def _make_solutepdb(atoms, masses, ligand):
"""
Make a solute PDB file
"""
mass2elem = {
1.0080000: "H",
12.0100000: "C",
14.0100000: "N",
16.0000000: "O",
32.0600000: "S",
35.4500000: "Cl",
19.0000000: "F",
79.9000000: "Br"
}
pdbout = pdb.PDBFile()
res = pdb.Residue()
res.resname = ligand
res.serial = 1
for i, (a, m) in enumerate(zip(atoms, masses), 1):
atom = pdb.Atom()
atom.serial = i
atom.hetatm = False
atom.name = "%s%d" % (mass2elem[m], i
) # Atom names from masses and serial number
atom.resname = ligand
atom.residue = 1
atom.set_xyz(a.xyz)
res.atoms.append(atom)
pdbout.atoms.append(atom)
pdbout.residues.append(res)
pdbout.write(ligand + ".pdb")
def write_singlepdb(filename, resname, atomname):
struct = pdb.PDBFile()
res = pdb.Residue()
atm = pdb.Atom()
atm.serial = 1
atm.name = atomname
atm.resname = resname
atm.residue = 1
res.append(atm)
struct.residues.append(res)
struct.write(filename)
def make(self, bd=3.0):
struct = pdb.PDBFile()
res = pdb.Residue()
for i, bead in enumerate(self.beads):
atom = pdb.Atom()
atom.idx = i
atom.serial = i + 1
atom.name = bead.name
atom.resname = self.name
atom.residue = 1
atom.set_xyz(bead.xyz * bd)
res.atoms.append(atom)
struct.atoms.append(atom)
struct.residues.append(res)
allcoord = np.asarray([a.xyz for a in struct.atoms])
offset = allcoord.mean(axis=0) + 50.0
for a in struct.atoms:
a.set_xyz(a.xyz + offset)
struct.box = np.asarray([100, 100, 100])
return struct
natomtypes - 1].mass
atom.set_mu([0.0, 0.0, 0.0])
conlist = [
aa_datafiles[res].bonds, aa_datafiles[res].angles,
aa_datafiles[res].dihedrals
]
for cons, ntypes in zip(conlist, contypes):
for con in cons:
con.param = con.param + ntypes
natomtypes = _ntypes(include.masses)
# Add a range of all-atom residues to the data file
moli = 0
if aa_range is not None:
first, last = map(lambda x: int(x) - 1, aa_range[1:].split("-"))
resall = pdb.Residue()
allres = []
for i in range(first, last + 1):
for atom in pdbfile.residues[i].atoms:
resall.append(atom)
allres.append(pdbfile.residues[i])
takeres[i] = False
_generate_aa_residue(resall, 1, aa_datafiles[aa_range], data)
moli = 1
if args.watrad is not None:
ninside = 0
com = [
np.asarray([res.collect("centerofmass")
for res in allres]).mean(axis=0)
]
rotate_struct(pdbfile, host, centroids[1]-centroids[0], 'z')
# Then rotate around the short axis of the host
host_xyz = host.collect("xyz")
rotate_struct(pdbfile, host, host_xyz[axis_indices[0][0],:]-
host_xyz[axis_indices[0][1],:], 'y')
# Next move G1 to the new origin
pdbfile.update_xyz(pdbfile.xyz-pdbfile.xyz[g1,:])
# And finally add three new residues with dummy atoms
new_xyz = [[0.000,3.500,-14.500],
[0.000,0.000,-11.000],
[0.000,0.000,-6.000]]
for i in range(3) :
res = pdb.Residue()
atom = pdb.Atom()
atom.idx = 1
atom.hetatm = False
atom.serial = 1
atom.name = " Pb "
atom.residue = 1
atom.resname = "DUM"
atom.set_xyz(new_xyz[i])
res.append(atom)
pdbfile.atoms.insert(0, atom)
pdbfile.residues.insert(0, res)
pdbfile.renumber()
if args.out is None :
args.out = os.path.splitext(args.file)[0]+"_apr.pdb"