            top.addBond(atoms[p0], atoms[p1])

        positions = positions*angstrom
        velocities = velocities*angstrom/femtosecond
        return top, positions, velocities

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def _createTopology(self):
        '''Build the topology of the system
        '''
        top = Topology()
        positions = []

        boxVectors = []
        for x, y, z in self._conn.execute('SELECT x, y, z FROM global_cell'):
            boxVectors.append(mm.Vec3(x, y, z)*angstrom)
        unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
        top.setUnitCellDimensions(unitCellDimensions)

        atoms = {}
        lastChain = None
        lastResId = None
        c = top.addChain()
        q = '''SELECT id, name, anum, resname, resid, chain, x, y, z
        FROM particle'''
        for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z) in self._conn.execute(q):
            if chain != lastChain:
                lastChain = chain
                c = top.addChain()
            if resId != lastResId:
                lastResId = resId
                if resName in PDBFile._residueNameReplacements:
                    resName = PDBFile._residueNameReplacements[resName]
                r = top.addResidue(resName, c)
                if resName in PDBFile._atomNameReplacements:
                    atomReplacements = PDBFile._atomNameReplacements[resName]
                else:
                    atomReplacements = {}

            if atomName in atomReplacements:
                atomName = atomReplacements[atomName]

            elem = Element.getByAtomicNumber(atomNumber)
            atoms[atomId] = top.addAtom(atomName, elem, r)
            positions.append(mm.Vec3(x, y, z)*angstrom)

        for p0, p1 in self._conn.execute('SELECT p0, p1 FROM bond'):
            top.addBond(atoms[p0], atoms[p1])

        return top, positions

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def delete(self, toDelete):
        """Delete chains, residues, atoms, and bonds from the model.

        You can specify objects to delete at any granularity: atoms, residues, or chains.  Passing
        in an Atom object causes that Atom to be deleted.  Passing in a Residue object causes that
        Residue and all Atoms it contains to be deleted.  Passing in a Chain object causes that
        Chain and all Residues and Atoms it contains to be deleted.

        In all cases, when an Atom is deleted, any bonds it participates in are also deleted.
        You also can specify a bond (as a tuple of Atom objects) to delete just that bond without
        deleting the Atoms it connects.

        Parameters:
         - toDelete (list) a list of Atoms, Residues, Chains, and bonds (specified as tuples of Atoms) to delete
        """
        newTopology = Topology()
        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
        newAtoms = {}
        newPositions = []*nanometer
        deleteSet = set(toDelete)
        for chain in self.topology.chains():
            if chain not in deleteSet:
                needNewChain = True;
                for residue in chain.residues():
                    if residue not in deleteSet:
                        needNewResidue = True
                        for atom in residue.atoms():
                            if atom not in deleteSet:
                                if needNewChain:
                                    newChain = newTopology.addChain()
                                    needNewChain = False;
                                if needNewResidue:
                                    newResidue = newTopology.addResidue(residue.name, newChain)
                                    needNewResidue = False;
                                newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
                                newAtoms[atom] = newAtom
                                newPositions.append(deepcopy(self.positions[atom.index]))
        for bond in self.topology.bonds():
            if bond[0] in newAtoms and bond[1] in newAtoms:
                if bond not in deleteSet and (bond[1], bond[0]) not in deleteSet:
                    newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
        self.topology = newTopology
        self.positions = newPositions

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def __init__(self, file):
        """Load a PDBx/mmCIF file.

        The atom positions and Topology can be retrieved by calling
        getPositions() and getTopology().

        Parameters
        ----------
        file : string
            the name of the file to load.  Alternatively you can pass an open
            file object.
        """
        top = Topology()
        ## The Topology read from the PDBx/mmCIF file
        self.topology = top
        self._positions = []

        # Load the file.

        inputFile = file
        if isinstance(file, str):
            inputFile = open(file)
        reader = PdbxReader(inputFile)
        data = []
        reader.read(data)
        block = data[0]

