def load_crd(filename, object=''):
"""
Load a fDynamo coordinates file (.crd)
Parameters
----------
filename : str
file path
object : str, optional
name of the object (def: filename prefix)
"""
if not object:
object = "".join(os.path.basename(filename).rpartition('.')[:-2])
# read file as list of strings
with open(filename, "rt") as f:
crd_file = f.readlines()
# remove comment lines, trailing comments and space split
crd_file = [
line.split("!")[0].split() for line in crd_file
if line.strip() and not line.startswith("!")
]
# reversed dictionary of atomic numbers to elements
atomic_number_inv = {n: elem for elem, n in atomic_number.items()}
# create new model and append crd's atoms
model = Indexed()
a = Atom()
a.hetatm = False
for line in crd_file:
if line[0].lower() == "subsystem":
a.segi = str(line[2])
elif line[0].lower() == "residue":
a.resi_number = int(line[1])
a.resn = str(line[2])
elif len(line) != 6:
continue
else:
a.name = str(line[1])
a.symbol = atomic_number_inv[int(line[2])]
a.coord = (float(line[3]), float(line[4]), float(line[5]))
model.add_atom(deepcopy(a))
model.update_index()
cmd.load_model(model, object)
cmd.rebond(object)
cmd.dss(object)
print(f" pyDYNAMON: \"{filename}\" loaded as \"{object}\"")
def fromList(self,list): # currently no handling of conect records
model = Indexed()
# read atoms
cnt = 0
at = None
for rec in list:
if (rec[0:4]=='ATOM') or (rec[0:6]=='HETATM'):
at = Atom()
if rec[0]=='A': at.hetatm=0 # default is 1
at.index = cnt
at.name = string.strip(rec[12:16])
at.alt = string.strip(rec[16:17])
at.resn = string.strip(rec[17:20])
at.chain = string.strip(rec[21:22])
at.resi = string.strip(rec[22:27]) # note: insertion is part of resi
at.resi_number = int(rec[22:26])
at.coord = [float(rec[30:38]),
float(rec[38:46]),
float(rec[46:54])]
try:
at.q = float(rec[54:60])
except ValueError:
at.q = 1.0
try:
at.b = float(rec[60:66])
except ValueError:
at.b = 0.0
at.segi = string.strip(rec[72:76])
at.symbol = string.strip(rec[76:78])
if not len(at.symbol):
at.symbol = at.name[0:1]
if at.symbol in '012345678':
at.symbol = at.name[1:2]
cnt = cnt + 1
model.add_atom(at)
elif (rec[0:3]=='TER'):
if at:
at.ter=1
return(model)
def fromList(self,list): # currently no handling of conect records
model = Indexed()
# read atoms
cnt = 0
at = None
for rec in list:
if (rec[0:4]=='ATOM') or (rec[0:6]=='HETATM'):
at = Atom()
if rec[0]=='A': at.hetatm=0 # default is 1
at.index = cnt
at.name = string.strip(rec[12:16])
at.alt = string.strip(rec[16:17])
at.resn = string.strip(rec[17:20])
at.chain = string.strip(rec[21:22])
at.resi = string.strip(rec[22:27]) # note: insertion is part of resi
at.resi_number = int(rec[22:26])
at.coord = [float(rec[30:38]),
float(rec[38:46]),
float(rec[46:54])]
try:
at.q = float(rec[54:60])
except ValueError:
at.q = 1.0
try:
at.b = float(rec[60:66])
except ValueError:
at.b = 0.0
at.segi = string.strip(rec[72:76])
at.symbol = string.strip(rec[76:78])
if not len(at.symbol):
at.symbol = at.name[0:1]
if at.symbol in '012345678':
at.symbol = at.name[1:2]
cnt = cnt + 1
model.add_atom(at)
elif (rec[0:3]=='TER'):
if at:
at.ter=1
return(model)
def convert_to_chempy_model(atom_array):
"""
Convert an :class:`AtomArray` into a :class:`chempy.models.Indexed`
object.
Returns
-------
chempy_model : Indexed
The converted structure.
"""
model = IndexedModel()
annot_cat = atom_array.get_annotation_categories()
for i in range(atom_array.array_length()):
atom = Atom()
atom.segi = atom_array.chain_id[i]
atom.chain = atom_array.chain_id[i]
atom.resi_number = atom_array.res_id[i]
atom.ins_code = atom_array.ins_code[i]
res_name = atom_array.res_name[i]
atom.resn = res_name
if len(res_name) == 1:
atom.resn_code = res_name
else:
try:
atom.resn_code = ProteinSequence.convert_letter_3to1(res_name)
except KeyError:
atom.resn_code = "X"
atom.hetatm = 1 if atom_array.hetero[i] else 0
atom.name = atom_array.atom_name[i]
atom.symbol = atom_array.element[i]
if "b_factor" in annot_cat:
atom.b = atom_array.b_factor[i]
if "occupancy" in annot_cat:
atom.q = atom_array.occupancy[i]
if "charge" in annot_cat:
atom.formal_charge = atom_array.charge[i]
atom.coord = tuple(atom_array.coord[..., i, :])
atom.index = i + 1
model.add_atom(atom)
if atom_array.bonds is not None:
for i, j, bond_type in atom_array.bonds.as_array():
bond = Bond()
bond.order = BOND_ORDER[bond_type]
bond.index = [i, j]
model.add_bond(bond)
else:
warnings.warn(
"The given atom array (stack) has no associated bond information")
return model
