import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
## molecule_name is the name of the residue that gets used in mbuild and gromacs
## so ensure molecule_name matches the itp file
#######################
xmlfile = "ecer3-hairpin.xml"
molecule_name = "ecer3"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[58, 104])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file),
overwrite=True,
residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
#######################
## Example script to convert an ITP file into an mBuild compound python module
## Note that the xyz coordinates must be pulled from another file
####################
ref_molecule = mb.load('ffa18.mol2')
#molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('ffa18.itp')
cmpd = itp_utils.coordinates_from_compound(ref_molecule, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [3, 17])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name],
overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
bilayer = mb.load('npt.pdb')
molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('dspc.itp')
cmpd = itp_utils.coordinates_from_compound(molecule, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [32,89])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name], overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
#first_tail = cmpd.children[3:54]
#second_tail = [a for a in cmpd.children[55:109] if 'C' in a.name]
# Doing simple tail rotations
#ref_vector = second_tail[-1].xyz - second_tail[0].xyz
#cmpd_vector = first_tail[-1].xyz - first_tail[0].xyz
#
#theta = mb.coordinate_transform.angle(cmpd_vector[0], ref_vector[0])
#normal = np.cross(cmpd_vector[0], ref_vector[0])
#
#for a in first_tail:
# a.rotate(theta-0.2, normal)
#cmpd.save('new_isis.gro', overwrite=True, residues='ISIS')
# Then run then run an EM
# Then reorient according to convention
cmpd = itp_utils.compound_from_itp("ISIS.itp")
coords = mb.load('em_nopbc.gro')
cmpd = itp_utils.coordinates_from_compound(coords, cmpd)
cmpd.name='ISIS'
first_tail = cmpd.children[3:54]
second_tail = [a for a in cmpd.children[55:109] if 'C' in a.name]
cmpd = xml_utils.align_cmpd(cmpd, [3, 51])
cmpd.save('isis.mol2',
residues=[cmpd.name], overwrite=True)
xml_utils.write_compound_py(cmpd, 'isis.mol2')
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
## molecule_name is the name of the residue that gets used in mbuild and gromacs
## so ensure molecule_name matches the itp file
#######################
xmlfile = "ucer2-extended.xml"
molecule_name = "ucer2"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[74, 70])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file), overwrite=True, residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
## molecule_name is the name of the residue that gets used in mbuild and gromacs
## so ensure molecule_name matches the itp file
#######################
xmlfile = "ecer2-hairpin.xml"
molecule_name = "ecer2"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[57, 101])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file), overwrite=True, residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
## molecule_name is the name of the residue that gets used in mbuild and gromacs
## so ensure molecule_name matches the itp file
#######################
xmlfile = "ecer2-extended.xml"
molecule_name = "ecer2"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[50, 46])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file),
overwrite=True,
residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
#######################
## Example script to convert an ITP file into an mBuild compound python module
## Note that the xyz coordinates must be pulled from another file
####################
bilayer = mb.load('npt.pdb')
molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('dppc.itp')
cmpd = itp_utils.coordinates_from_compound(molecule, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [83, 47])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name],
overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
#######################
xmlfile = "cholesterol.xml"
molecule_name = "chol"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[0, 64])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file), overwrite=True, residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
#######################
## Example script to convert an ITP file into an mBuild compound python module
## Note that the xyz coordinates must be pulled from another file
####################
ref_molecule = mb.load('oh16.pdb')
#molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('oh16.itp')
cmpd = itp_utils.coordinates_from_compound(ref_molecule, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [46, 24])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name],
overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
#######################
## Example script to convert an ITP file into an mBuild compound python module
## Note that the xyz coordinates must be pulled from another file
####################
ref_molecule = mb.load('oh18.pdb')
#molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('oh18.itp')
cmpd = itp_utils.coordinates_from_compound(ref_molecule, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [55,25])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name], overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
#######################
## Example script to convert an ITP file into an mBuild compound python module
## Note that the xyz coordinates must be pulled from another file
####################
bilayer = mb.load('oh12.pdb')
#molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('oh12.itp')
cmpd = itp_utils.coordinates_from_compound(bilayer, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [34, 18])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name],
overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
#######################
xmlfile = "cer-eos-hairpin.xml"
molecule_name = "cer1"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[24,195])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file), overwrite=True, residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
#######################
xmlfile = "c16ffa.xml"
molecule_name = "ffa16"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[15, 0])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file), overwrite=True, residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
## molecule_name is the name of the residue that gets used in mbuild and gromacs
## so ensure molecule_name matches the itp file
#######################
xmlfile = "ucer2-hairpin-charmm.xml"
molecule_name = "ucer2"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd, align_indices=[81, 125])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file),
overwrite=True,
residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
#######################
## Example script to convert an ITP file into an mBuild compound python module
## Note that the xyz coordinates must be pulled from another file
####################
charmmgui = mb.load('oh24.pdb')
#molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('oh24.itp')
cmpd = itp_utils.coordinates_from_compound(charmmgui, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [70, 36])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name],
overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
import scripts.xml_utils as xml_utils
import mbuild as mb
import pdb
#########################
## This is a code to generate an mBuild compound from prototype.xml
## While the prototype.xml may not be properly aligned,
## the resulting mBuild compound is aligned
## Tail tip is origin, headgroup at highest Z coordinate
## molecule_name is the name of the residue that gets used in mbuild and gromacs
## so ensure molecule_name matches the itp file
#######################
xmlfile = "tip3p.xml"
molecule_name = "SOL"
structure_file = molecule_name + ".mol2"
cmpd = xml_utils.compound_from_xml(xmlfile, a_to_nm=True, name=molecule_name)
# Perform aligning
cmpd = xml_utils.align_cmpd(cmpd,
align_indices=[0, int(cmpd.n_particles / 2), -1])
# Save structure and bonding information
cmpd.save('{}'.format(structure_file),
overwrite=True,
residues=[molecule_name])
# Write compound.py file
xml_utils.write_compound_py(cmpd, structure_file)
import mbuild as mb
import scripts.xml_utils as xml_utils
dopc = mb.load('dopc.gro')
dopc.name = 'DOPC'
chl = mb.load('new_chl1.gro')
chl.name = 'CHL1'
new_dopc = xml_utils.align_cmpd(dopc, [0, 87])
new_dopc.name = dopc.name
new_chl = xml_utils.align_cmpd(chl, [1, 64])
new_chl.name = chl.name
new_dopc.save('aligned_dopc.gro', residues='DOPC')
new_chl.save('aligned_chl.gro', residues='CHL1')
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
#######################
## Example script to convert an ITP file into an mBuild compound python module
## Note that the xyz coordinates must be pulled from another file
####################
ref_molecule = mb.load('oh20.pdb')
#molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('oh20.itp')
cmpd = itp_utils.coordinates_from_compound(ref_molecule, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [30, 57])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name],
overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
import mbuild as mb
import scripts.xml_utils as xml_utils
import scripts.itp_utils as itp_utils
import pdb
bilayer = mb.load('npt.pdb')
molecule = bilayer.children[0]
cmpd = itp_utils.compound_from_itp('dppc.itp')
cmpd = itp_utils.coordinates_from_compound(molecule, cmpd)
aligned_cmpd = xml_utils.align_cmpd(cmpd, [44, 83])
aligned_cmpd.save('{}.mol2'.format(aligned_cmpd.name),
residues=[aligned_cmpd.name],
overwrite=True)
xml_utils.write_compound_py(aligned_cmpd, '{}.mol2'.format(aligned_cmpd.name))