        # Build the topology.

        atomData = block.getObj('atom_site')
        atomNameCol = atomData.getAttributeIndex('auth_atom_id')
        atomIdCol = atomData.getAttributeIndex('id')
        resNameCol = atomData.getAttributeIndex('auth_comp_id')
        resNumCol = atomData.getAttributeIndex('auth_seq_id')
        resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code')
        chainIdCol = atomData.getAttributeIndex('auth_asym_id')
        elementCol = atomData.getAttributeIndex('type_symbol')
        altIdCol = atomData.getAttributeIndex('label_alt_id')
        modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
        xCol = atomData.getAttributeIndex('Cartn_x')
        yCol = atomData.getAttributeIndex('Cartn_y')
        zCol = atomData.getAttributeIndex('Cartn_z')
        lastChainId = None
        lastResId = None
        atomTable = {}
        atomsInResidue = set()
        models = []
        for row in atomData.getRowList():
            atomKey = ((row[resNumCol], row[chainIdCol], row[atomNameCol]))
            model = ('1' if modelCol == -1 else row[modelCol])
            if model not in models:
                models.append(model)
                self._positions.append([])
            modelIndex = models.index(model)
            if row[altIdCol] != '.' and atomKey in atomTable and len(self._positions[modelIndex]) > atomTable[atomKey].index:
                # This row is an alternate position for an existing atom, so ignore it.

                continue
            if modelIndex == 0:
                # This row defines a new atom.

                if lastChainId != row[chainIdCol]:
                    # The start of a new chain.
                    chain = top.addChain(row[chainIdCol])
                    lastChainId = row[chainIdCol]
                    lastResId = None
                if lastResId != row[resNumCol] or lastChainId != row[chainIdCol] or (lastResId == '.' and row[atomNameCol] in atomsInResidue):
                    # The start of a new residue.
                    resId = (None if resNumCol == -1 else row[resNumCol])
                    resIC = ('' if resInsertionCol == -1 else row[resInsertionCol])
                    res = top.addResidue(row[resNameCol], chain, resId, resIC)
                    lastResId = row[resNumCol]
                    atomsInResidue.clear()
                element = None
                try:
                    element = elem.get_by_symbol(row[elementCol])
                except KeyError:
                    pass
                atom = top.addAtom(row[atomNameCol], element, res, row[atomIdCol])
                atomTable[atomKey] = atom
                atomsInResidue.add(row[atomNameCol])
            else:
                # This row defines coordinates for an existing atom in one of the later models.

                try:
                    atom = atomTable[atomKey]
                except KeyError:
                    raise ValueError('Unknown atom %s in residue %s %s for model %s' % (row[atomNameCol], row[resNameCol], row[resNumCol], model))
                if atom.index != len(self._positions[modelIndex]):
                    raise ValueError('Atom %s for model %s does not match the order of atoms for model %s' % (row[atomIdCol], model, models[0]))
            self._positions[modelIndex].append(Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol]))*0.1)
        for i in range(len(self._positions)):
            self._positions[i] = self._positions[i]*nanometers
        ## The atom positions read from the PDBx/mmCIF file.  If the file contains multiple frames, these are the positions in the first frame.
        self.positions = self._positions[0]
        self.topology.createStandardBonds()
        self._numpyPositions = None

        # Record unit cell information, if present.

#.........这里部分代码省略.........

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]

#.........这里部分代码省略.........
        includeDir : string=None
            A directory in which to look for other files included from the
            top file. If not specified, we will attempt to locate a gromacs
            installation on your system. When gromacs is installed in
            /usr/local, this will resolve to /usr/local/gromacs/share/gromacs/top
        defines : dict={}
            preprocessor definitions that should be predefined when parsing the file
         """
        if includeDir is None:
            includeDir = _defaultGromacsIncludeDir()
        self._includeDirs = (os.path.dirname(file), includeDir)
        # Most of the gromacs water itp files for different forcefields,
        # unless the preprocessor #define FLEXIBLE is given, don't define
        # bonds between the water hydrogen and oxygens, but only give the
        # constraint distances and exclusions.
        self._defines = OrderedDict()
        self._defines['FLEXIBLE'] = True
        self._genpairs = True
        if defines is not None:
            for define, value in defines.iteritems():
                self._defines[define] = value

        # Parse the file.

        self._currentCategory = None
        self._ifStack = []
        self._elseStack = []
        self._moleculeTypes = {}
        self._molecules = []
        self._currentMoleculeType = None
        self._atomTypes = {}
        self._bondTypes= {}
        self._angleTypes = {}
        self._dihedralTypes = {}
        self._implicitTypes = {}
        self._pairTypes = {}
        self._cmapTypes = {}
        self._processFile(file)

