def perform_orca(self, commandline, memory, execution_string, **kwargs):
"""Generate the orca input, run orca, assign new attributes and
update attribute values."""
orca_object = OrcaObject(commandline, memory, **kwargs)
orca_object.clean()
orca_object.generate_input(self.sdf_string)
orca_object.run_orca(execution_string)
orca_object.clean()
self.energy = orca_object.get_energy()
self.initial_sdf_string = self.sdf_string
self.sdf_string = xyz2sdf(orca_object.get_xyz_string_opt(),
self.mol_info.template_sdf_string)
for dof in self.dof:
setattr(dof, "initial_values", dof.values)
dof.update_values(self.sdf_string)
def perform_nwchem(self, functional, basis_set, execution_string):
"""Generate the NWChem input, run NWChem, assign new attributes and
update attribute values."""
nwchem_object = NWChemObject(functional, basis_set)
nwchem_object.clean()
nwchem_object.generate_input(self.sdf_string)
nwchem_object.run_nwchem(execution_string)
nwchem_object.clean()
self.energy = nwchem_object.get_energy()
self.initial_sdf_string = self.sdf_string
self.sdf_string = xyz2sdf(nwchem_object.get_xyz_string_opt(),
self.mol_info.template_sdf_string)
for dof in self.dof:
setattr(dof, "initial_values", dof.values)
dof.update_values(self.sdf_string)
def perform_orca(self, commandline, memory, execution_string, **kwargs):
"""Generate the orca input, run orca, assign new attributes and
update attribute values."""
orca_object = OrcaObject(commandline, memory, **kwargs)
orca_object.clean()
orca_object.generate_input(self.sdf_string)
orca_object.run_orca(execution_string)
orca_object.clean()
self.energy = orca_object.get_energy()
self.initial_sdf_string = self.sdf_string
self.sdf_string = xyz2sdf(orca_object.get_xyz_string_opt(),
self.mol_info.template_sdf_string)
for dof in self.dof:
setattr(dof, "initial_values", dof.values)
dof.update_values(self.sdf_string)
def perform_nwchem(self, functional, basis_set, execution_string):
"""Generate the NWChem input, run NWChem, assign new attributes and
update attribute values."""
nwchem_object = NWChemObject(functional, basis_set)
nwchem_object.clean()
nwchem_object.generate_input(self.sdf_string)
nwchem_object.run_nwchem(execution_string)
nwchem_object.clean()
self.energy = nwchem_object.get_energy()
self.initial_sdf_string = self.sdf_string
self.sdf_string = xyz2sdf(nwchem_object.get_xyz_string_opt(),
self.mol_info.template_sdf_string)
for dof in self.dof:
setattr(dof, "initial_values", dof.values)
dof.update_values(self.sdf_string)
def pyranosering_set(sdf_string, position, new_dih, new_ang):
""" Set the pyranosering.
Args:
sdf_string (string)
position (list): 7 atoms defining the ring, i.e. positions of
['C0','C1','C2','C3','C4','O', 'O0']
new_dih (list) : 5 values for the dihedral angles
new_ang (list): 5 values for the bond angles
Returns:
modified sdf_string
Raises:
ValueError: If the lenght of the position is not equal 7 ot if the
length of new_dih/new_ang is not equal to 5.
"""
if len(position) != 7:
raise ValueError("The position needs to be defined by 7 integers")
if len(new_dih) != 5:
raise ValueError("Five dihedral angles are needed for the new ring "
"conformation.")
if len(new_ang) != 5:
raise ValueError("Five bond angles are needed for the new ring "
"conformation.")
from scipy.linalg import expm3
atoms_ring = {}
for n, name in zip(range(len(position)),
['C0', 'C1', 'C2', 'C3', 'C4', 'O', 'O0']):
atoms_ring[name] = position[n]
def initialize(sdf_string):
molecule = Chem.MolFromMolBlock(sdf_string, removeHs=False)
return molecule
def calculate_normal_vector(list_of_atoms, xyz):
"""Calculate the normal vector of a plane by
cross product of two vectors belonging to it.
