def get_object_sequence(selection='sele'):
'''
DESCRIPTION
:param selection: the selected object in pymol
:return: the object's sequence
'''
print cmd.get_fastastr(
hf.get_selection_details(selection)['pdb_object_name'])
def testDoubleRNAFASTA(self):
rna = "AUUUUUUUCG"
cmd.fnab(input=rna, mode="RNA", form="B", dbl_helix=1)
fasta_str = cmd.get_fastastr().splitlines()
self.assertEqual(len(fasta_str), 2)
sense_strand = fasta_str[1]
self.assertEqual(rna, sense_strand)
def testDoubleRNAFASTA(self):
rna = "AUUUUUUUCG"
cmd.fnab(input=rna, mode="RNA", form="B", dbl_helix=1)
fasta_str = cmd.get_fastastr().splitlines()
self.assertEqual(len(fasta_str), 2)
sense_strand = fasta_str[1]
self.assertEqual(rna, sense_strand)
def get_sequence(obj):
seq = ''
for chain in cmd.get_chains(obj):
seq_ = cmd.get_fastastr(f'{obj} and chain {chain} and polymer.protein')
seq_ = seq_.split()[1:]
seq_ = ''.join(seq_)
seq += seq_
return seq
def testDoubleDNAFASTA(self):
dna = "ATCCCCG"
revcomp = "CGGGGAT"
cmd.fnab(input=dna, dbl_helix=1)
fasta_str = cmd.get_fastastr().splitlines()
fasta_raw = (fasta_str[1], fasta_str[3])
sense_strand = fasta_raw[0]
antisense_strand = fasta_raw[1]
self.assertEqual(dna, sense_strand)
self.assertEqual(revcomp, antisense_strand)
cmd.delete('all')
cmd.fnab(input=dna)
fasta_str = cmd.get_fastastr().splitlines()
fasta_raw = (fasta_str[1], fasta_str[3])
sense_strand = fasta_raw[0]
antisense_strand = fasta_raw[1]
self.assertEqual(dna, sense_strand)
self.assertEqual(revcomp, antisense_strand)
def testDoubleDNAFASTA(self):
dna = "ATCCCCG"
revcomp = "CGGGGAT"
cmd.fnab(input=dna, dbl_helix=1)
fasta_str = cmd.get_fastastr().splitlines()
fasta_raw = (fasta_str[1], fasta_str[3])
sense_strand = fasta_raw[0]
antisense_strand = fasta_raw[1]
self.assertEqual(dna, sense_strand)
self.assertEqual(revcomp, antisense_strand)
cmd.delete('all')
cmd.fnab(input=dna)
fasta_str = cmd.get_fastastr().splitlines()
fasta_raw = (fasta_str[1], fasta_str[3])
sense_strand = fasta_raw[0]
antisense_strand = fasta_raw[1]
self.assertEqual(dna, sense_strand)
self.assertEqual(revcomp, antisense_strand)
def test_CanGetNewRNASequence(self):
cmd.load(self.datafile("1rna.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1rna/A/A/14")
cmd.get_wizard().mode = "Guanine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1rna/A/A").splitlines()[1]
self.assertEqual(seq, "UUAUAUAUAUAUAG")
def test_CanGetNewDNASequence(self):
cmd.load(self.datafile("1bna.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1bna/A/A/1")
cmd.get_wizard().mode = "Adenine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1bna/A/A").splitlines()[1]
self.assertEqual(seq, "AGCGAATTCGCG")
def test_CanMutateNonCanonicalNucleo(self):
cmd.load(self.datafile("1k5e.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1k5e/A/A/6")
cmd.get_wizard().mode = "Adenine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1k5e/A/A").splitlines()[1]
self.assertEqual(seq, "CGGACAAGAAG")
def test_CanGetNewDNASequence(self):
cmd.load(self.datafile("1bna.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1bna/A/A/1")
cmd.get_wizard().mode = "Adenine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1bna/A/A").splitlines()[1]
self.assertEqual(seq, "AGCGAATTCGCG")
def test_CanGetNewRNASequence(self):
cmd.load(self.datafile("1rna.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1rna/A/A/14")
cmd.get_wizard().mode = "Guanine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1rna/A/A").splitlines()[1]
self.assertEqual(seq, "UUAUAUAUAUAUAG")
def test_CanMutateNonCanonicalNucleo(self):
cmd.load(self.datafile("1k5e.cif"))