        # Create the Topology from it.

        top = Topology()
        ## The Topology read from the prmtop file
        self.topology = top
        if periodicBoxVectors is not None:
            if unitCellDimensions is not None:
                raise ValueError("specify either periodicBoxVectors or unitCellDimensions, but not both")
            top.setPeriodicBoxVectors(periodicBoxVectors)
        else:
            top.setUnitCellDimensions(unitCellDimensions)
        PDBFile._loadNameReplacementTables()
        for moleculeName, moleculeCount in self._molecules:
            if moleculeName not in self._moleculeTypes:
                raise ValueError("Unknown molecule type: "+moleculeName)
            moleculeType = self._moleculeTypes[moleculeName]
            if moleculeCount > 0 and moleculeType.has_virtual_sites:
                raise ValueError('Virtual sites not yet supported by Gromacs parsers')

            # Create the specified number of molecules of this type.

            for i in range(moleculeCount):
                atoms = []
                lastResidue = None
                c = top.addChain()
                for index, fields in enumerate(moleculeType.atoms):
                    resNumber = fields[2]
                    if resNumber != lastResidue:
                        lastResidue = resNumber
                        resName = fields[3]
                        if resName in PDBFile._residueNameReplacements:
                            resName = PDBFile._residueNameReplacements[resName]
                        r = top.addResidue(resName, c)
                        if resName in PDBFile._atomNameReplacements:
                            atomReplacements = PDBFile._atomNameReplacements[resName]
                        else:
                            atomReplacements = {}
                    atomName = fields[4]
                    if atomName in atomReplacements:
                        atomName = atomReplacements[atomName]

                    # Try to guess the element.

                    upper = atomName.upper()
                    if upper.startswith('CL'):
                        element = elem.chlorine
                    elif upper.startswith('NA'):
                        element = elem.sodium
                    elif upper.startswith('MG'):
                        element = elem.magnesium
                    else:
                        try:
                            element = elem.get_by_symbol(atomName[0])
                        except KeyError:
                            element = None
                    atoms.append(top.addAtom(atomName, element, r))

                # Add bonds to the topology

                for fields in moleculeType.bonds:
                    top.addBond(atoms[int(fields[0])-1], atoms[int(fields[1])-1])

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def __init__(self, file):
        """Load a PDB file.

        The atom positions and Topology can be retrieved by calling getPositions() and getTopology().

        Parameters
        ----------
        file : string
            the name of the file to load
        """
        top = Topology()
        ## The Topology read from the PDB file
        self.topology = top

        # Load the PDB file

        if isinstance(file, PdbStructure):
            pdb = file
        else:
            inputfile = file
            own_handle = False
            if isinstance(file, str):
                inputfile = open(file)
                own_handle = True
            pdb = PdbStructure(inputfile, load_all_models=True)
            if own_handle:
                inputfile.close()
        PDBFile._loadNameReplacementTables()

        # Build the topology

        atomByNumber = {}
        for chain in pdb.iter_chains():
            c = top.addChain(chain.chain_id)
            for residue in chain.iter_residues():
                resName = residue.get_name()
                if resName in PDBFile._residueNameReplacements:
                    resName = PDBFile._residueNameReplacements[resName]
                r = top.addResidue(resName, c, str(residue.number))
                if resName in PDBFile._atomNameReplacements:
                    atomReplacements = PDBFile._atomNameReplacements[resName]
                else:
                    atomReplacements = {}
                for atom in residue.atoms:
                    atomName = atom.get_name()
                    if atomName in atomReplacements:
                        atomName = atomReplacements[atomName]
                    atomName = atomName.strip()
                    element = atom.element
                    if element is None:
                        # Try to guess the element.

                        upper = atomName.upper()
                        if upper.startswith('CL'):
                            element = elem.chlorine
                        elif upper.startswith('NA'):
                            element = elem.sodium
                        elif upper.startswith('MG'):
                            element = elem.magnesium
                        elif upper.startswith('BE'):
                            element = elem.beryllium
                        elif upper.startswith('LI'):
                            element = elem.lithium
                        elif upper.startswith('K'):
                            element = elem.potassium
                        elif upper.startswith('ZN'):
                            element = elem.zinc
                        elif( len( residue ) == 1 and upper.startswith('CA') ):
                            element = elem.calcium
                        else:
                            try:
                                element = elem.get_by_symbol(atomName[0])
                            except KeyError:
                                pass
                    newAtom = top.addAtom(atomName, element, r, str(atom.serial_number))
                    atomByNumber[atom.serial_number] = newAtom
        self._positions = []
        for model in pdb.iter_models(True):
            coords = []
            for chain in model.iter_chains():
                for residue in chain.iter_residues():
                    for atom in residue.atoms:
                        pos = atom.get_position().value_in_unit(nanometers)
                        coords.append(Vec3(pos[0], pos[1], pos[2]))
            self._positions.append(coords*nanometers)
        ## The atom positions read from the PDB file.  If the file contains multiple frames, these are the positions in the first frame.
        self.positions = self._positions[0]
        self.topology.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
        self.topology.createStandardBonds()
        self.topology.createDisulfideBonds(self.positions)
        self._numpyPositions = None

