Exemplo n.º 1
0
    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)
        self._numpyPositions = None

        # Add bonds based on CONECT records. Bonds between metals of elements specified in metalElements and residues in standardResidues are not added.

        connectBonds = []
        for connect in pdb.models[-1].connects:
            i = connect[0]
            for j in connect[1:]:
                if i in atomByNumber and j in atomByNumber:    
                    if atomByNumber[i].element is not None and atomByNumber[j].element is not None:
                        if atomByNumber[i].element.symbol not in metalElements and atomByNumber[j].element.symbol not in metalElements:
                            connectBonds.append((atomByNumber[i], atomByNumber[j])) 
                        elif atomByNumber[i].element.symbol in metalElements and atomByNumber[j].residue.name not in PDBFile._standardResidues:
                            connectBonds.append((atomByNumber[i], atomByNumber[j])) 
                        elif atomByNumber[j].element.symbol in metalElements and atomByNumber[i].residue.name not in PDBFile._standardResidues:
                            connectBonds.append((atomByNumber[i], atomByNumber[j]))     
                    else:
                        connectBonds.append((atomByNumber[i], atomByNumber[j]))         
        if len(connectBonds) > 0:
            # Only add bonds that don't already exist.
            existingBonds = set(top.bonds())
            for bond in connectBonds:
                if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
                    top.addBond(bond[0], bond[1])
                    existingBonds.add(bond)
Exemplo n.º 2
0
    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),
                                   residue.insertion_code)
                if resName in PDBFile._atomNameReplacements:
                    atomReplacements = PDBFile._atomNameReplacements[resName]
                else:
                    atomReplacements = {}
                for atom in residue.iter_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.iter_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. Bonds between metals of elements specified in metalElements and residues in standardResidues are not added.

        connectBonds = []
        for connect in pdb.models[-1].connects:
            i = connect[0]
            for j in connect[1:]:
                if i in atomByNumber and j in atomByNumber:
                    if atomByNumber[i].element is not None and atomByNumber[
                            j].element is not None:
                        if atomByNumber[
                                i].element.symbol not in metalElements and atomByNumber[
                                    j].element.symbol not in metalElements:
                            connectBonds.append(
                                (atomByNumber[i], atomByNumber[j]))
                        elif atomByNumber[
                                i].element.symbol in metalElements and atomByNumber[
                                    j].residue.name not in PDBFile._standardResidues:
                            connectBonds.append(
                                (atomByNumber[i], atomByNumber[j]))
                        elif atomByNumber[
                                j].element.symbol in metalElements and atomByNumber[
                                    i].residue.name not in PDBFile._standardResidues:
                            connectBonds.append(
                                (atomByNumber[i], atomByNumber[j]))
                    else:
                        connectBonds.append((atomByNumber[i], atomByNumber[j]))
        if len(connectBonds) > 0:
            # Only add bonds that don't already exist.
            existingBonds = set(top.bonds())
            for bond in connectBonds:
                if bond not in existingBonds and (
                        bond[1], bond[0]) not in existingBonds:
                    top.addBond(bond[0], bond[1])
                    existingBonds.add(bond)
Exemplo n.º 3
0
    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]))
        if len(connectBonds) > 0:
            # Only add bonds that don't already exist.
            existingBonds = set(top.bonds())
            for bond in connectBonds:
                if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
                    top.addBond(bond[0], bond[1])
                    existingBonds.add(bond)
Exemplo n.º 4
0
    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]))
        if len(connectBonds) > 0:
            # Only add bonds that don't already exist.
            existingBonds = set(top.bonds())
            for bond in connectBonds:
                if bond not in existingBonds and (
                        bond[1], bond[0]) not in existingBonds:
                    top.addBond(bond[0], bond[1])
                    existingBonds.add(bond)