cmd.wizard("nucmutagenesis")
cmd.select("/1k5e/A/A/6")
cmd.get_wizard().mode = "Adenine"
cmd.get_wizard().do_select("sele")
cmd.get_wizard().apply()
seq = cmd.get_fastastr("/1k5e/A/A").splitlines()[1]
self.assertEqual(seq, "CGGACAAGAAG")
def Mutagenesis(kinase1, model, template,peptide_instance):
"""superposition the model and template, remove template and leave peptide behind """
"""replace peptide with instance peptide"""
list_name = peptide_instance
with open(input_data_folder+list_name,'r') as f:
instances = f.readlines()
instance = [x.strip() for x in instances]
print "your peptide: ", instance
for pep in instance:
cmd.delete('all')
cmd.fetch(model) # model_candidate, ex.chk1,chk2...
cmd.remove("hetatm") #remove the nonstandard residues
cmd.fetch(template) #mutagenesis template, ex.2phk
peptide_template = cmd.get_fastastr( "/"+template+'//B') #get the peptide from the template and generate another one for mutagenesis
peptide_template = peptide_template + 'G' #peptide of 2phk is 7 amino acid long, when our input peptide is 8 aa, we need to plus one character
for aa in peptide_template[6:].lower(): #creat template_peptide for mutagenesis
cmd._alt(aa)
firstaa = AAcode_1_to_3(peptide_template[6]) #translate template_peptide to 3 letter
low_firstaa = firstaa[0].lower()
cmd.alter(low_firstaa, 'chain = "B"') #select this template_peptide
cmd.show_as("cartoon")
cmd.align(model, template) #superpostion of model and template
cmd.align(low_firstaa,template) #superpostion of template_peptide and template
remove_part = "("+template+" and not resn ATP"+")"
cmd.select("remove_part",remove_part)
cmd.remove("remove_part") #remove the template except for ATP, there are only model and template_peptide
cmd.remove("resn hoh") #remove water
cmd.wizard("mutagenesis")
peptide_position = 0
for i in pep:
#the peptide_position starting point depends the first position of mutagenesis peptide
#pymol's peptide start from 1, not 0
mutagenesis_template = '/'+low_firstaa+ '///' + str(peptide_position + 2) # because of 2phk start at 2nd of peptide
#mutagenesis_template = '/' + template + '//B/' + str(peptide_position + 2)
cmd.get_wizard().do_select(mutagenesis_template) # select peptide position of mutation
replace_aminoacid = AAcode_1_to_3(pep)[peptide_position]
cmd.get_wizard().set_mode(replace_aminoacid) # select which residue want to mutate to
cmd.get_wizard().apply()
peptide_position += 1
filename = kinase1 + '_' + model + 'model_' + template + 'muta_' + pep + '.pdb' #build the canonical name
cmd.save(filename)
ATPchange(filename) #change ATP naming to the format of ATP.params
cmd.wizard(None)
return
def testGetFastastr(self):
seq, name = 'ACD', 'm1'
cmd.fab(seq, name)
s = cmd.get_fastastr()
lines = s.split()
self.assertTrue(lines[0] in (
'>' + name,
'>' + name + '_',
))
self.assertEqual(lines[1:], [seq])
def testGetFastastr(self):
seq, name = 'ACD', 'm1'
cmd.fab(seq, name)
s = cmd.get_fastastr()
lines = s.split()
self.assertTrue(lines[0] in (
'>' + name,
'>' + name + '_',
))
self.assertEqual(lines[1:], [seq])
def find_mutations(obj1, obj2, sel_name='mutations'):
from pymol import stored, CmdException
if cmd.count_atoms(obj1) == 0:
print '%s is empty'%obj1
return
if cmd.count_atoms(obj2) == 0:
print '%s is empty'%obj2
return
seq1 = ''.join(cmd.get_fastastr(obj1).split('\n')[1:])
seq2 = ''.join(cmd.get_fastastr(obj2).split('\n')[1:])
muts = []
for i, aa in enumerate(seq1):
if aa != seq2[i]:
muts.append(i)
if not muts:
print('no mutations')
return
percent = 100 * float(len(muts)) / float(len(seq1))
print 'found %i mutations with %s, which is %.2f' % (len(muts), obj2,
percent)