        # Add bonds based on CONECT records.

        connectBonds = []
        for connect in pdb.models[0].connects:
            i = connect[0]
            for j in connect[1:]:
                if i in atomByNumber and j in atomByNumber:
                    connectBonds.append((atomByNumber[i], atomByNumber[j]))
#.........这里部分代码省略.........

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def addExtraParticles(self, forcefield):
        """Add missing extra particles to the model that are required by a force field.

        Some force fields use "extra particles" that do not represent actual atoms, but still need to be included in
        the System.  Examples include lone pairs, Drude particles, and the virtual sites used in some water models
        to adjust the charge distribution.  Extra particles can be recognized by the fact that their element is None.

        This method is primarily used to add extra particles, but it can also remove them.  It tries to match every
        residue in the Topology to a template in the force field.  If there is no match, it will both add and remove
        extra particles as necessary to make it match.

        Parameters:
         - forcefield (ForceField) the ForceField defining what extra particles should be present
        """
        # Create copies of all residue templates that have had all extra points removed.

        templatesNoEP = {}
        for resName, template in forcefield._templates.iteritems():
            if any(atom.element is None for atom in template.atoms):
                index = 0
                newIndex = {}
                newTemplate = ForceField._TemplateData(resName)
                for i, atom in enumerate(template.atoms):
                    if atom.element is not None:
                        newIndex[i] = index
                        index += 1
                        newTemplate.atoms.append(ForceField._TemplateAtomData(atom.name, atom.type, atom.element))
                for b1, b2 in template.bonds:
                    if b1 in newIndex and b2 in newIndex:
                        newTemplate.bonds.append((newIndex[b1], newIndex[b2]))
                        newTemplate.atoms[newIndex[b1]].bondedTo.append(newIndex[b2])
                        newTemplate.atoms[newIndex[b2]].bondedTo.append(newIndex[b1])
                for b in template.externalBonds:
                    if b in newIndex:
                        newTemplate.externalBonds.append(newIndex[b])
                templatesNoEP[template] = newTemplate

        # Record which atoms are bonded to each other atom, with and without extra particles.

        bondedToAtom = []
        bondedToAtomNoEP = []
        for atom in self.topology.atoms():
            bondedToAtom.append(set())
            bondedToAtomNoEP.append(set())
        for atom1, atom2 in self.topology.bonds():
            bondedToAtom[atom1.index].add(atom2.index)
            bondedToAtom[atom2.index].add(atom1.index)
            if atom1.element is not None and atom2.element is not None:
                bondedToAtomNoEP[atom1.index].add(atom2.index)
                bondedToAtomNoEP[atom2.index].add(atom1.index)

        # If the force field has a DrudeForce, record the types of Drude particles and their parents since we'll
        # need them for picking particle positions.

        drudeTypeMap = {}
        for force in forcefield._forces:
            if isinstance(force, DrudeGenerator):
                for type in force.typeMap:
                    drudeTypeMap[type] = force.typeMap[type][0]

        # Create the new Topology.

        newTopology = Topology()
        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
        newAtoms = {}
        newPositions = []*nanometer
        for chain in self.topology.chains():
            newChain = newTopology.addChain()
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain)

                # Look for a matching template.

                matchFound = False
                signature = _createResidueSignature([atom.element for atom in residue.atoms()])
                if signature in forcefield._templateSignatures:
                    for t in forcefield._templateSignatures[signature]:
                        if _matchResidue(residue, t, bondedToAtom) is not None:
                            matchFound = True
                if matchFound:
                    # Just copy the residue over.

                    for atom in residue.atoms():
                        newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
                        newAtoms[atom] = newAtom
                        newPositions.append(deepcopy(self.positions[atom.index]))
                else:
                    # There's no matching template.  Try to find one that matches based on everything except
                    # extra points.

                    template = None
                    residueNoEP = Residue(residue.name, residue.index, residue.chain)
                    residueNoEP._atoms = [atom for atom in residue.atoms() if atom.element is not None]
                    if signature in forcefield._templateSignatures:
                        for t in forcefield._templateSignatures[signature]:
                            if t in templatesNoEP:
                                matches = _matchResidue(residueNoEP, templatesNoEP[t], bondedToAtomNoEP)
                                if matches is not None:
                                    template = t;
                                    # Record the corresponding atoms.
#.........这里部分代码省略.........

