def test_Write_6(self):
if not haveStride: return
from MolKit import Read
self.mol = Read("Data/1crn.pdb")[0]
self.mol.secondaryStructureFromStride()
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_writer.pdb', self.mol,
records=['ATOM', 'HETATM', 'CONECT',
'TURN','HELIX', 'SHEET'],
bondOrigin='all', ssOrigin='Stride')
# Make sure that the ss information has been written out
# properly.
nmol = Read("Data/1crn_writer.pdb")[0]
nmol.secondaryStructureFromFile()
nsset = nmol.chains[0].secondarystructureset
osset = self.mol.chains[0].secondarystructureset
self.assertEqual(len(nsset), len(osset))
for nss, oss in map(None, nsset, osset):
self.assertEqual(nss.name, oss.name)
self.assertEqual(nss.start.name,oss.start.name)
self.assertEqual(nss.end.name, oss.end.name)
self.assertEqual(len(nss.residues), len(oss.residues))
os.system("rm Data/1crn_writer.pdb")
def __init__(self, filename):
self.input_file = Read(filename)[0]
self.output = filename.split('.')[0] + '.pdb'
writer = PdbWriter()
writer.write(self.output,
self.input_file.allAtoms,
records=['ATOM', 'HETATM'])
def __init__(self, original_pdb, pqr_file, metal):
self.ori_pdb = Read(original_pdb)[0]
self.pqr = Read(pqr_file)[0]
self.metal = metal
self.new_pdb = pqr_file.split('.')[0] + '.pdb'
if self.metal:
zn = self.ori_pdb.allAtoms.get(lambda x: x.element == 'Zn')
# remove hydrogens added to HYS residues near ZN atoms
close_atoms = self.pqr.closerThan(zn[0].coords, self.pqr.allAtoms,
2.3)
# FIXME: only take the first atoms in list
for a in close_atoms:
if a.element == 'H':
# print a.name
for b in a.bonds:
at2 = b.atom1
if at2 == a: at2 = b.atom2
at2.bonds.remove(b)
a.bonds.remove(b)
a.parent.remove(a)
del a
self.pqr.allAtoms = self.pqr.chains.residues.atoms + zn
writer = PdbWriter()
writer.write(self.new_pdb,
self.pqr.allAtoms,
records=['ATOM', 'HETATM'])
def write_pdb(pdbqt_parser, outfile): mol = pdbqt_parser[0] mol.buildBondsByDistance() mol.allAtoms.number = range(1, len(mol.allAtoms) + 1) writer = PdbWriter() writer.write(outfile, mol.allAtoms, records=['HETATM'], sort=1, bondOrigin=0)
def __init__(self, original_pdb, pqr_file, metals):
self.ori_pdb = Read(original_pdb)[0]
self.pqr = Read(pqr_file)[0]
self.metals = metals
self.new_pdb = pqr_file.split('.')[0] + '.pdb'
uniq_list = {} # to avoid redundancy
if self.metals:
for met in self.metals:
ele = met[1][:3].strip().lower()
if ele not in uniq_list.keys():
uniq_list[ele] = met[2]
else:
continue
met_atoms = self.ori_pdb.allAtoms.get(lambda x: x.element.lower() in uniq_list)
for atm in met_atoms:
atm.charge = uniq_list[atm.element.lower()]
print 'atoms charge', atm.element, uniq_list[atm.element.lower()]
for met_atm in met_atoms:
close_atoms = self.pqr.closerThan(met_atm.coords, self.pqr.allAtoms, 2.8)
for a in close_atoms:
if a.element == 'H':
for b in a.bonds:
at2 = b.atom1
if at2 == a: at2 = b.atom2
at2.bonds.remove(b)
a.bonds.remove(b)
a.parent.remove(a)
del a
self.pqr.allAtoms = self.pqr.chains.residues.atoms
self.pqr.allAtoms = self.pqr.chains.residues.atoms + met_atoms
writer = PdbWriter()
writer.write(self.new_pdb, self.pqr.allAtoms, records=['ATOM', 'HETATM'])
def test_write(self):
"""
test writing a pdb file
"""
writer = PdbWriter()
writer.write('test_pdbWriter.pdb', self.mol, bondOrigin=('File',))
ans, errors = self.compare('Data/1crn.pdb', 'test_pdbWriter.pdb')
self.assertEquals(errors, None)
self.assertEquals(ans, True)
def buildPdb(map_dict,
npts,
name='DlgBuilt',
ctr=0,
outputfile='results.pdb',
scale=1.0):
if debug: print "in buildPdb: tolerance=", tolerance
name = 'DlgBuilt'
mol = Protein(name=name)
mol.curChain = Chain()
mol.chains = ChainSet([mol.curChain])
mol.curRes = Residue()
mol.curChain.adopt(mol.curRes)
mol.allAtoms = AtomSet()
mol.curRes.atoms = mol.allAtoms
nzpts = nypts = nxpts = npts
#nxpts, nypts, nzpts = npts