# this is a correction for PDBs that are not renumbered, also if there's
# a MEM residue in the middle of the numbering...
stored.resis = []
stored.resns = []
cmd.iterate(obj1, 'stored.resis.append(resi)')
cmd.iterate(obj1, 'stored.resns.append(resn)')
resnums = sorted(list(set([int(a) for a, n in zip(stored.resis,
stored.resns)
if n != 'MEM'])))
seq_num_resnum = {ind+1: val for ind, val in enumerate(resnums)}
muts_s = ['%s' % str(seq_num_resnum[a+1]) for a in muts]
muts_sel = '((%s and resi %s) or (%s and resi %s))' % (obj1,
'+'.join(muts_s),
obj2,
'+'.join(muts_s))
cmd.select(sel_name, muts_sel)
def testMixedCase(self):
dna = "AtG"
revcomp = "CAT"
cmd.fnab(input=dna)
fasta_str = cmd.get_fastastr().splitlines()
fasta_raw = (fasta_str[1], fasta_str[3])
sense_strand = fasta_raw[0]
antisense_strand = fasta_raw[1]
self.assertEqual(dna.upper(), sense_strand)
self.assertEqual(revcomp, antisense_strand)
def testMixedCase(self):
dna = "AtG"
revcomp = "CAT"
cmd.fnab(input=dna)
fasta_str = cmd.get_fastastr().splitlines()
fasta_raw = (fasta_str[1], fasta_str[3])
sense_strand = fasta_raw[0]
antisense_strand = fasta_raw[1]
self.assertEqual(dna.upper(), sense_strand)
self.assertEqual(revcomp, antisense_strand)
def get_chain_sequence(selection='sele'):
'''
DESCRIPTION:
:param selection: the selected object in pymol
:return: fasta sequence for the selection's chain
'''
selection_details = hf.get_selection_details(selection)
seq = cmd.get_fastastr('chain ' + selection_details['chain']).rstrip()
seq = seq.split('\n')
seq = seq[0] + '_' + selection_details['chain'] + '\n' + ''.join(seq[1:])
print seq
def testIdentifiers(self):
seq = 'ACD'
segi = 'foo'
chain = 'F'
resv = 10
cmd.fab(seq, 'm1', 'peptide', resv, chain, segi)
cmd.iterate('first m1', 'stored.v = (segi, chain, resv, resn)')
self.assertEqual(stored.v, (segi, chain, resv, 'ALA'))
cmd.iterate('last m1', 'stored.v = (segi, chain, resv, resn)')
self.assertEqual(stored.v, (segi, chain, resv + 2, 'ASP'))
v = cmd.get_fastastr().splitlines()[1]
self.assertEqual(v, seq)
def get_sequence(obj):
aa1 = list("ACDEFGHIKLMNPQRSTVWY")
aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR".split(
)
aa123 = dict(zip(aa1, aa3))
# aa321 = dict(zip(aa3, aa1))
chains = cmd.get_chains(obj)
seq_cat = ''
for chain in chains:
seq = cmd.get_fastastr(f'{obj} and chain {chain}')
seq = seq.split()[1:]
seq = ''.join(seq)
seq_cat += seq
seq_cat = np.asarray([aa123[r] for r in seq_cat])
return seq_cat
def testIdentifiers(self):
seq = 'ACD'
segi = 'foo'
chain = 'F'
resv = 10
cmd.fab(seq, 'm1', 'peptide', resv, chain, segi)
cmd.iterate('first m1', 'stored.v = (segi, chain, resv, resn)')
self.assertEqual(stored.v, (segi, chain, resv, 'ALA'))
cmd.iterate('last m1', 'stored.v = (segi, chain, resv, resn)')
self.assertEqual(stored.v, (segi, chain, resv + 2, 'ASP'))
v = cmd.get_fastastr().splitlines()[1]
self.assertEqual(v, seq)
def get_sequence(query_object, verbose=True):
"""
USAGE
get_sequence OBJECT
Returns a single string with the aminoacid sequence of the object.
