def parse(self, filename):
filename = pmx_data_file(filename)
self.filename = filename
l = open(filename).readlines()
self.lines = kickOutComments(l,';')
self.__get_residue_names()
for key in self.keys:
rtp_lines = self.__read_residue_entry( key)
# read atoms
al = readSection(rtp_lines,'[ atoms ]','[')
atoms = self.__read_rtp_atoms(key, al )
# read bonds
bl = readSection(rtp_lines,'[ bonds ]','[')
bonds = self.__read_rtp_bonds( key, bl )
# read dihedrals
dl = readSection(rtp_lines,'[ dihedrals ]','[')
diheds = self.__read_rtp_dihedrals(key, dl)
# read impropers
il = readSection(rtp_lines,'[ impropers ]','[')
improps = self.__read_rtp_impropers(key, il)
# read cmap (only for charmm)
cmap = readSection(rtp_lines,'[ cmap ]','[')
#print cmap
#cmap = self.__read_rtp_cmap(key, cl)
self.entries[key] = {
'atoms': atoms,
'bonds': bonds,
'diheds': diheds,
'improps': improps,
'cmap' : cmap
}
def build_rna_strand(seq):
dic = pmx_data_file('rna.pkl')
seq = seq.lower()
ss = []
for x in seq:
ss.append(x)
new = []
new.extend(dic[ss[0]].residues)
ss.pop(0)
while ss:
newbp = ss.pop(0)
newm = dic[newbp].copy()
add_bp(newm, new, True)
new.extend(newm.residues)
chA = []
a = 1
for r in new:
r.set_resid(a)
a += 1
chA.append(r)
mm = Model(residues=chA)
mm.chains[0].set_chain_id('A')
for chain in mm.chains:
r = chain.residues[0]
r.set_resname(r.resname + '5')
make_5ter(r)
r = chain.residues[-1]
r.set_resname(r.resname + '3')
make_3ter(r)
return mm
def parse(self, filename):
filename = pmx_data_file(filename)
self.filename = filename
l = open(filename).readlines()
self.lines = kickOutComments(l,';')
self.__get_residue_names()
for key in self.keys:
rtp_lines = self.__read_residue_entry( key)
# read atoms
al = readSection(rtp_lines,'[ atoms ]','[')
atoms = self.__read_rtp_atoms(key, al )
# read bonds
bl = readSection(rtp_lines,'[ bonds ]','[')
bonds = self.__read_rtp_bonds( key, bl )
# read dihedrals
dl = readSection(rtp_lines,'[ dihedrals ]','[')
diheds = self.__read_rtp_dihedrals(key, dl)
# read impropers
il = readSection(rtp_lines,'[ impropers ]','[')
improps = self.__read_rtp_impropers(key, il)
# read cmap (only for charmm)
cmap = readSection(rtp_lines,'[ cmap ]','[')
#print cmap
#cmap = self.__read_rtp_cmap(key, cl)
self.entries[key] = {
'atoms': atoms,
'bonds': bonds,
'diheds': diheds,
'improps': improps,
'cmap' : cmap
}
def parse(self, filename, version):
if not hasattr(filename,"append"): # not a list
filename = pmx_data_file(filename)
l = open(filename).readlines()
self.filename = filename
else:
l = filename
self.filename = '< from list >'
self.lines = kickOutComments(l,';')
self.__parse_atomtypes(version)
def parse(self, filename, version):
if not hasattr(filename,"append"): # not a list
filename = pmx_data_file(filename)
l = open(filename).readlines()
self.filename = filename
else:
l = filename
self.filename = '< from list >'
self.lines = kickOutComments(l,';')
self.__parse_atomtypes(version)
def parse(self, filename):
if not hasattr(filename,"append"): # not a list
filename = pmx_data_file(filename)
self.filename = filename
l = open(filename).readlines()
else:
l = filename
self.filename = '< from list >'
self.lines = kickOutComments(l,';')
self.__parse_directives()
self.__parse_bondtypes()
self.__parse_angletypes()
self.__parse_dihedraltypes()
def parse(self, filename):
if not hasattr(filename,"append"): # not a list
filename = pmx_data_file(filename)
self.filename = filename
l = open(filename).readlines()
else:
l = filename
self.filename = '< from list >'
self.lines = kickOutComments(l,';')
self.__parse_directives()
self.__parse_bondtypes()
self.__parse_angletypes()
self.__parse_dihedraltypes()
def build_dna_strand(seq):
dic = pmx_data_file('bp.pkl')
seq = seq.lower()
ss = []
for x in seq:
ss.append(x)
new = []
new.extend(dic[ss[0]].residues)
ss.pop(0)
while ss:
newbp = ss.pop(0)
newm = dic[newbp].copy()
add_bp(newm, new)
new.extend(newm.residues)
chA = []
chB = []
a = 1
b = 1
for r in new:
if r.chain_id == 'B':
r.set_resid(a)
a += 1
chA.append(r)
else:
chB.append(r)
chB.reverse()
for r in chB:
r.set_resid(b)
b += 1
mm = Model(residues=chA + chB)
mm.chains[1].set_chain_id('C')
mm.chains[0].set_chain_id('A')
mm.chains[1].set_chain_id('B')
for chain in mm.chains:
r = chain.residues[0]
r.set_resname(r.resname + '5')
make_5ter(r)
r = chain.residues[-1]
r.set_resname(r.resname + '3')
make_3ter(r)
return mm
def build_dna_strand(seq):
dic = pmx_data_file('bp.pkl')
seq = seq.lower()
ss = []
for x in seq:
ss.append(x)
new = []
new.extend(dic[ss[0]].residues)
ss.pop(0)
while ss:
newbp = ss.pop(0)
newm = dic[newbp].copy()
add_bp(newm, new)
new.extend(newm.residues)
chA = []
chB = []
a = 1
b = 1
for r in new:
if r.chain_id == 'B':
r.set_resid(a)
a+=1
chA.append(r)
else:
chB.append(r)
chB.reverse()
for r in chB:
r.set_resid(b)
b+=1
mm = Model(residues=chA+chB)
mm.chains[1].set_chain_id('C')
mm.chains[0].set_chain_id('A')
mm.chains[1].set_chain_id('B')
for chain in mm.chains:
r = chain.residues[0]
r.set_resname(r.resname+'5')
make_5ter(r)
r = chain.residues[-1]
r.set_resname(r.resname+'3')
make_3ter(r)
return mm
def get_fragments():
dic = pmx_data_file('fragments.pkl')
n = len(dic.keys())
print >> sys.stderr, "pmx__> # Fragments loaded: %d" % n
return dic
def load_bbdep():
return pmx_data_file('bbdep.pkl')
def get_fragments():
dic = pmx_data_file('fragments.pkl')
n = len(dic.keys())
print >>sys.stderr,"pmx__> # Fragments loaded: %d" % n
return dic