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]

#.........这里部分代码省略.........
                                nd1IsBonded = False
                                ne2IsBonded = False
                                for acceptor in acceptors:
                                    if acceptor.residue != residue:
                                        acceptorPos = self.positions[acceptor.index]
                                        if isHbond(nd1Pos, hd1Pos, acceptorPos):
                                            nd1IsBonded = True
                                            break
                                        if isHbond(ne2Pos, he2Pos, acceptorPos):
                                            ne2IsBonded = True
                                if ne2IsBonded and not nd1IsBonded:
                                    variant = 'HIE'
                                else:
                                    variant = 'HID'
                        elif residue.name == 'HIS':
                            variant = 'HIP'
                    if variant is not None and variant not in spec.variants:
                        raise ValueError('Illegal variant for %s residue: %s' % (residue.name, variant))
                    actualVariants[residue.index] = variant

                    # Make a list of hydrogens that should be present in the residue.

                    parents = [atom for atom in residue.atoms() if atom.element != elem.hydrogen]
                    parentNames = [atom.name for atom in parents]
                    hydrogens = [h for h in spec.hydrogens if (variant is None and pH <= h.maxph) or (h.variants is None and pH <= h.maxph) or (h.variants is not None and variant in h.variants)]
                    hydrogens = [h for h in hydrogens if h.terminal is None or (isNTerminal and h.terminal == 'N') or (isCTerminal and h.terminal == 'C')]
                    hydrogens = [h for h in hydrogens if h.parent in parentNames]

                    # Loop over atoms in the residue, adding them to the new topology along with required hydrogens.

                    for parent in residue.atoms():
                        # Add the atom.

                        newAtom = newTopology.addAtom(parent.name, parent.element, newResidue)
                        newAtoms[parent] = newAtom
                        newPositions.append(deepcopy(self.positions[parent.index]))
                        if parent in parents:
                            # Match expected hydrogens with existing ones and find which ones need to be added.

                            existing = [atom for atom in bonded[parent] if atom.element == elem.hydrogen]
                            expected = [h for h in hydrogens if h.parent == parent.name]
                            if len(existing) < len(expected):
                                # Try to match up existing hydrogens to expected ones.

                                matches = []
                                for e in existing:
                                    match = [h for h in expected if h.name == e.name]
                                    if len(match) > 0:
                                        matches.append(match[0])
                                        expected.remove(match[0])
                                    else:
                                        matches.append(None)

                                # If any hydrogens couldn't be matched by name, just match them arbitrarily.

                                for i in range(len(matches)):
                                    if matches[i] is None:
                                        matches[i] = expected[-1]
                                        expected.remove(expected[-1])

                                # Add the missing hydrogens.

                                for h in expected:
                                    newH = newTopology.addAtom(h.name, elem.hydrogen, newResidue)
                                    newIndices.append(newH.index)
                                    delta = Vec3(0, 0, 0)*nanometer

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def addSolvent(self, forcefield, model='tip3p', boxSize=None, padding=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar):
        """Add solvent (both water and ions) to the model to fill a rectangular box.

        The algorithm works as follows:
        1. Water molecules are added to fill the box.
        2. Water molecules are removed if their distance to any solute atom is less than the sum of their van der Waals radii.
        3. If the solute is charged, enough positive or negative ions are added to neutralize it.  Each ion is added by
           randomly selecting a water molecule and replacing it with the ion.
        4. Ion pairs are added to give the requested total ionic strength.

        The box size can be specified in three ways.  First, you can explicitly give a box size to use.  Alternatively, you can
        give a padding distance.  The largest dimension of the solute (along the x, y, or z axis) is determined, and a cubic
        box of size (largest dimension)+2*padding is used.  Finally, if neither a box size nor a padding distance is specified,
        the existing Topology's unit cell dimensions are used.

