def rotate_a_nucleic_group(this_group, rotate_type, residue_to_rotate, angle,
theta, backward, residues_in_group,
segnames_in_group, seg_type_in_group, txtOutput):
if (rotate_type == 'protein_backbone_dihedral'):
rotate_a_group(this_group, rotate_type, residue_to_rotate, angle,
theta, backward)
if (rotate_type == 'ds_nucleic'):
theta = theta * 180 / numpy.pi
# cg the group to rotate
assert seg_type_in_group[0] == seg_type_in_group[
1] == 'nucleic', 'flexible DNA should be first two segments in the group'
flex_resids = [residues_in_group[0]]
dna_resids = [[residues_in_group[0][0], residues_in_group[0][-1]],
[residues_in_group[1][-1], residues_in_group[1][0]]]
dna_segnames = [segnames_in_group[0], segnames_in_group[1]]
rigid_group = [segnames_in_group[2:]]
bp_per_bead = 1
(cg_dna, aa_dna, rigid_mol, vecXYZ, trialbeads, beadgroups,
rigid_move_masks, all_beads, dna_bead_masks, rigid_group_masks,
rigid_group_mols, aa_all, rigid_mask, aa_dna_mask, bp_per_bead_array,
pkl_file) = ddmc.get_cg_parameters(flex_resids,
dna_resids,
dna_segnames,
'this_group.dcd',
'this_group.pdb',
bp_per_bead,
txtOutput,
rigid_groups=rigid_group,
rm_pkl=True)
# determine which bead contains the residue to rotate
trial_bead = int(numpy.ceil(residue_to_rotate / float(bp_per_bead)))
# perform the rotation on that bead and subsequent DNA
d_coor = numpy.copy(cg_dna.coor()[0])
thetaXYZ = [theta, 0, 0]
r_coor = numpy.copy(rigid_mol.coor()[0])
(d_coor[trial_bead:], vecXYZ[:, trial_bead:],
r_coor) = ddmc.beadRotate(d_coor[trial_bead - 1:],
vecXYZ[:,
trial_bead - 1:], thetaXYZ, r_coor)
cg_dna.setCoor(numpy.array([d_coor]))
rigid_mol.setCoor(numpy.array([r_coor]))
# reverse cg the DNA
error = ddmc.recover_aaDNA_model(cg_dna, aa_dna, vecXYZ, all_beads,
dna_bead_masks)
aa_all.set_coor_using_mask(aa_dna, 0, aa_dna_mask)
aa_all.set_coor_using_mask(rigid_mol, 0, rigid_mask)
this_group.setCoor(aa_all.coor())
return
def rotate_a_nucleic_group(this_group, rotate_type, residue_to_rotate, angle,
theta, backward, residues_in_group,
segnames_in_group, seg_type_in_group, txtOutput):
if(rotate_type == 'protein_backbone_dihedral'):
rotate_a_group(
this_group, rotate_type, residue_to_rotate, angle, theta, backward)
if(rotate_type == 'ds_nucleic'):
theta = theta * 180 / numpy.pi
# cg the group to rotate
assert seg_type_in_group[0] == seg_type_in_group[
1] == 'nucleic', 'flexible DNA should be first two segments in the group'
flex_resids = [residues_in_group[0]]
dna_resids = [[residues_in_group[0][0], residues_in_group[0][-1]],
[residues_in_group[1][-1], residues_in_group[1][0]]]
dna_segnames = [segnames_in_group[0], segnames_in_group[1]]
rigid_group = [segnames_in_group[2:]]
bp_per_bead = 1
(cg_dna, aa_dna, rigid_mol, vecXYZ, trialbeads, beadgroups,
rigid_move_masks, all_beads, dna_bead_masks, rigid_group_masks,
rigid_group_mols, aa_all, rigid_mask, aa_dna_mask,
bp_per_bead_array, pkl_file) = ddmc.get_cg_parameters(flex_resids,
dna_resids, dna_segnames, 'this_group.dcd', 'this_group.pdb',
bp_per_bead, txtOutput, rigid_groups=rigid_group, rm_pkl=True)