ctr = 0
for ADtype, m in map_dict.items():
if debug:
print "PROCESSING ", ADtype, " array:", max(m.ravel()), ':', min(
m.ravel())
vals = []
tctr = 0 #for number of each type
for z in range(nzpts):
for y in range(nypts):
for x in range(nxpts):
val = scale * abs(m[x, y, z])
vals.append(val)
#if abs(val)>.005:
if val > tolerance * scale:
ctr += 1
name = ADtype + str(ctr)
#version3:
#info_lo = (xcen - numxcells*spacing,
# ycen - numycells*spacing,
# zcen - numzcells *spacing)
#using lower back pt of cube, i think
#xcoord = (x-info_lo[0])/spacing
#ycoord = (y-info_lo[1])/spacing
#zcoord = (z-info_lo[2])/spacing
#version2:
xcoord = (x - numxcells) * spacing + xcen
ycoord = (y - numycells) * spacing + ycen
zcoord = (z - numzcells) * spacing + zcen
coords = (xcoord, ycoord, zcoord)
tctr += 1
# #print "addAtom: name=",name,"ADtype=", ADtype," val=", val, "coords=", coords,"ctr=", ctr
addAtom(mol, name, ADtype, val, coords, ctr)
print "added ", tctr, '<-', ADtype, " atoms"
if debug:
print ADtype, ':', tctr, ' ', ctr
print "total atoms=", ctr
writer = PdbWriter()
writer.write(outputfile, mol.allAtoms, records=['ATOM'])
def test_write_2(self):
"""
Tests that PdbWriter can write molecule parsed by MMCIFParser
"""
# read a molecule
parser = MMCIFParser(filename='Data/1CRN.cif')
mol = parser.parse()
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_mmcifwriter.pdb', mol)
os.remove('Data/1crn_mmcifwriter.pdb')
def get_ligand(self, sel, filename):
selection = sel.split(':')
new_mol = None
for chain in self.mol.chains:
for res in chain.residues:
# exclude water residues
if res.name[:3] in ['WAT', 'HOH', 'SOL', ' ZN']:
continue
if selection == [chain.name, res.name[:3], res.name[3:]]:
new_mol = makeMoleculeFromAtoms('ligand', res.atoms)
writer = PdbWriter()
writer.write(filename, new_mol.allAtoms, records=['ATOM', 'HETATM'])
return new_mol
def test_write_2(self):
"""
Tests that PdbWriter can write molecule parsed by MMCIFParser
"""
# read a molecule
parser = MMCIFParser(filename='Data/1CRN.cif')
mol = parser.parse()
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_mmcifwriter.pdb', mol)
os.remove('Data/1crn_mmcifwriter.pdb')
def buildPdb(map_dict, npts, name='DlgBuilt', ctr=0, outputfile='results.pdb',
scale=1.0):
if debug: print "in buildPdb: tolerance=", tolerance
name = 'DlgBuilt'
mol = Protein(name=name)
mol.curChain = Chain()
mol.chains = ChainSet([mol.curChain])
mol.curRes = Residue()
mol.curChain.adopt(mol.curRes)
mol.allAtoms = AtomSet()
mol.curRes.atoms = mol.allAtoms
nzpts=nypts=nxpts = npts
#nxpts, nypts, nzpts = npts
ctr = 0
for ADtype, m in map_dict.items():
if debug:
print "PROCESSING ", ADtype, " array:", max(m.ravel()), ':', min(m.ravel())
vals = []
tctr = 0 #for number of each type
for z in range(nzpts):
for y in range(nypts):
for x in range(nxpts):
val = scale * abs(m[x,y,z])
vals.append(val)
#if abs(val)>.005:
if val>tolerance*scale:
ctr += 1
name = ADtype + str(ctr)
#version3:
#info_lo = (xcen - numxcells*spacing,
# ycen - numycells*spacing,
# zcen - numzcells *spacing)
#using lower back pt of cube, i think
#xcoord = (x-info_lo[0])/spacing
#ycoord = (y-info_lo[1])/spacing
#zcoord = (z-info_lo[2])/spacing
#version2:
xcoord = (x-numxcells)*spacing + xcen
ycoord = (y-numycells)*spacing + ycen
zcoord = (z-numzcells)*spacing + zcen
coords = (xcoord,ycoord,zcoord)
tctr += 1
# #print "addAtom: name=",name,"ADtype=", ADtype," val=", val, "coords=", coords,"ctr=", ctr
addAtom(mol, name, ADtype, val, coords, ctr)
print "added ",tctr, '<-', ADtype, " atoms"
if debug:
print ADtype, ':', tctr , ' ', ctr
print "total atoms=", ctr
writer = PdbWriter()
writer.write(outputfile, mol.allAtoms, records=['ATOM'])
def test_Write_2(self):
"""
Test writing out CONECT records for the bonds described in
the pdb file and built by distance.
