def strandinfo(self):
for i in range(len(self.strands) - 1, -1, -1):
print self.startpos[i] + len(self.strands[i]) - 1
for j in range(len(self.strands[i]) - 1, -1, -1):
print str(self.strands[i][j][Ball.p_resseqid]).zfill(3) + aminoacid.getaacode(
self.strands[i][j][Ball.p_aaid]
)
print "~~~~~~~~~~~~~"
def writepdb(pdbfn, barrel, structname = '', pdb = False, sticks = False, supp = False):
balls = barrel.balls
if pdb:
supp = False
balls = barrel.pdbballs
chain = Bio.PDB.Chain.Chain("A")
for i in range(barrel.aanum):
res_id = (' ', balls[i][Ball.p_resseqid], ' ')
res_type = aminoacid.getaacode(balls[i][Ball.p_aaid])
res = Bio.PDB.Residue.Residue(res_id, res_type, ' ')
coord = (balls[i][Ball.p_coordx], balls[i][Ball.p_coordy], balls[i][Ball.p_coordz])
atom = Bio.PDB.Atom.Atom('CA', coord, 0, 0, ' ', 'CA', balls[i][Ball.p_resseqid], 'C')
res.add(atom)
chain.add(res)
if supp:
for i in range(barrel.aanum, len(balls)):
res_id = (' ', balls[i][Ball.p_resseqid], ' ')
res_type = 'X'
res = Bio.PDB.Residue.Residue(res_id, res_type, ' ')
coord = (balls[i][Ball.p_coordx], balls[i][Ball.p_coordy], balls[i][Ball.p_coordz])
atom = Bio.PDB.Atom.Atom('CA', coord, 0, 0, ' ', 'CA', balls[i][Ball.p_resseqid], 'C')
res.add(atom)
chain.add(res)
model = Bio.PDB.Model.Model(1)
model.add(chain)
structure = Bio.PDB.Structure.Structure(structname)
structure.add(model)
io = Bio.PDB.PDBIO()
io.set_structure(structure)
io.save(pdbfn, write_end=False)
with open(pdbfn, 'a') as fout:
if sticks:
if supp:
stknum = len(barrel.sticks)
else:
stknum = barrel.bondnum
for i in range(stknum):
id1 = barrel.sticks[i][Stick.p_ball1id]
id2 = barrel.sticks[i][Stick.p_ball2id]
#fout.write( 'CONECT%5d%5d\n' % (barrel.balls[id1][Ball.p_resseqid], barrel.balls[id2][Ball.p_resseqid]) )
fout.write( 'CONECT%5d%5d\n' % (id1+1, id2+1) )
fout.write('END\n')