Python PDBFile._loadNameReplacementTables方法代码示例

# 需要导入模块: from simtk.openmm.app import PDBFile [as 别名]
# 或者: from simtk.openmm.app.PDBFile import _loadNameReplacementTables [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 PDBFile [as 别名]
# 或者: from simtk.openmm.app.PDBFile import _loadNameReplacementTables [as 别名]
    def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
        """Load a top file.

        Parameters
        ----------
        file : str
            the name of the file to load
        periodicBoxVectors : tuple of Vec3=None
            the vectors defining the periodic box
        unitCellDimensions : Vec3=None
            the dimensions of the crystallographic unit cell.  For
            non-rectangular unit cells, specify periodicBoxVectors instead.
        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'):
#.........这里部分代码省略.........

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

        # 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]

            # Get the element from the prmtop file if available
            if prmtop.has_atomic_number:
                try:
                    element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
                except KeyError:
                    element = None
            else:
                # Try to guess the element from the atom name.

                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('ZN'):
                    element = elem.zinc
                else:
                    try:
                        element = elem.get_by_symbol(atomName[0])
                    except KeyError:
                        element = None

            top.addAtom(atomName, element, r)
            self.elements.append(element)

        # 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():
            box = prmtop.getBoxBetaAndDimensions()
            top.setPeriodicBoxVectors(computePeriodicBoxVectors(*(box[1:4] + box[0:1]*3)))

# 需要导入模块: from simtk.openmm.app import PDBFile [as 别名]
# 或者: from simtk.openmm.app.PDBFile import _loadNameReplacementTables [as 别名]
    def __init__(self, file, unitCellDimensions=None, includeDir='/usr/local/gromacs/share/gromacs/top', defines={}):
        """Load a top file.

        Parameters:
         - file (string) the name of the file to load
         - unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell
         - includeDir (string=/usr/local/gromacs/share/gromacs/top) a directory in which to look for other files
           included from the top file
         - defines (map={}) preprocessor definitions that should be predefined when parsing the file
         """
        self._includeDirs = (os.path.dirname(file), includeDir)
        self._defines = defines

        # Parse the file.

        self._currentCategory = None
        self._ifStack = []
        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
        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]

            # 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])