        Parameters:
         - forcefield (ForceField) the ForceField to use for determining van der Waals radii and atomic charges
         - model (string='tip3p') the water model to use.  Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
         - boxSize (Vec3=None) the size of the box to fill with water
         - padding (distance=None) the padding distance to use
         - positiveIon (string='Na+') the type of positive ion to add.  Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
         - negativeIon (string='Cl-') the type of negative ion to add.  Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
           that not all force fields support all ion types.
         - ionicString (concentration=0*molar) the total concentration of ions (both positive and negative) to add.  This
           does not include ions that are added to neutralize the system.
        """
        # Pick a unit cell size.

        if boxSize is not None:
            if is_quantity(boxSize):
                boxSize = boxSize.value_in_unit(nanometer)
            box = Vec3(boxSize[0], boxSize[1], boxSize[2])*nanometer
        elif padding is not None:
            maxSize = max(max((pos[i] for pos in self.positions))-min((pos[i] for pos in self.positions)) for i in range(3))
            box = (maxSize+2*padding)*Vec3(1, 1, 1)
        else:
            box = self.topology.getUnitCellDimensions()
            if box is None:
                raise ValueError('Neither the box size nor padding was specified, and the Topology does not define unit cell dimensions')
        box = box.value_in_unit(nanometer)
        invBox = Vec3(1.0/box[0], 1.0/box[1], 1.0/box[2])

        # Identify the ion types.

        posIonElements = {'Cs+':elem.cesium, 'K+':elem.potassium, 'Li+':elem.lithium, 'Na+':elem.sodium, 'Rb+':elem.rubidium}
        negIonElements = {'Cl-':elem.chlorine, 'Br-':elem.bromine, 'F-':elem.fluorine, 'I-':elem.iodine}
        if positiveIon not in posIonElements:
            raise ValueError('Illegal value for positive ion: %s' % positiveIon)
        if negativeIon not in negIonElements:
            raise ValueError('Illegal value for negative ion: %s' % negativeIon)
        positiveElement = posIonElements[positiveIon]
        negativeElement = negIonElements[negativeIon]

        # Load the pre-equilibrated water box.

        vdwRadiusPerSigma = 0.5612310241546864907
        if model == 'tip3p':
            waterRadius = 0.31507524065751241*vdwRadiusPerSigma
        elif model == 'spce':
            waterRadius = 0.31657195050398818*vdwRadiusPerSigma
        elif model == 'tip4pew':
            waterRadius = 0.315365*vdwRadiusPerSigma
        elif model == 'tip5p':
            waterRadius = 0.312*vdwRadiusPerSigma
        else:
            raise ValueError('Unknown water model: %s' % model)
        pdb = PDBFile(os.path.join(os.path.dirname(__file__), 'data', model+'.pdb'))
        pdbTopology = pdb.getTopology()
        pdbPositions = pdb.getPositions().value_in_unit(nanometer)
        pdbResidues = list(pdbTopology.residues())
        pdbBoxSize = pdbTopology.getUnitCellDimensions().value_in_unit(nanometer)

        # Have the ForceField build a System for the solute from which we can determine van der Waals radii.

        system = forcefield.createSystem(self.topology)
        nonbonded = None
        for i in range(system.getNumForces()):
            if isinstance(system.getForce(i), NonbondedForce):
                nonbonded = system.getForce(i)
        if nonbonded is None:
            raise ValueError('The ForceField does not specify a NonbondedForce')
        cutoff = [nonbonded.getParticleParameters(i)[1].value_in_unit(nanometer)*vdwRadiusPerSigma+waterRadius for i in range(system.getNumParticles())]
        waterCutoff = waterRadius
        if len(cutoff) == 0:
            maxCutoff = waterCutoff
        else:
            maxCutoff = max(waterCutoff, max(cutoff))

        # Copy the solute over.

        newTopology = Topology()
        newTopology.setUnitCellDimensions(box)
        newAtoms = {}
        newPositions = []*nanometer
        for chain in self.topology.chains():
            newChain = newTopology.addChain()
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain)
                for atom in residue.atoms():
                    newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
#.........这里部分代码省略.........

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def convertWater(self, model='tip3p'):
        """Convert all water molecules to a different water model.