Args:
list_of_atoms: list of 3 atoms
xyz: numpy array with atoms xyz position
"""
r0 = xyz[list_of_atoms[1], :] - xyz[list_of_atoms[0], :]
r1 = xyz[list_of_atoms[2], :] - xyz[list_of_atoms[1], :]
cross_product = np.cross(r1, r0)
return cross_product
def measure_angle(list_of_atoms, xyz):
"""Calculate an angle between three atoms:
angle = acos(dot(X,Y)/(norm(X)*norm(Y)))
Args:
list_of_atoms: list of 3 atoms
xyz: numpy array with atoms xyz positions
"""
r0 = xyz[list_of_atoms[0], :] - xyz[list_of_atoms[1], :]
r1 = xyz[list_of_atoms[2], :] - xyz[list_of_atoms[1], :]
norm_r0 = np.sqrt(np.sum(r0**2))
norm_r1 = np.sqrt(np.sum(r1**2))
norm = norm_r0*norm_r1
dot_product = np.dot(r0, r1)/norm
angle = np.arccos(dot_product)
#Calculate the axis of rotation (axor):
axor = np.cross(r0, r1)
return angle*180.0/np.pi, axor
def measure_dihedral(list_of_atoms, xyz):
"""Calculate a dihedral angle between two planes defined by
a list of four atoms. It returns the angle and the rotation axis
required to set a new dihedral.
Args:
list_of_atoms: list of 4 atoms
xyz: numpy array with atom xyz positions
"""
plane1 = calculate_normal_vector(list_of_atoms[:3], xyz)
plane2 = calculate_normal_vector(list_of_atoms[1:], xyz)
#Calculate the axis of rotation (axor)
axor = np.cross(plane1, plane2)
#Calculate a norm of normal vectors:
norm_plane1 = np.sqrt(np.sum(plane1**2))
norm_plane2 = np.sqrt(np.sum(plane2**2))
norm = norm_plane1 * norm_plane2
#Measure the angle between two planes:
dot_product = np.dot(plane1, plane2)/norm
alpha = np.arccos(dot_product)
#The cosine function is symetric thus, to distinguish between
#negative and positive angles, one has to calculate if the fourth
#point is above or below the plane defined by first 3 points:
ppoint = - np.dot(plane1, xyz[list_of_atoms[0], :])
dpoint = (np.dot(plane1, xyz[list_of_atoms[3], :])+ppoint)/norm_plane1
if dpoint >= 0:
return -(alpha*180.0)/np.pi, axor
else:
return (alpha*180.0)/np.pi, axor
def determine_carried_atoms(at1, at2, conn_mat):
"""Find all atoms necessary to be carried over during rotation
of an atom 2:
Args:
at1, at2: two atoms number
"""
#1. Zero the connections in connectivity matrix
tmp_conn = np.copy(conn_mat)
tmp_conn[at1, at2] = 0
tmp_conn[at2, at1] = 0
#2. Determine the connected atoms:
carried_atoms = [at2]
s = True
while s:
s = False
#Always iterate over entire list because I might have branching
for at in carried_atoms:
#List of indexes of connected atoms:
conn_atoms = np.where(tmp_conn[at] != 0)[0]
conn_atoms.tolist
for x in conn_atoms:
if x not in carried_atoms:
carried_atoms.append(x)
s = True
return carried_atoms
def set_angle(list_of_atoms, new_ang, atoms_ring, xyz, conn_mat):
"""Set a new angle between three atoms
Args:
list_of_atoms: list of three atoms
new_ang: value of dihedral angle (in degrees) to be set
atoms_ring: dictionary of atoms in the ring. It recognizes
if the last atom is 'C0O' (obsolete)
xyz: numpy array with atoms xyz positions
conn_mat: connectivity matrix
Returns:
xyz: modified numpy array with new atoms positions
"""
#Determine the axis of rotation:
old_ang, axor = measure_angle(list_of_atoms, xyz)
norm_axor = np.sqrt(np.sum(axor**2))
normalized_axor = axor/norm_axor
#Determine which atoms should be dragged along with the bond:
carried_atoms = determine_carried_atoms(list_of_atoms[1],
list_of_atoms[2], conn_mat)
#Each carried_atom is rotated by euler-rodrigues formula:
#Also, I move the midpoint of the bond to the mid atom
#the rotation step and then move the atom back.
rot_angle = np.pi*(new_ang - old_ang)/180.
