def createHTMLTypeMap(self, definition, outfilename):
"""
Create an HTML typemap file at the desired location. If a
type cannot be found for an atom a blank is listed.
Parameters
definition: The definition objects.
outfilename: The name of the file to write (string)
"""
from forcefield import Forcefield
from server import STYLESHEET
# Cache the initial atom numbers
numcache = {}
for atom in self.getAtoms():
numcache[atom] = atom.serial
self.reSerialize()
amberff = Forcefield("amber", definition, None)
charmmff = Forcefield("charmm", definition, None)
file = open(outfilename, "w")
file.write("<HTML>\n")
file.write("<HEAD>\n")
file.write("<TITLE>PQR Typemap (beta)</TITLE>\n")
file.write('<link rel="stylesheet" href="%s" type="text/css">\n' % STYLESHEET)
file.write("</HEAD>\n")
file.write("<BODY>\n")
file.write("<H3>This is a developmental page including the atom type for the atoms in the PQR file.</H3><P>\n")
file.write("<TABLE CELLSPACING=2 CELLPADDING=2 BORDER=1>\n")
file.write(
"<tr><th>Atom Number</th><th>Atom Name</th><th>Residue Name</th><th>Chain ID</th><th>AMBER Atom Type</th><th>CHARMM Atom Type</th></tr>\n"
)
for atom in self.getAtoms():
if isinstance(atom.residue, Amino) or isinstance(atom.residue, WAT) or isinstance(atom.residue, Nucleic):
resname = atom.residue.ffname
else:
resname = atom.residue.name
ambergroup = amberff.getGroup(resname, atom.name)
charmmgroup = charmmff.getGroup(resname, atom.name)
file.write(
"<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>\n"
% (atom.serial, atom.name, resname, atom.chainID, ambergroup, charmmgroup)
)
file.write("</table>\n")
file.write("</BODY></HTML>\n")
file.close()
# Return the original numbers back
for atom in self.getAtoms():
atom.serial = numcache[atom]
del numcache
del amberff
del charmmff
def __init__(self, db_file=None):
if not db_file and db_file is not False:
db_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, os.pardir, 'dat', 'forcefields', 'tip3p.xml')
Forcefield.__init__(self, db_file)
self.ff_name = 'tip3p'
self.pair_style = 'lj'
self.ff_class = '1'
def __init__(self, db_file=None):
if not db_file and db_file is not False:
db_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, os.pardir, 'dat', 'forcefields', 'gaff.json')
Forcefield.__init__(self, db_file)
self.name = 'gaff'
self.pair_style = 'lj'
self.bond_style = 'harmonic'
self.angle_style = 'harmonic'
self.dihedral_style = 'fourier'
self.improper_style = 'cvff'
self.ff_class = '1'
def __init__(self, db_file=None):
if not db_file and db_file is not False:
db_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, os.pardir, 'dat', 'forcefields', 'pcff.xml')
Forcefield.__init__(self, db_file)
self.name = 'pcff'
self.ff_class = '2'
self.pair_style = 'class2'
self.bond_style = 'class2'
self.angle_style = 'class2'
self.dihedral_style = 'class2'
self.improper_style = 'class2'
self.nb_mixing = 'sixth'
def __init__(self, db_file=None):
if not db_file and db_file is not False:
db_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, os.pardir, 'dat', 'forcefields',
'dreiding.xml')
Forcefield.__init__(self, db_file)
self.ff_name = 'dreiding'
self.pair_style = 'buck'
self.bond_style = 'harmonic'
self.angle_style = 'harmonic'
self.dihedral_style = 'harmonic'
self.improper_style = 'harmonic'
self.ff_class = '1'
def createHTMLTypeMap(self, definition, outfilename):
"""
Create an HTML typemap file at the desired location. If a
type cannot be found for an atom a blank is listed.
Parameters
definition: The definition objects.
outfilename: The name of the file to write (string)
"""
from forcefield import Forcefield
from aconf import STYLESHEET
# Cache the initial atom numbers
numcache = {}
for atom in self.getAtoms():
numcache[atom] = atom.serial
self.reSerialize()
amberff = Forcefield("amber", definition, None)
charmmff = Forcefield("charmm", definition, None)
file = open(outfilename, "w")
file.write("<HTML>\n")
file.write("<HEAD>\n")
file.write("<TITLE>PQR Typemap (beta)</TITLE>\n")
file.write("<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET)
file.write("</HEAD>\n")
file.write("<BODY>\n")
file.write("<H3>This is a developmental page including the atom type for the atoms in the PQR file.</H3><P>\n")
file.write("<TABLE CELLSPACING=2 CELLPADDING=2 BORDER=1>\n")
file.write("<tr><th>Atom Number</th><th>Atom Name</th><th>Residue Name</th><th>Chain ID</th><th>AMBER Atom Type</th><th>CHARMM Atom Type</th></tr>\n")
for atom in self.getAtoms():
if isinstance(atom.residue, (Amino, WAT, Nucleic)):
resname = atom.residue.ffname
else:
resname = atom.residue.name
ambergroup = amberff.getGroup(resname, atom.name)
charmmgroup = charmmff.getGroup(resname, atom.name)
file.write("<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>\n" % (atom.serial, atom.name, resname, atom.chainID, ambergroup, charmmgroup))
file.write("</table>\n")
file.write("</BODY></HTML>\n")
file.close()
# Return the original numbers back
for atom in self.getAtoms():
atom.serial = numcache[atom]
del numcache
del amberff
del charmmff