import packages.binana.peel as peel
import packages.pymolecule.pymolecule as pymolecule
part_1 = pymolecule.Molecule()
part_1.fileio.load_pdb_into('helixPt1.pdb')
part_2 = pymolecule.Molecule()
part_2.fileio.load_pdb_into('helixPt2.pdb')
#peel_1.write_vmd_script_file('peel1.vmd'')
peel_1 = peel.peel(part_1, peel.defaultParams)
fmaps_1 = peel_1.create_feature_maps([25, 55, -25, 5, -15, 15], 1,
['hbondDonor', 'hbondAcceptor'])
peel_2 = peel.peel(part_2, peel.defaultParams)
fmaps_2 = peel_2.create_feature_maps([25, 55, -25, 5, -15, 15], 1,
['hbondDonor', 'hbondAcceptor'])
#peel_1.write_vmd_script_file('peel_1.vmd')
#peel_2.write_vmd_script_file('peel_2.vmd')
fmaps_1['hbondDonor'].write_dx_file('hbd1.dx')
fmaps_1['hbondAcceptor'].write_dx_file('hba1.dx')
fmaps_2['hbondDonor'].write_dx_file('hbd2.dx')
fmaps_2['hbondAcceptor'].write_dx_file('hba2.dx')
my_algebra = peel.algebra()
my_algebra.setScoreFuncs(
['hbondAcceptor_A * hbondDonor_B', 'hbondAcceptor_B * hbondDonor_A'])
my_score_maps, my_scores = my_algebra.scoreAll(fmaps_1, fmaps_2)
import packages.binana.peel as peel
import packages.pymolecule.pymolecule as pymolecule
my_params = peel.defaultParams
trp = pymolecule.Molecule()
trp.fileio.load_pdb_into('trp.pdb',
bonds_by_distance=True,
serial_reindex=True,
resseq_reindex=False)
my_peel = peel.peel(trp, my_params)
my_peel.write_vmd_script('visualize_trp.vmd', peel.defaultParams)
my_feature_maps = my_peel.create_feature_maps([-20, 20, -20, 20, -20, 20], 0.5)
my_feature_maps['hbondAcceptor'].write_pdb('HBA.pdb')
my_feature_maps['hbondDonor'].write_pdb('HBD.pdb')
my_feature_maps['aromatic'].write_pdb('ARO.pdb')
print "Done!"
import packages.binana.peel as peel
import packages.pymolecule.pymolecule as pymolecule
import numpy
features = [
'aromatic', 'hbondDonor', 'hbondAcceptor', 'hydrophobic', 'hydrophilic',
'hydrophobicity', 'occupancy'
]
mostly_empty = pymolecule.Molecule()
mostly_empty.fileio.load_pdb_into('mostly_empty.pdb')
my_peel = peel.peel(mostly_empty, peel.defaultParams)
one_point_fmaps_1 = my_peel.create_feature_maps([0, 0, 0, 0, 0, 0], 1,
features)
one_point_fmaps_2 = my_peel.create_feature_maps([0, 0, 0, 0, 0, 0], 1,
features)
print
print '======Beginning scoring ======'
for i in range(len(features)):
#So the point of featuremap_1 for aromatic will be set to 0, hBondDonor 2, etc...
one_point_fmaps_1[features[i]].setData(numpy.array([[[2 * i]]]))
#So the point of featuremap_2 for aromatic will be set to 1, hBondDonor 3, etc...
one_point_fmaps_2[features[i]].setData(numpy.array([[[(2 * i) + 1]]]))
print 'Setting %s to be %i for featuremap_A and %i for featuremap_B' % (
features[i], i * 2, (i * 2) + 1)
my_algebra = peel.algebra()
my_score_funcs = [
'hbondAcceptor_A * hbondDonor_B', 'hbondAcceptor_B * hbondDonor_A'
import numpy
import random
import os
import shutil
# This program demonstrates all the features of pymolecule 2.0, a python framework
# for loading, saving, and manipulating 3D molecular data.
########## First, set up the example directory ##########
if os.path.exists('./example_output'): shutil.rmtree('./example_output')
os.mkdir('./example_output')