#Shake it, baby! Rotation matrix:
#print old_ang, new_ang, rot_angle*180./np.pi
rot1 = expm3(np.cross(np.eye(3), normalized_axor*rot_angle))
translation = xyz[list_of_atoms[1], :]
for at in carried_atoms:
xyz[at, :] = np.dot(rot1, xyz[at, :]-translation)
xyz[at, :] = xyz[at, :]+translation
return xyz
def set_dihedral(list_of_atoms, new_dih, atoms_ring, xyz, conn_mat):
"""Set a new dihedral angle between two planes defined by
atoms first and last three atoms of the supplied list.
Args:
list_of_atoms: list of four atoms
new_dih: value of dihedral angle (in degrees) to be set
atoms_ring: dictionary of atoms in the ring. It recognizes
if the last atom is 'C0O'
xyz: numpy array with atoms xyz positions
conn_mat: connectivity matrix
Returns:
xyz: modified numpy array with new atoms positions
"""
#Determine the axis of rotation:
old_dih, axor = measure_dihedral(list_of_atoms, xyz)
norm_axor = np.sqrt(np.sum(axor**2))
normalized_axor = axor/norm_axor
#Check if the bond is the last bond, next to broken one.
#If yes, refer to the oxygen:
if 'O0a' in atoms_ring.keys():
if list_of_atoms[-1] == atoms_ring['O0a']:
new_dih += 120.0
else:
if list_of_atoms[-1] == atoms_ring['O0b']:
new_dih -= 120.0
#Determine which atoms should be dragged along with the bond:
carried_atoms = determine_carried_atoms(list_of_atoms[1],
list_of_atoms[2], conn_mat)
#Each carried_atom is rotated by Euler-Rodrigues formula:
#Reverse if the angle is less than zero, so it rotates in
#right direction.
#Also, I move the midpoint of the bond to the center for
#the rotation step and then move the atom back.
if old_dih >= 0.0:
rot_angle = np.pi*(new_dih - old_dih)/180.
else:
rot_angle = -np.pi*(new_dih - old_dih)/180.
#Shake it, baby! Rotation matrix:
rot1 = expm3(np.cross(np.eye(3), normalized_axor*rot_angle))
translation = (xyz[list_of_atoms[1], :]+xyz[list_of_atoms[2], :])/2
for at in carried_atoms:
xyz[at, :] = np.dot(rot1, xyz[at, :]-translation)
xyz[at, :] = xyz[at, :]+translation
return xyz
def mutate_ring(molecule, new_dih, new_ang):
"""Mutate a ring to given conformation defined as a list of torsional
angles accoring to the 10.1016/S0040-4020(00)01019-X (IUPAC) paper
"""
n_at = molecule.GetNumAtoms()
n_bonds = molecule.GetNumBonds()
m_string = Chem.MolToMolBlock(molecule)
#Split the string to xyz, connectivity matrix and atom list
m_coords = m_string.split('\n')[4:4+n_at]
xyz = np.zeros((n_at, 3))
atom_list = []
n = 0
for line in m_coords:
xyz[n, :] += np.array(map(float, line.split()[:3]))
atom_list.append(line.split()[3])
n += 1
#Molecule Connectivity Matrix
m_conn = m_string.split('\n')[4+n_at:4+n_at+n_bonds]
conn_mat = np.zeros((n_at, n_at))
for line in m_conn:
at1 = int(line.split()[0])
at2 = int(line.split()[1])
conn_mat[at1-1, at2-1] = 1
conn_mat[at2-1, at1-1] = 1
#Introduce a cut between ring C0 and C1:
#I chose these atoms according to the torsion
#definitions in the IUPAC paper
#doi: 10.1016/S0040-4020(00)01019-X
conn_mat[atoms_ring['C0'], atoms_ring['C1']] = 0
conn_mat[atoms_ring['C1'], atoms_ring['C0']] = 0
#Construct a list of atoms in order:
#C0, C1, C2, C3, C4, O, C0, O0a/b (oxygen at anomeric carbon)
#I use this list to rotate bonds.