Similar to print(cmd.get_fastastr(OBJECT)) but does not separate and add
chain ID names.
"""
query_seq = ""
# Retrieve the fasta string, while removing newlines
fasta_seq = cmd.get_fastastr(query_object).replace("\n", "")
# Remove the chain ID name headers
for chain in cmd.get_chains(query_object):
fasta_seq = fasta_seq.replace(">%s_%s" % (query_object, chain), "")
# Print (by default) and return the sequence
if verbose:
print(fasta_seq)
return fasta_seq
def get_seq(obj1):
seq1 = ''.join(cmd.get_fastastr(obj1).split('\n')[1:])
print(seq1)
def get_seq(file_name, chain):
pymol.finish_launching()
cmd.delete('all')
cmd.load(file_name)
cmd.select('seq_chain', 'chain ' + chain)
return cmd.get_fastastr('seq_chain')
def test_CanGetSourceSequence(self):
cmd.load(self.datafile("1rna.cif"))
seq = cmd.get_fastastr('/1rna/A/A').splitlines()[1]
self.assertEqual(seq, "UUAUAUAUAUAUAA")
def testSingleDNAFASTA(self):
dna = "ATGC"
cmd.fnab(input=dna, mode="DNA", form="B", dbl_helix=-1)
fasta_str = cmd.get_fastastr().splitlines()
self.assertEqual(dna, fasta_str[1])
def testSingleRNAFASTA(self):
rna = "AUGC"
cmd.fnab(input=rna, mode="RNA")
fasta_str = cmd.get_fastastr().splitlines()
self.assertEqual(rna, fasta_str[1])
def get_sequence(chain):
seq = cmd.get_fastastr(f'inpdb and chain {chain} and polymer.protein')
seq = seq.split()[1:]
seq = ''.join(seq)
return seq
def print_seq():
print cmd.get_fastastr('all')
def testSingleDNAFASTA(self):
dna = "ATGC"
cmd.fnab(input=dna, mode="DNA", form="B", dbl_helix=-1)
fasta_str = cmd.get_fastastr().splitlines()
self.assertEqual(dna, fasta_str[1])
def color_sensitivity(file,
column=None,
show_hetatm=True,
show_chains=True,
on_chain=None,
reload=True,
normalize=True,
min_val=-1,
max_val=1,
on_pdb=None):
_, pdbid, chain, _ = file.split('_')
if on_chain:
chain = on_chain
if on_pdb:
pdbid = on_pdb
if not stored.pdbid == pdbid or reload:
stored.pdbid = pdbid
stored.chain = chain
stored.df = pd.read_csv(os.path.join(label_path, file), sep='\t')
stored.col_pos = 0
get_pdb_file(pdbid)
cmd.load(os.path.join(pdb_path, '{}.pdb'.format(pdbid)))
print('Columns:\n{}'.format(', '.join(stored.df.columns)))
# actual coloring
cmd.alter("sele", "b=0.0")
cmd.select("all")
cmd.hide("everything")
cmd.select("sele", "chain {}".format(chain))
cmd.show("cartoon", "sele")
cmd.color("grey", "sele")
if show_hetatm:
cmd.select("het", "hetatm")
cmd.show("sticks", "het")
cmd.color("yellow", "het")
if show_chains:
cmd.select("other", "not chain {}".format(chain))
cmd.show("cartoon", "other")
cmd.color("orange", "other")
if not column:
column = stored.df.columns[stored.col_pos % len(stored.df.columns)]
print('Showing {}'.format(column))
seq_df = ''.join(stored.df['AA'][1:])
seq_pdb = cmd.get_fastastr('chain {}'.format(chain))
seq_pdb = ''.join(seq_pdb.split()[1:])
print('Seq sensitivity:\n{}\n\nSeq pdb:\n{}\n\n'.format(seq_df, seq_pdb))