"""
from MolKit import Read
self.mol = Read("Data/1crn.pdb")[0]
self.mol.buildBondsByDistance()
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_writer.pdb', self.mol)
from MolKit.pdbParser import PdbParser
nmol = Read("Data/1crn_writer.pdb")[0]
os.system("rm Data/1crn_writer.pdb")
def test_Write_1(self):
"""
Test the default option of the write method of a PdbWriter.
Just write the ATOM, HETATM and CONECT records and bondOrigin
is File.
"""
# read a molecule
from MolKit import Read
self.mol = Read("Data/1crn.pdb")[0]
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_writer.pdb', self.mol)
# This should write only the ATOM and CONECT records
# The TER records are automatically created with the ATOM records
# 1- Make sure that the file has been created
import os
self.failUnless(os.path.exists('Data/1crn_writer.pdb'))
# 2- Make sure that the file created the proper records
# Get the default records from the new pdb files
from MolKit.pdbParser import PdbParser
nmol = Read("Data/1crn_writer.pdb")[0]
# COMPARE
ncoords = nmol.allAtoms.coords
ocoords = self.mol.allAtoms.coords
self.assertEqual(ncoords, ocoords)
nname = nmol.allAtoms.name
oname = nmol.allAtoms.name
self.assertEqual(nname, oname)
nbonds = nmol.allAtoms.bonds[0]
obonds = self.mol.allAtoms.bonds[0]
self.assertEqual(len(nbonds), len(obonds))
nbatms = nbonds.atom1+nbonds.atom2
nbatms = nbatms.uniq()
nbatms.sort()
nbatms = nbonds.atom1+nbonds.atom2
nbatms = nbatms.uniq()
nbatms.sort()
os.system("rm Data/1crn_writer.pdb")
def test_Write_4(self):
"""
Test writing out the ATOM records and the CONECT records
without the HETATM
"""
from MolKit import Read
self.mol = Read("Data/1bsr.pdb")[0]
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1bsr_writer.pdb', self.mol,
records=['ATOM', 'CONECT'], bondOrigin=('File',))
nmol = Read("Data/1bsr_writer.pdb")[0]
nhoh = nmol.chains.residues.get(lambda x: x.type=="HOH")
ohoh = self.mol.chains.residues.get(lambda x: x.type=="HOH")
self.failUnless(len(nhoh)==0)
os.system("rm Data/1bsr_writer.pdb")
def test_Write_4Char_AtomNames(self):
""" check that atoms with names of 4+char are written properly"""
from MolKit import Read
self.mol = Read("Data/HTet.mol2")[0]
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/test_HTet.pdb', self.mol)
testmol = Read("Data/test_HTet.pdb")[0]
self.assertEqual(len(self.mol.allAtoms), len(testmol.allAtoms))
#check the 4char atoms have correct element types
self.assertEqual(testmol.allAtoms[0].element, 'C')
self.assertEqual(testmol.allAtoms[1].element, 'Cl')
self.assertEqual(testmol.allAtoms[22].element, 'N')
self.assertEqual(testmol.allAtoms[23].element, 'H')
#check the 4char atoms have reasonable names
self.assertEqual(testmol.allAtoms[0].name, 'C11')
self.assertEqual(testmol.allAtoms[1].name, 'Cl22')
self.assertEqual(testmol.allAtoms[22].name, 'N61')
self.assertEqual(testmol.allAtoms[23].name, 'HN61')
os.system("rm Data/test_HTet.pdb")
def writeCoords(self,score=None,filename1=None,filename2=None,
sort=True, transformed=False,
pdbRec=['ATOM', 'HETATM', 'CONECT'],
bondOrigin='all', ssOrigin=None):
""" write the coords of the molecules in pdb file
pdb is file will have the molecule name follow by number of conformation
"""
writer = PdbWriter()
if score is None:
score = min( self.confcoords.keys())