atoms_list = []
for x in range(0, 5):
atoms_list.append(atoms_ring['C'+str(x)])
atoms_list.append(atoms_ring['O'])
atoms_list.append(atoms_ring['C0'])
atoms_list.append(atoms_ring['O0'])
#Determine the anomer - alpha/beta, based on improper
#dihedral angle C1-C0-O-O0
imdih = []
for at in ['C1', 'C0', 'O', 'O0']:
imdih.append(atoms_ring[at])
test_anomer = measure_dihedral(imdih, xyz)[0]
if test_anomer > 0.0:
atoms_ring['O0b'] = atoms_ring.pop('O0')
else:
atoms_ring['O0a'] = atoms_ring.pop('O0')
#Adjust the 'internal' angles in the ring:
for n in range(len(new_ang)):
xyz = set_angle(atoms_list[n:n+3], new_ang[n], atoms_ring, xyz,
conn_mat)
#Rotate the dihedral angles in the ring:
for n in range(len(new_dih)):
xyz = set_dihedral(atoms_list[n:n+4], new_dih[n], atoms_ring, xyz,
conn_mat)
a = []
a.append("%10s\n" % n_at)
for n in new_dih:
a.append("%10.4f" % n)
a.append("\n")
for n in range(n_at):
a.append("%10s%10.4f%10.4f%10.4f\n" % (atom_list[n], xyz[n, 0],
xyz[n, 1], xyz[n, 2]))
xyz_string = ''.join(a)
return xyz_string
molecule = initialize(sdf_string)
sdf_string = xyz2sdf(mutate_ring(molecule, new_dih, new_ang), sdf_string)
return sdf_string
def pyranosering_set(sdf_string, position, new_dih, new_ang):
""" Set the pyranosering.
Args:
sdf_string (string)
position (list): 7 atoms defining the ring, i.e. positions of
['C0','C1','C2','C3','C4','O', 'O0']
new_dih (list) : 5 values for the dihedral angles
new_ang (list): 5 values for the bond angles
Returns:
modified sdf_string
Raises:
ValueError: If the lenght of the position is not equal 7 ot if the
length of new_dih/new_ang is not equal to 5.
"""
if len(position) != 7:
raise ValueError("The position needs to be defined by 7 integers")
if len(new_dih) != 5:
raise ValueError("Five dihedral angles are needed for the new ring "
"conformation.")
if len(new_ang) != 5:
raise ValueError("Five bond angles are needed for the new ring "
"conformation.")
from scipy.linalg import expm3
atoms_ring = {}
for n, name in zip(range(len(position)),
['C0', 'C1', 'C2', 'C3', 'C4', 'O', 'O0']):
atoms_ring[name] = position[n]
def initialize(sdf_string):
molecule = Chem.MolFromMolBlock(sdf_string, removeHs=False)
return molecule
def calculate_normal_vector(list_of_atoms, xyz):
"""Calculate the normal vector of a plane by
cross product of two vectors belonging to it.
Args:
list_of_atoms: list of 3 atoms
xyz: numpy array with atoms xyz position
"""
r0 = xyz[list_of_atoms[1], :] - xyz[list_of_atoms[0], :]
r1 = xyz[list_of_atoms[2], :] - xyz[list_of_atoms[1], :]
cross_product = np.cross(r1, r0)
return cross_product
def measure_angle(list_of_atoms, xyz):
"""Calculate an angle between three atoms:
angle = acos(dot(X,Y)/(norm(X)*norm(Y)))
Args:
list_of_atoms: list of 3 atoms
xyz: numpy array with atoms xyz positions
"""
r0 = xyz[list_of_atoms[0], :] - xyz[list_of_atoms[1], :]
r1 = xyz[list_of_atoms[2], :] - xyz[list_of_atoms[1], :]
norm_r0 = np.sqrt(np.sum(r0**2))
norm_r1 = np.sqrt(np.sum(r1**2))
norm = norm_r0 * norm_r1
dot_product = np.dot(r0, r1) / norm
angle = np.arccos(dot_product)
#Calculate the axis of rotation (axor):
axor = np.cross(r0, r1)
return angle * 180.0 / np.pi, axor
def measure_dihedral(list_of_atoms, xyz):
"""Calculate a dihedral angle between two planes defined by
a list of four atoms. It returns the angle and the rotation axis
required to set a new dihedral.