alignment_obj = pairwise2.align.globalms(seq_df, seq_pdb, 1, 0, -.5,
-.1)[0] #one_alignment_only=True,
print(alignment_obj)
aligned_df, aligned_pdb = alignment_obj[:2]
stored.aligned_values = []
current_pos = 0
for aa_df, aa_pdb in zip(aligned_df, aligned_pdb):
if aa_df == '-':
stored.aligned_values.append(float('nan'))
elif aa_pdb == '-':
current_pos += 1
continue
else:
stored.aligned_values.append(stored.df.loc[current_pos + 1,
column])
current_pos += 1
if normalize:
stored.aligned_values = list(
np.asarray(stored.aligned_values /
np.nanmax(np.abs(stored.aligned_values))))
else:
pass
for idx in range(len(stored.aligned_values)):
if np.isnan(stored.aligned_values[idx]):
stored.aligned_values[idx] = -1000
stored.aligned_values = iter(stored.aligned_values)
stored.last_resi = -1
def helper(resi):
try:
if resi != stored.last_resi:
stored.b = next(stored.aligned_values)
except StopIteration:
stored.b = np.nan
stored.last_resi = resi
return stored.b
stored.helper = helper
cmd.alter("sele", "b = stored.helper(resi)")
cmd.spectrum("b", "red_white_blue", "sele", str(min_val), str(max_val))
cmd.select("nan", "b=-1000")
cmd.color("grey", "nan")
stored.col_pos += 1
def testGetFastastr(self):
seq, name = 'ACD', 'm1'
cmd.fab(seq, name)
s = cmd.get_fastastr()
self.assertEqual(s.split(), ['>' + name, seq])
def annotate_v(selection, scheme):
aaseq = "".join(cmd.get_fastastr(selection).split("\n")[1:])
obj = annotate(aaseq, scheme)
result = obj.retrieve()
for i in result.keys():
cmd.select(i, "pepseq %s" % result[i])
import sys
from pymol import cmd
protein = sys.argv[1] # PDB file
outfile = sys.argv[2] # Outfile
cmd.load(protein, 'Protein')
chains = cmd.get_chains('Protein')
N_res = len(cmd.get_fastastr("chain A").split('\n')[1])
for n in range(len(chains)):
cmd.select('AA', '/Protein//' + chains[n] + '/1/N')
cmd.edit('AA')
cmd.editor.attach_amino_acid("pk1", 'ace')
cmd.unpick()
cmd.select('AA', '/Protein//' + chains[n] + '/' + str(N_res) + '/C')
cmd.edit('AA')
cmd.editor.attach_amino_acid("pk1", 'nhh')
cmd.unpick()
# Rename NHH to NH2 (GROMACS format)
cmd.select("NH2s", "resn NHH")
cmd.alter("NH2s", "resn='NH2'")
cmd.delete("NH2s")
cmd.save(outfile, 'Protein')
def testSingleRNAFASTA(self):
rna = "AUGC"
cmd.fnab(input=rna, mode="RNA")
fasta_str = cmd.get_fastastr().splitlines()
self.assertEqual(rna, fasta_str[1])
def compare_10gs_11gs():
# it is possible to download proteins from RCSB (Protein Data Bank) to fetch_path, which is current working
# directory by default
cmd.set('fetch_path', cmd.exp_path(PATH_data))
cmd.fetch('10gs')
cmd.fetch('11gs')
cmd.load('{0}10gs.cif'.format(PATH_data), '10gs')
cmd.load('{0}11gs.cif'.format(PATH_data), '11gs')
# proteins
# pymol has several options for proteins alignment, align is better for proteins with high homology
align_command = cmd.align # or super, or cealign