        Parameters:
         - model (string='tip3p') the water model to convert to.  Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
        
        @deprecated Use addExtraParticles() instead.  It performs the same function but in a more general way.
        """
        if model in ('tip3p', 'spce'):
            sites = 3
        elif model == 'tip4pew':
            sites = 4
        elif model == 'tip5p':
            sites = 5
        else:
            raise ValueError('Unknown water model: %s' % model)
        newTopology = Topology()
        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
        newAtoms = {}
        newPositions = []*nanometer
        for chain in self.topology.chains():
            newChain = newTopology.addChain()
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain)
                if residue.name == "HOH":
                    # Copy the oxygen and hydrogens
                    oatom = [atom for atom in residue.atoms() if atom.element == elem.oxygen]
                    hatoms = [atom for atom in residue.atoms() if atom.element == elem.hydrogen]
                    if len(oatom) != 1 or len(hatoms) != 2:
                        raise ValueError('Illegal water molecule (residue %d): contains %d oxygen(s) and %d hydrogen(s)' % (residue.index, len(oatom), len(hatoms)))
                    o = newTopology.addAtom(oatom[0].name, oatom[0].element, newResidue)
                    h1 = newTopology.addAtom(hatoms[0].name, hatoms[0].element, newResidue)
                    h2 = newTopology.addAtom(hatoms[1].name, hatoms[1].element, newResidue)
                    newAtoms[oatom[0]] = o
                    newAtoms[hatoms[0]] = h1
                    newAtoms[hatoms[1]] = h2
                    po = deepcopy(self.positions[oatom[0].index])
                    ph1 = deepcopy(self.positions[hatoms[0].index])
                    ph2 = deepcopy(self.positions[hatoms[1].index])
                    newPositions.append(po)
                    newPositions.append(ph1)
                    newPositions.append(ph2)

                    # Add virtual sites.

                    if sites == 4:
                        newTopology.addAtom('M', None, newResidue)
                        newPositions.append(0.786646558*po + 0.106676721*ph1 + 0.106676721*ph2)
                    elif sites == 5:
                        newTopology.addAtom('M1', None, newResidue)
                        newTopology.addAtom('M2', None, newResidue)
                        v1 = (ph1-po).value_in_unit(nanometer)
                        v2 = (ph2-po).value_in_unit(nanometer)
                        cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
                        newPositions.append(po - (0.34490826*v1 - 0.34490826*v2 - 6.4437903*cross)*nanometer)
                        newPositions.append(po - (0.34490826*v1 - 0.34490826*v2 + 6.4437903*cross)*nanometer)
                else:
                    # Just copy the residue over.
                    for atom in residue.atoms():
                        newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
                        newAtoms[atom] = newAtom
                        newPositions.append(deepcopy(self.positions[atom.index]))
        for bond in self.topology.bonds():
            if bond[0] in newAtoms and bond[1] in newAtoms:
                newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
        self.topology = newTopology
        self.positions = newPositions

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]

#.........这里部分代码省略.........
        For Amber topology files this is the same as the normal LJ parameters,
        but is done here so that OpenMMChamberParm can inherit and override this
        behavior without having to duplicate all of the system creation code.
        """
        return self.openmm_LJ()

    @property
    def topology(self):
        """
        The OpenMM Topology object. Cached when possible, but any changes to the
        topology object lists results in the topology being deleted and rebuilt
        """
        # If anything changed, rebuild the topology
        if not self._topology_changed():
            try:
                return self._topology
            except AttributeError:
                pass
        else:
            self.remake_parm()
      
        self._topology = Topology()

        # Add all of the atoms to the topology file in the same chain
        chain = self._topology.addChain()
        last_residue = None
        for i, atm in enumerate(self.atom_list):
            resnum = atm.residue.idx
            if last_residue != resnum:
                last_residue = resnum
                resname = atm.residue.resname
                res = self._topology.addResidue(resname, chain)
            elem = element.get_by_symbol(pt.Element[atm.element])
            self._topology.addAtom(atm.atname, elem, res)

        # Add bonds to the topology (both with and without hydrogen)
        atoms = list(self._topology.atoms())
        for bnd in self.bonds_inc_h + self.bonds_without_h:
            self._topology.addBond(atoms[bnd.atom1.starting_index],
                                   atoms[bnd.atom2.starting_index])
      