Args:
list_of_atoms: list of 4 atoms
xyz: numpy array with atom xyz positions
"""
plane1 = calculate_normal_vector(list_of_atoms[:3], xyz)
plane2 = calculate_normal_vector(list_of_atoms[1:], xyz)
#Calculate the axis of rotation (axor)
axor = np.cross(plane1, plane2)
#Calculate a norm of normal vectors:
norm_plane1 = np.sqrt(np.sum(plane1**2))
norm_plane2 = np.sqrt(np.sum(plane2**2))
norm = norm_plane1 * norm_plane2
#Measure the angle between two planes:
dot_product = np.dot(plane1, plane2) / norm
alpha = np.arccos(dot_product)
#The cosine function is symetric thus, to distinguish between
#negative and positive angles, one has to calculate if the fourth
#point is above or below the plane defined by first 3 points:
ppoint = -np.dot(plane1, xyz[list_of_atoms[0], :])
dpoint = (np.dot(plane1, xyz[list_of_atoms[3], :]) +
ppoint) / norm_plane1
if dpoint >= 0:
return -(alpha * 180.0) / np.pi, axor
else:
return (alpha * 180.0) / np.pi, axor
def determine_carried_atoms(at1, at2, conn_mat):
"""Find all atoms necessary to be carried over during rotation
of an atom 2:
Args:
at1, at2: two atoms number
"""
#1. Zero the connections in connectivity matrix
tmp_conn = np.copy(conn_mat)
tmp_conn[at1, at2] = 0
tmp_conn[at2, at1] = 0
#2. Determine the connected atoms:
carried_atoms = [at2]
s = True
while s:
s = False
#Always iterate over entire list because I might have branching
for at in carried_atoms:
#List of indexes of connected atoms:
conn_atoms = np.where(tmp_conn[at] != 0)[0]
conn_atoms.tolist
for x in conn_atoms:
if x not in carried_atoms:
carried_atoms.append(x)
s = True
return carried_atoms
def set_angle(list_of_atoms, new_ang, atoms_ring, xyz, conn_mat):
"""Set a new angle between three atoms
Args:
list_of_atoms: list of three atoms
new_ang: value of dihedral angle (in degrees) to be set
atoms_ring: dictionary of atoms in the ring. It recognizes
if the last atom is 'C0O' (obsolete)
xyz: numpy array with atoms xyz positions
conn_mat: connectivity matrix
Returns:
xyz: modified numpy array with new atoms positions
"""
#Determine the axis of rotation:
old_ang, axor = measure_angle(list_of_atoms, xyz)
norm_axor = np.sqrt(np.sum(axor**2))
normalized_axor = axor / norm_axor
#Determine which atoms should be dragged along with the bond:
carried_atoms = determine_carried_atoms(list_of_atoms[1],
list_of_atoms[2], conn_mat)
#Each carried_atom is rotated by euler-rodrigues formula:
#Also, I move the midpoint of the bond to the mid atom
#the rotation step and then move the atom back.
rot_angle = np.pi * (new_ang - old_ang) / 180.
#Shake it, baby! Rotation matrix:
#print old_ang, new_ang, rot_angle*180./np.pi
rot1 = expm3(np.cross(np.eye(3), normalized_axor * rot_angle))
translation = xyz[list_of_atoms[1], :]
for at in carried_atoms:
xyz[at, :] = np.dot(rot1, xyz[at, :] - translation)
xyz[at, :] = xyz[at, :] + translation
return xyz
def set_dihedral(list_of_atoms, new_dih, atoms_ring, xyz, conn_mat):
"""Set a new dihedral angle between two planes defined by
atoms first and last three atoms of the supplied list.
Args:
list_of_atoms: list of four atoms
new_dih: value of dihedral angle (in degrees) to be set
atoms_ring: dictionary of atoms in the ring. It recognizes
if the last atom is 'C0O'
xyz: numpy array with atoms xyz positions
conn_mat: connectivity matrix
Returns:
xyz: modified numpy array with new atoms positions
"""
#Determine the axis of rotation:
old_dih, axor = measure_dihedral(list_of_atoms, xyz)
norm_axor = np.sqrt(np.sum(axor**2))
normalized_axor = axor / norm_axor
#Check if the bond is the last bond, next to broken one.