########## Saving and Loading Molecular Data ##########
# First, create a molecule object.
molecule = pymolecule.Molecule()
#molecule.fileio.load_pym_into('./example_output/pym_example.pym') # remove this later
# Now, load a PDB file into that object. Calculate the bonds by distance, and
# reindex the serial and resseq fields. Definitions used::
# pymolecule.Molecule.fileio.load_pdb_into
# pymolecule.Molecule.fileio.load_pdb_into_using_file_object
# pymolecule.Molecule.fileio.serial_reindex
# pymolecule.Molecule.fileio.resseq_reindex
# pymolecule.Molecule.atoms_and_bonds.create_bonds_by_distance
# pymolecule.Molecule.selections.select_all_atoms_bound_to_selection
molecule.fileio.load_pdb_into('./example.pdb', True, True, True)
# Save the molecule object as a PDB file. The serial and resseq fields have
# already been reindexed, so we'll skip that. Definitions used:
# pymolecule.Molecule.fileio.save_pdb
centerCoords[proteinPdbPrefix] = [
numpy.mean(allCoords[proteinPdbPrefix][:, 0]),
numpy.mean(allCoords[proteinPdbPrefix][:, 1]),
numpy.mean(allCoords[proteinPdbPrefix][:, 2])
]
# Generate the PDB map
sideLength = 30
protein_boundaries = [
centerCoords[proteinPdbPrefix][0] - sideLength,
centerCoords[proteinPdbPrefix][0] + sideLength,
centerCoords[proteinPdbPrefix][1] - sideLength,
centerCoords[proteinPdbPrefix][1] + sideLength,
centerCoords[proteinPdbPrefix][2] - sideLength,
centerCoords[proteinPdbPrefix][2] + sideLength
]
protein_molecule = pymolecule.Molecule()
protein_molecule.fileio.load_pdb_into(pdbFileName,
serial_reindex=True,
resseq_reindex=False)
protein_peel = peel.peel(protein_molecule, my_params)
protein_feature_maps = protein_peel.create_feature_maps(
protein_boundaries, gridResolution, features=features)
# Now save the featureMaps for this protein
#with gzip.open('%s/%s_featureMaps.cPickle.gz' %(proteinFmOutputDir, proteinPdbPrefix),'wb') as my_file:
my_file = gzip.open(
'%s/%s_featureMaps.cPickle.gz' %
(proteinFmOutputDir, proteinPdbPrefix), 'wb')
cPickle.dump(protein_feature_maps, my_file, protocol=2)
my_file.close()
else:
#If the job is marked as started, let's see if it's finished. If so, load that receptor map
import packages.binana.peel as peel
import packages.pymolecule.pymolecule as pymolecule
#import numpy
my_params = peel.defaultParams
my_protein = pymolecule.Molecule()
my_protein.fileio.load_pdb_into('2gfc_reduced.pdb',
serial_reindex=True,
resseq_reindex=False)
my_peel = peel.peel(my_protein, my_params)
my_peel.write_vmd_script('visualize_2gfc.vmd', peel.defaultParams)
#povmeMap = numpy.ones((13,13,13))
#my_peel.color_povme_map(povmeMap, [0,13,0,13,0,13], 1)
# If given no "features" argument, create_feature_maps will create maps of all features
my_feature_maps = my_peel.create_feature_maps([10, 80, -30, 45, -30, 30], 1)
my_feature_maps['hbondAcceptor'].write_pdb('HBA.pdb')
my_feature_maps['hbondAcceptor'].write_dx_file('HBA.dx')
my_feature_maps['hbondDonor'].write_pdb('HBD.pdb')
my_feature_maps['hbondDonor'].write_dx_file('HBD.dx')
my_feature_maps['aromatic'].write_pdb('ARO.pdb')
my_feature_maps['aromatic'].write_dx_file('ARO.dx')
my_feature_maps['hydrophobic'].write_pdb('HPB.pdb')
my_feature_maps['hydrophobic'].write_dx_file('HPB.dx')
my_feature_maps['hydrophilic'].write_pdb('HPL.pdb')
my_feature_maps['hydrophilic'].write_dx_file('HPL.dx')
#my_feature_maps['hydrophobicity'].write_pdb('HPBTY.pdb')
#my_feature_maps['hydrophobicity'].write_dx_file('HPBTY.dx')
#import numpy
import packages.pymolecule.pymolecule as pymolecule
import packages.binana.peel as peel
import sys
#print sys.modules
my_params = peel.defaultParams
#DEFAULT
#arg = pymolecule.FileIO.load_pdb_into( 'arg.pdb', bonds_by_distance=True, serial_reindex = True, resseq_reindex=False)
arg = pymolecule.Molecule()
arg.fileio.load_pdb_into('arg.pdb',
bonds_by_distance=True,
serial_reindex=True,
resseq_reindex=False)
my_peel = peel.peel(arg, my_params)
my_peel.write_vmd_script('visualize_arg.vmd', peel.defaultParams)
my_feature_maps = my_peel.create_feature_maps([-10, 15, -5, 15, -10, 15], 1)
my_feature_maps['hbondAcceptor'].write_pdb('HBA.pdb')
my_feature_maps['hbondAcceptor'].write_dx_file('HBA.dx')
my_feature_maps['hbondDonor'].write_pdb('HBD.pdb')
my_feature_maps['hbondDonor'].write_dx_file('HBD.dx')
my_feature_maps['occupancy'].write_dx_file('OCC.dx')
#my_feature_maps['aromatic'].write_pdb('ARO.pdb') #don't bother with this
my_feature_maps['hydrophobic'].write_pdb('HBC.pdb')
my_feature_maps['hydrophilic'].write_pdb('HPL.pdb')
#my_feature_maps['hydrophobicity'].write_pdb('HPBTY.pdb')
#my_feature_maps['hydrophobicity'].write_dx_file('HPBTY.dx')
#HBAMap = my_feature_maps[0].data