align_res = align_command('10gs', '11gs')
if align_command == cmd.align:
print('aligned with rmsd {0}'.format(align_res[0]))
# cmd.create creates a separate object (copies everything to it)
# het stands for heteroatoms (non-protein)
cmd.create('10gs_protein', '10gs and not het')
cmd.create('11gs_protein', '11gs and not het')
# print protein sequences for fun
fasta_10gs = cmd.get_fastastr(selection='10gs_protein')
fasta_11gs = cmd.get_fastastr(selection='11gs_protein')
print('10gs sequence:{0}'.format(fasta_10gs))
print('11gs sequence:{0}'.format(fasta_11gs))
cmd.delete('*_protein') # delete objects
# ligands
cmd.select('10gs_ligands', '10gs and not resname HOH and het')
cmd.select('11gs_ligands', '11gs and not resname HOH and het')
space_10gs = {'lig_names': []} # or simpy lig_names = []
space_11gs = {'lig_names': []}
# strange pymol interface to iterate over atoms
cmd.iterate('10gs_ligands', 'lig_names.append(resn)', space=space_10gs)
cmd.iterate('11gs_ligands', 'lig_names.append(resn)', space=space_11gs)
ligs_10gs = set(space_10gs['lig_names'])
ligs_11gs = set(space_11gs['lig_names'])
# by the way, in both 10gs and 11gs we have MSE, which is actually a modified residue and not a ligand
print('ligands found in 10gs: {0}'.format(ligs_10gs))
print('ligands found in 11gs: {0}'.format(ligs_11gs))
for ligand_unique in ligs_10gs.symmetric_difference(ligs_11gs):
cmd.save(
'{0}{1}_{2}_ligand.sdf'.format(
PATH_data, '10gs' if ligand_unique in ligs_10gs else '11gs',
ligand_unique), 'resname {0}'.format(ligand_unique))
# deleting selection, objects remain unchanged
cmd.delete('ligs*')
print('drawing a figure (this will take some time)')
cmd.set('transparency_mode', 1)
cmd.bg_color('white')
cmd.show('sticks', 'het and not resname HOH')
cmd.color('white', 'not het')
cmd.show('surface', 'not het')
cmd.hide('lines')
cmd.set('transparency', '0.7')
cmd.show('spheres', 'resname HOH')
cmd.color('palecyan', 'resname HOH')
cmd.hide('nonbonded', 'resname HOH')
cmd.set('sphere_transparency', '0.7')
cmd.ray()
cmd.png('{0}fig.png'.format(PATH_data))
mutant = aa_mapping[to_aa]
selection = 'A/{}/'.format(location)
print('PDB path:', pdb_path)
print('Raw AA substitution:', aa_sub)
print('Selection:', selection)
print('New amino acid:', mutant)
print('Starting mutagenesis')
cmd.wizard('mutagenesis')
print('Loading PDB')
cmd.load(pdb_path)
seq_str = cmd.get_fastastr('all')
if verbose:
print(seq_str)
lines = seq_str.splitlines()
sequence = ''.join(lines[1:])
residue_indexes = []
def append_residue_index(resi, resn, name):
residue_indexes.append(resi)
namespace = {'append_residue_index': append_residue_index}
def fasta(selection="all"):
print(cmd.get_fastastr(selection))
def test_CanGetSourceSequence(self):
cmd.load(self.datafile("1rna.cif"))
seq = cmd.get_fastastr('/1rna/A/A').splitlines()[1]
self.assertEqual(seq, "UUAUAUAUAUAUAA")