if not self.confcoords.has_key(float(score)): return
c1 = self.confcoords[score][0]
c2 = self.confcoords[score][1]
if filename1 is None:
filename1 = self.mol1.name + '_1.pdb'
prev_conf = self.setCoords(self.atomset1,c1)
writer.write(filename1, self.atomset1, sort=sort, records=pdbRec,
bondOrigin=bondOrigin, ssOrigin=ssOrigin)
self.atomset1.setConformation(prev_conf)
if filename2 is None:
filename2 = self.mol2.name + '_1.pdb'
prev_conf = self.setCoords(self.atomset2,c2)
writer.write(filename2, self.atomset2, sort=sort, records=pdbRec,
bondOrigin=bondOrigin, ssOrigin=ssOrigin)
self.atomset2.setConformation(prev_conf)
usage()
sys.exit()
mol = Read(filename)[0]
if verbose: print('read ', filename)
filetype = os.path.splitext(os.path.basename(filename))[1]
if verbose: print("filetype=", filetype)
writer = None
if filetype == '.pdbqt':
writer = PdbqtWriter()
elif filetype == '.pdbq':
writer = PdbqWriter()
elif filetype == '.pdbqs':
writer = PdbqsWriter()
elif filetype == '.pdb':
writer = PdbWriter()
else:
print('Sorry! Unable to write this filetype->', filetype)
center = numpy.add.reduce(mol.allAtoms.coords) / len(mol.allAtoms)
crds = numpy.array(mol.allAtoms.coords)
center = numpy.add.reduce(crds) / len(mol.allAtoms)
crds = crds - center
crds = crds.tolist()
mol.allAtoms.updateCoords(crds)
lenCoords = len(crds)
#rotate the atoms here
if axis is not None and angle is not None:
rot = (float(angle) * 3.14159 / 180.) % (2 * numpy.pi)
x = numpy.array([0., 0., 0.])
y = numpy.array(list(map(float, axis.split(','))))
usage()
sys.exit()
if not pdbqt_filename:
print 'pdbqt_to_pdb: pdbqt_filename must be specified.'
usage()
sys.exit()
mols = Read(pdbqt_filename)
if verbose: print 'read ', pdbqt_filename
mol = mols[0]
mol.buildBondsByDistance()
#fix number for problem files with alternative positions
mol.allAtoms.number = range(1, len(mol.allAtoms)+1)
#pdb_filename = mol.name + '.pdb'
writer = PdbWriter()
writer.write(pdb_filename, mol.allAtoms, records=['ATOM', 'HETATM'])
if verbose:
print "wrote ", 'ctr', " atoms to", pdb_filename
# To execute this command type:
# pdbqt_to_pdb.py -f pdbqt_filename_stem [-o outputfilename] -v
def WritePDB(filename, node):
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write(filename, node)
def save_pdb(self, filename):
""" avoid errors when visualize entry protein in pdbqt format"""
mol = Read(filename)[0]
writer = PdbWriter()
writer.write(self.pdb, mol.allAtoms, records=['ATOM', 'HETATM'])
def WritePDB(filename,node):
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write(filename, node)
usage()
sys.exit()
if not pdbqt_filename:
print 'pdbqt_to_pdb: pdbqt_filename must be specified.'
usage()
sys.exit()
mols = Read(pdbqt_filename)
if verbose: print 'read ', pdbqt_filename
mol = mols[0]
mol.buildBondsByDistance()
#fix number for problem files with alternative positions
mol.allAtoms.number = range(1, len(mol.allAtoms)+1)
#pdb_filename = mol.name + '.pdb'
writer = PdbWriter()
writer.write(pdb_filename, mol.allAtoms, records=['ATOM', 'HETATM'])
if verbose:
print "wrote ", ctr, " atoms to", pdb_filename
# To execute this command type:
# pdbqt_to_pdb.py -f pdbqt_filename_stem [-o outputfilename] -v
def test_constructor(self):
"""
instantiate an PdbWriter
"""
writer = PdbWriter()
self.assertEquals(writer.__class__, PdbWriter)