#If yes, refer to the oxygen:
if 'O0a' in atoms_ring.keys():
if list_of_atoms[-1] == atoms_ring['O0a']:
new_dih += 120.0
else:
if list_of_atoms[-1] == atoms_ring['O0b']:
new_dih -= 120.0
#Determine which atoms should be dragged along with the bond:
carried_atoms = determine_carried_atoms(list_of_atoms[1],
list_of_atoms[2], conn_mat)
#Each carried_atom is rotated by Euler-Rodrigues formula:
#Reverse if the angle is less than zero, so it rotates in
#right direction.
#Also, I move the midpoint of the bond to the center for
#the rotation step and then move the atom back.
if old_dih >= 0.0:
rot_angle = np.pi * (new_dih - old_dih) / 180.
else:
rot_angle = -np.pi * (new_dih - old_dih) / 180.
#Shake it, baby! Rotation matrix:
rot1 = expm3(np.cross(np.eye(3), normalized_axor * rot_angle))
translation = (xyz[list_of_atoms[1], :] + xyz[list_of_atoms[2], :]) / 2
for at in carried_atoms:
xyz[at, :] = np.dot(rot1, xyz[at, :] - translation)
xyz[at, :] = xyz[at, :] + translation
return xyz
def mutate_ring(molecule, new_dih, new_ang):
"""Mutate a ring to given conformation defined as a list of torsional
angles accoring to the 10.1016/S0040-4020(00)01019-X (IUPAC) paper
"""
n_at = molecule.GetNumAtoms()
n_bonds = molecule.GetNumBonds()
m_string = Chem.MolToMolBlock(molecule)
#Split the string to xyz, connectivity matrix and atom list
m_coords = m_string.split('\n')[4:4 + n_at]
xyz = np.zeros((n_at, 3))
atom_list = []
n = 0
for line in m_coords:
xyz[n, :] += np.array(map(float, line.split()[:3]))
atom_list.append(line.split()[3])
n += 1
#Molecule Connectivity Matrix
m_conn = m_string.split('\n')[4 + n_at:4 + n_at + n_bonds]
conn_mat = np.zeros((n_at, n_at))
for line in m_conn:
at1 = int(line.split()[0])
at2 = int(line.split()[1])
conn_mat[at1 - 1, at2 - 1] = 1
conn_mat[at2 - 1, at1 - 1] = 1
#Introduce a cut between ring C0 and C1:
#I chose these atoms according to the torsion
#definitions in the IUPAC paper
#doi: 10.1016/S0040-4020(00)01019-X
conn_mat[atoms_ring['C0'], atoms_ring['C1']] = 0
conn_mat[atoms_ring['C1'], atoms_ring['C0']] = 0
#Construct a list of atoms in order:
#C0, C1, C2, C3, C4, O, C0, O0a/b (oxygen at anomeric carbon)
#I use this list to rotate bonds.
atoms_list = []
for x in range(0, 5):
atoms_list.append(atoms_ring['C' + str(x)])
atoms_list.append(atoms_ring['O'])
atoms_list.append(atoms_ring['C0'])
atoms_list.append(atoms_ring['O0'])
#Determine the anomer - alpha/beta, based on improper
#dihedral angle C1-C0-O-O0
imdih = []
for at in ['C1', 'C0', 'O', 'O0']:
imdih.append(atoms_ring[at])
test_anomer = measure_dihedral(imdih, xyz)[0]
if test_anomer > 0.0:
atoms_ring['O0b'] = atoms_ring.pop('O0')
else:
atoms_ring['O0a'] = atoms_ring.pop('O0')
#Adjust the 'internal' angles in the ring:
for n in range(len(new_ang)):
xyz = set_angle(atoms_list[n:n + 3], new_ang[n], atoms_ring, xyz,
conn_mat)
#Rotate the dihedral angles in the ring:
for n in range(len(new_dih)):
xyz = set_dihedral(atoms_list[n:n + 4], new_dih[n], atoms_ring,
xyz, conn_mat)
a = []
a.append("%10s\n" % n_at)
for n in new_dih:
a.append("%10.4f" % n)
a.append("\n")
for n in range(n_at):
a.append("%10s%10.4f%10.4f%10.4f\n" %
(atom_list[n], xyz[n, 0], xyz[n, 1], xyz[n, 2]))
xyz_string = ''.join(a)
return xyz_string
molecule = initialize(sdf_string)
sdf_string = xyz2sdf(mutate_ring(molecule, new_dih, new_ang), sdf_string)
return sdf_string