        # Set the box dimensions
        if self.ptr('ifbox'):
            if hasattr(self, 'rst7'):
                self._topology.setUnitCellDimensions(
                        self.rst7.box[:3]*u.angstrom
                )
            else:
                self._topology.setUnitCellDimensions(
                        self.parm_data['BOX_DIMENSIONS'][1:4]*u.angstrom
                )

        return self._topology
   
    def _get_gb_params(self, gb_model=HCT):
        """ Gets the GB parameters. Need this method to special-case GB neck """
        if gb_model is GBn:
            screen = [0.5 for atom in self.atom_list]
            for i, atom in enumerate(self.atom_list):
                if atom.element == 6:
                    screen[i] = 0.48435382330
                elif atom.element == 1:
                    screen[i] = 1.09085413633
                elif atom.element == 7:
                    screen[i] = 0.700147318409
                elif atom.element == 8:

# 需要导入模块: from simtk.openmm.app import Topology [as 别名]
# 或者: from simtk.openmm.app.Topology import addAtom [as 别名]
    def __init__(self, file, extraParticleIdentifier='EP'):
        """Load a PDB file.

        The atom positions and Topology can be retrieved by calling getPositions() and getTopology().

        Parameters
        ----------
        file : string
            the name of the file to load
        extraParticleIdentifier : string='EP'
            if this value appears in the element column for an ATOM record, the Atom's element will be set to None to mark it as an extra particle
        """
        
        metalElements = ['Al','As','Ba','Ca','Cd','Ce','Co','Cs','Cu','Dy','Fe','Gd','Hg','Ho','In','Ir','K','Li','Mg',
        'Mn','Mo','Na','Ni','Pb','Pd','Pt','Rb','Rh','Sm','Sr','Te','Tl','V','W','Yb','Zn']
        
        top = Topology()
        ## The Topology read from the PDB file
        self.topology = top

        # Load the PDB file

        if isinstance(file, PdbStructure):
            pdb = file
        else:
            inputfile = file
            own_handle = False
            if isinstance(file, str):
                inputfile = open(file)
                own_handle = True
            pdb = PdbStructure(inputfile, load_all_models=True, extraParticleIdentifier=extraParticleIdentifier)
            if own_handle:
                inputfile.close()
        PDBFile._loadNameReplacementTables()

        # Build the topology

        atomByNumber = {}
        for chain in pdb.iter_chains():
            c = top.addChain(chain.chain_id)
            for residue in chain.iter_residues():
                resName = residue.get_name()
                if resName in PDBFile._residueNameReplacements:
                    resName = PDBFile._residueNameReplacements[resName]
                r = top.addResidue(resName, c, str(residue.number))
                if resName in PDBFile._atomNameReplacements:
                    atomReplacements = PDBFile._atomNameReplacements[resName]
                else:
                    atomReplacements = {}
                for atom in residue.atoms:
                    atomName = atom.get_name()
                    if atomName in atomReplacements:
                        atomName = atomReplacements[atomName]
                    atomName = atomName.strip()
                    element = atom.element
                    if element == 'EP':
                        element = None
                    elif element is None:
                        # Try to guess the element.

                        upper = atomName.upper()
                        while len(upper) > 1 and upper[0].isdigit():
                            upper = upper[1:]
                        if upper.startswith('CL'):
                            element = elem.chlorine
                        elif upper.startswith('NA'):
                            element = elem.sodium
                        elif upper.startswith('MG'):
                            element = elem.magnesium
                        elif upper.startswith('BE'):
                            element = elem.beryllium
                        elif upper.startswith('LI'):
                            element = elem.lithium
                        elif upper.startswith('K'):
                            element = elem.potassium
                        elif upper.startswith('ZN'):
                            element = elem.zinc
                        elif( len( residue ) == 1 and upper.startswith('CA') ):
                            element = elem.calcium
                        else:
                            try:
                                element = elem.get_by_symbol(upper[0])
                            except KeyError:
                                pass
                    newAtom = top.addAtom(atomName, element, r, str(atom.serial_number))
                    atomByNumber[atom.serial_number] = newAtom
        self._positions = []
        for model in pdb.iter_models(True):
            coords = []
            for chain in model.iter_chains():
                for residue in chain.iter_residues():
                    for atom in residue.atoms:
                        pos = atom.get_position().value_in_unit(nanometers)
                        coords.append(Vec3(pos[0], pos[1], pos[2]))
            self._positions.append(coords*nanometers)
        ## The atom positions read from the PDB file.  If the file contains multiple frames, these are the positions in the first frame.
        self.positions = self._positions[0]
        self.topology.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
        self.topology.createStandardBonds()
        self.topology.createDisulfideBonds(self.positions)
#.........这里部分代码省略.........