Example #1
0
def PDBFromGrofile(grofile,
                   stripWaters=False,
                   stripIons=False,
                   stripDummy=False):
    """Take in a *.gro Grofile file and write it as a PDB file."""

    gstruct = GromacsStructure(name=grofile, header="title")
    gstruct.load(grofile)

    p = PDBStructure()

    for gatom in gstruct.atoms:

        atom = {}
        atom["serial"] = gatom.atomnum
        atom["name"] = '%-4s' % (gatom.atomname.strip())
        atom["altLoc"] = ' '
        atom["resName"] = '%-4s' % (gatom.resname.strip())
        atom["chainID"] = ' '
        atom["resSeq"] = gatom.resnum
        atom["iCode"] = ' '
        atom["x"] = gatom.x * 10.  # *.gro files are in nm
        atom["y"] = gatom.y * 10.
        atom["z"] = gatom.z * 10.
        atom["occupancy"] = 1.0
        atom["tempFactor"] = 0.0
        atom["segID"] = '    '
        atom["element"] = '  '
        atom["charge"] = '   '

        if (atom["resName"].count('HOH') > 0) or (atom["resName"].count('SOL')
                                                  > 0):
            if not stripWaters:
                atoms.append(atom)
        elif (atom["resName"].count('Cl') > 0) or (atom["resName"].count('Na')
                                                   > 0):
            if not stripIons:
                atoms.append(atom)
        elif (atom["resName"].count('DMM') > 0):
            if not stripDummy:
                p.atoms.append(atom)
        else:
            p.atoms.append(atom)

    return p
Example #2
0
def PDBFromGrofile(grofile, stripWaters=False, stripIons=False, stripDummy=False):
    """Take in a *.gro Grofile file and write it as a PDB file."""
    
    gstruct = GromacsStructure(name=grofile, header="title" )
    gstruct.load(grofile)
    
    p = PDBStructure()
    
    for gatom in gstruct.atoms:

        atom = { }
        atom["serial"] = gatom.atomnum
        atom["name"] = '%-4s'%(gatom.atomname.strip())
        atom["altLoc"] = ' '
        atom["resName"] = '%-4s'%(gatom.resname.strip())
        atom["chainID"] = ' '        
        atom["resSeq"] = gatom.resnum
        atom["iCode"] = ' '
        atom["x"] = gatom.x*10.    # *.gro files are in nm
        atom["y"] = gatom.y*10.
        atom["z"] = gatom.z*10.
        atom["occupancy"] = 1.0
        atom["tempFactor"] = 0.0
        atom["segID"] = '    '
        atom["element"] = '  '
        atom["charge"] = '   '

        if (atom["resName"].count('HOH')>0) or (atom["resName"].count('SOL')>0):
          if not stripWaters:
            atoms.append(atom)
        elif (atom["resName"].count('Cl')>0) or (atom["resName"].count('Na')>0):
          if not stripIons:
            atoms.append(atom)
        elif (atom["resName"].count('DMM')>0):
          if not stripDummy:
            p.atoms.append(atom)
        else:
            p.atoms.append(atom)

    return p
Example #3
0
def GromacsStructureFromGrofile(grofile):
    """Create a GromacsStructure objects from a grofile."""

    gstruct = GromacsStructure(name=grofile, header="title")
    gstruct.load(grofile)
    return gstruct
Example #4
0
def GromacsStructureFromGrofile(grofile):
    """Create a GromacsStructure objects from a grofile."""
    
    gstruct = GromacsStructure(name=grofile, header="title" )
    gstruct.load(grofile)
    return gstruct