# determine which bead contains the residue to rotate
trial_bead = int(numpy.ceil(residue_to_rotate / float(bp_per_bead)))
# perform the rotation on that bead and subsequent DNA
d_coor = numpy.copy(cg_dna.coor()[0])
thetaXYZ = [theta, 0, 0]
r_coor = numpy.copy(rigid_mol.coor()[0])
(d_coor[trial_bead:], vecXYZ[:, trial_bead:], r_coor) = ddmc.beadRotate(
d_coor[trial_bead - 1:], vecXYZ[:, trial_bead - 1:], thetaXYZ, r_coor)
cg_dna.setCoor(numpy.array([d_coor]))
rigid_mol.setCoor(numpy.array([r_coor]))
# reverse cg the DNA
error = ddmc.recover_aaDNA_model(
cg_dna, aa_dna, vecXYZ, all_beads, dna_bead_masks)
aa_all.set_coor_using_mask(aa_dna, 0, aa_dna_mask)
aa_all.set_coor_using_mask(rigid_mol, 0, rigid_mask)
this_group.setCoor(aa_all.coor())
return
def dna_main(pdb_file_name, number_of_groups, residues_in_groups, rotate_type,
group_to_rotate, residue_to_rotate, angle, theta, backward,
dna_segnames, dna_resids, bp_per_bead):
if rotate_type == 'ds_dna':
# determine which bead has the 'residue_to_rotate' in it
bead_to_rotate = 9
for i in xrange(100):
# treating this as thetaX
theta = theta + (5.0 * numpy.pi / 180.0)
thetaXYZ = [theta, 0, 0]
# rotate that bead
rotate_a_group_2(this_group, rotate_type, residue_to_rotate, angle,
theta, backward)
(cg_dna.coor()[0][bead_to_rotate:], vecXYZ[:, bead_to_rotate:],
dummy) = ddmc.beadRotate(cg_dna.coor()[0][bead_to_rotate - 1:],
vecXYZ[:, bead_to_rotate - 1:], thetaXYZ,
numpy.zeros((0, 3)))
# s rotate_dna_group(this_group, rotate_type, residue_to_rotate,
# angle, theta, backward)
else:
mol = sasmol.SasMol(0)
mol.read_pdb(pdb_file_name)
groups, group_masks = make_groups(mol, number_of_groups,
residues_in_groups)
this_group = groups[group_to_rotate]
itheta = theta
for i in xrange(100):
theta = theta + (5.0 * numpy.pi / 180.0)
rotate_a_group(this_group, rotate_type, residue_to_rotate, angle,
theta, backward)
return
def dna_main(pdb_file_name, number_of_groups, residues_in_groups,
rotate_type, group_to_rotate, residue_to_rotate, angle, theta,
backward, dna_segnames, dna_resids, bp_per_bead):
if rotate_type == 'ds_dna':
# determine which bead has the 'residue_to_rotate' in it
bead_to_rotate = 9
for i in xrange(100):
# treating this as thetaX
theta = theta + (5.0 * numpy.pi / 180.0)
thetaXYZ = [theta, 0, 0]
# rotate that bead
rotate_a_group_2(
this_group, rotate_type, residue_to_rotate, angle, theta, backward)
(cg_dna.coor()[0][bead_to_rotate:], vecXYZ[:, bead_to_rotate:], dummy
) = ddmc.beadRotate(cg_dna.coor()[0][bead_to_rotate - 1:],
vecXYZ[:, bead_to_rotate - 1:], thetaXYZ,
numpy.zeros((0, 3)))
# s rotate_dna_group(this_group, rotate_type, residue_to_rotate,
# angle, theta, backward)
else:
mol = sasmol.SasMol(0)
mol.read_pdb(pdb_file_name)
groups, group_masks = make_groups(
mol, number_of_groups, residues_in_groups)
this_group = groups[group_to_rotate]
itheta = theta
for i in xrange(100):
theta = theta + (5.0 * numpy.pi / 180.0)
rotate_a_group(
this_group, rotate_type, residue_to_rotate, angle, theta, backward)
return
