def pdb2psf_CA(pdb_name_in, psf_name_out, bonds=True, angles=True):
mol = Molecule(pdb_name_in)
mol.filter("name CA")
n = mol.numAtoms
atom_types = []
for i in range(n):
atom_types.append(CA_MAP[(mol.resname[i], mol.name[i])])
if bonds:
bonds = np.concatenate(
(
np.arange(n - 1).reshape([n - 1, 1]),
(np.arange(1, n).reshape([n - 1, 1])),
),
axis=1,
)
else:
bonds = np.empty([0, 2], dtype=np.int32)
if angles:
angles = np.concatenate(
(
np.arange(n - 2).reshape([n - 2, 1]),
(np.arange(1, n - 1).reshape([n - 2, 1])),
(np.arange(2, n).reshape([n - 2, 1])),
),
axis=1,
)
else:
angles = np.empty([0, 3], dtype=np.int32)
mol.atomtype = np.array(atom_types)
mol.bonds = bonds
mol.angles = angles
mol.write(psf_name_out)
def pdb2psf_CACB(pdb_name_in, psf_name_out, bonds=True, angles=True):
mol = Molecule(pdb_name_in)
mol.filter("name CA CB")
n = mol.numAtoms
atom_types = []
for i in range(n):
atom_types.append(CACB_MAP[(mol.resname[i], mol.name[i])])
CA_idx = []
CB_idx = []
for i, name in enumerate(mol.name):
if name[:2] == "CA":
CA_idx.append(i)
else:
CB_idx.append(i)
if bonds:
CA_bonds = np.concatenate(
(
np.array(CA_idx)[:-1].reshape([len(CA_idx) - 1, 1]),
np.array(CA_idx)[1:].reshape([len(CA_idx) - 1, 1]),
),
axis=1,
)
CB_bonds = np.concatenate(
(
np.array(CB_idx).reshape(len(CB_idx), 1) - 1,
np.array(CB_idx).reshape(len(CB_idx), 1),
),
axis=1,
)
bonds = np.concatenate((CA_bonds, CB_bonds))
else:
bonds = np.empty([0, 2], dtype=np.int32)
if angles:
CA_angles = np.concatenate(
(
np.array(CA_idx)[:-2].reshape([len(CA_idx) - 2, 1]),
np.array(CA_idx)[1:-1].reshape([len(CA_idx) - 2, 1]),
np.array(CA_idx)[2:].reshape([len(CA_idx) - 2, 1]),
),
axis=1,
)
CB_angles = []
cbn = 0
for i in CA_idx:
if mol.resname[i] != "GLY":
if i != 0:
CB_angles.append(
[CA_idx[CA_idx.index(i) - 1], i, CB_idx[cbn]])
if i != CA_idx[-1]:
CB_angles.append(
[CA_idx[CA_idx.index(i) + 1], i, CB_idx[cbn]])
cbn += 1
CB_angles = np.array(CB_angles)
angles = np.concatenate((CA_angles, CB_angles))
else:
angles = np.empty([0, 3], dtype=np.int32)
mol.atomtype = np.array(atom_types)
mol.bonds = bonds
mol.angles = angles
mol.write(psf_name_out)