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pdb_parser_lib.py
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pdb_parser_lib.py
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#!/usr/bin/env python
"""Main lib file"""
AMINOACID_CODES = ["ALA", "ARG", "ASN", "ASP", "CYS", "GLU", "GLN", "GLY",
"HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR",
"TRP", "TYR", "VAL"]
RES = ['DA', 'DG', 'DT', 'DC']
RES += ['A', 'G', 'U', 'C']
RESS = ['A', 'C', 'G', 'U', 'ADE', 'CYT', 'GUA', 'URY', 'URI', 'U34', 'U31', 'C31', '4SU', 'H2U', 'QUO', 'G7M', '5MU', '5MC', 'PSU', '2MG', '1MG', '1MA', 'M2G', '5BU', 'FHU', 'FMU', 'IU', 'OMG', 'OMC', 'OMU', 'A2M', 'A23', 'CCC', 'I'] + ['RC', 'RU', 'RA', 'RG', 'RT']
#DNA = ['DA', 'DG', 'DT', 'DC']
#RNA = ['A', 'G', 'U', 'C']
IONS = ['NA', 'MG', 'MN']
HYDROGEN_NAMES = ["H", "H5'", "H5''", "H4'", "H3'", "H2'", "HO2'", "H1'", "H3", "H5", "H6", "H5T", "H41", "1H5'",
"2H5'", "HO2'", "1H4", "2H4", "1H2", "2H2", "H1", "H8", "H2", "1H6", "2H6",
"HO5'", "H21", "H22", "H61", "H62", "H42", "HO3'", "1H2'", "2HO'", "HO'2", "H2'1" , "HO'2", "HO'2",
"H2", "H2'1", "H1", "H2", "1H5*","2H5*", "H4*", "H3*", "H1*", "1H2*", "2HO*", "1H2", "2H2", "1H4", "2H4", "1H6", "2H6", "H1", "H2", "H3", "H5", "H6", "H8", "H5'1", "H5'2", "H3T"]
import os
import sys
from collections import OrderedDict
import re
import string
ignore_op3 = False
def get_version(currfn='', verbose=False): #dupa
"""Get version of the tool based on state of the git repository.
Return version.
If currfn is empty, then the path is '.'. Hmm.. I think it will work. We will see.
The version is not printed!
https://github.com/m4rx9/curr_version/"""
from commands import getoutput
if currfn == '':
path = '.'
else:
path = os.path.dirname(currfn)
if verbose: print 'get_version::path', path
if os.path.islink(currfn):#path + os.sep + os.path.basename(__file__)):
path = os.path.dirname(os.readlink(path + os.sep + os.path.basename(currfn)))
if not path: path = '.'
if verbose: print 'get_version::path2', path
curr_path = os.getcwd()
os.chdir(os.path.abspath(path))
version = getoutput('git describe --long --tags --dirty --always')
os.chdir(curr_path)
if version.find('not found')>-1:
return ' unknown' # > install git to get versioning based on git'
else:
return version
class StrucFile:
"""StrucFile"""
def __init__(self, fn):
self.fn = fn
self.report = []
self.report.append('The RNAStrucFile report: %s ' % fn)
self.mol2_format = False
self.lines = []
lines = open(fn).read().strip().split('\n')
has_many_models = False
for l in lines:
# multi-models pdb files
if l.startswith('MODEL'):
has_many_models = True
if l.startswith('ENDMDL'):
break
if l.startswith('ATOM') or l.startswith('HETATM') or l.startswith('TER') or l.startswith('END'):
self.lines.append(l.strip())
if l.startswith("@<TRIPOS>"):
self.mol2_format = True
self.report.append('This is mol2 format')
self.res = self.get_resn_uniq()
def is_it_pdb(self):
"""Return True if the files is in PDB format."""
if len(self.lines):
return True
else:
return False
def is_mol2(self):
"""Return True if is_mol2 based on the presence of ```@<TRIPOS>```."""
return self.mol2_format
def decap_gtp(self):
lines = []
for l in self.lines:
if l.startswith('ATOM') or l.startswith('HETATM') :
if l[12:16].strip() in ['PG', 'O1G', 'O2G', 'O3G', 'O3B', 'PB','O1B','O2B', 'O3A']:
continue
if l[12:16].strip() == 'PA':
l = l.replace('PA', 'P ')
if l[12:16].strip() == 'O1A':
l = l.replace('O1A', 'O1P')
if l[12:16].strip() == 'O2A':
l = l.replace('O2A', 'O2P')
if l[17:20].strip() == 'GTP':
l = l[:17] + ' G' + l[20:]
l = l.replace('HETATM', 'ATOM ')
lines.append(l)
self.lines = lines
def is_amber_like(self):
"""Use self.lines and check if there is XX line
"""
for l in self.lines:
if l.startswith('ATOM') or l.startswith('HETATM') :
rn = l[17:20]
if rn in ['RU5', 'RC5', 'RA5', 'RT5', 'RG5']:
self.report.append('This is amber-like format')
return True
return False
def mol2toPDB(self, outfn=""):
try:
import pybel
except ImportError:
print 'pybel is needed for mol2 to pdb convertion'
#sys.exit(1)
sys.exit(0)
if not outfn:
outfn = self.fn.replace('.mol2', '.pdb')
for mol in pybel.readfile("mol2", self.fn):
mol.write("pdb", outfn, overwrite=True)
print 'outfn: ', outfn
self.report.append(' Converted from mol2 to PDB')
return outfn
def get_no_lines(self):
return len(self.lines)
def get_text(self, add_end=True):
txt = ''
for l in self.lines:
if l.startswith('END'):
continue # skip end
txt += l.strip() + '\n'
if add_end:
if not l.startswith('END'):
txt += 'END'
return txt.strip()
def get_chain(self, chain_id='A'):
txt = ''
for l in self.lines:
if l.startswith('ATOM') or l.startswith('HETATM') :
if l[21] == chain_id:
txt += l.strip() + '\n'
txt += 'TER'
return txt
def get_resn_uniq(self):
res = set()
for l in self.lines:
r = l[17:20].strip().upper()
res.add(r)
return res
def check_res_if_std_na(self):
wrong = []
for r in self.res:
if r not in RES:
wrong.append(r)
return wrong
def get_seq(self):
"""
You get `chains` such as:
OrderedDict([('A', {'header': 'A:1-47', 'seq': 'CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAU'}), ('B', {'header': 'B:48-58', 'seq': 'AUCAGGUGCAA'})])"""
seq = ''
curri = int(self.lines[0][22:26])
seq = self.lines[0][19]
chains = OrderedDict()
curri = -100000000000000 #ugly
chain_prev = None
for l in self.lines:
if l.startswith('ATOM') or l.startswith('HETATM') :
resi = int(l[22:26])
if curri != resi:
resname = l[17:20].strip()
if len(resname) == 'GTP': # DG -> g GTP
resname = 'g'
if len(resname) > 1: # DG -> g GTP
resname = resname[-1].lower()
seq += resname
chain_curr = l[21]
if chain_prev != chain_curr and chain_prev:
chains[chain_prev]['header'] += '-' + str(resi_prev)
if chains.has_key(chain_curr):
chains[chain_curr]['seq'] += resname
else:
chains[chain_curr] = dict()
chains[chain_curr]['header'] = chain_curr + ':' + str(resi)#resi_prev)
chains[chain_curr]['seq'] = resname
resi_prev = resi
chain_prev = chain_curr
curri = resi
chains[chain_prev]['header'] += '-' + str(resi_prev)
seq = ''
for c in chains.keys():
seq += '> ' + os.path.basename(self.fn) + ' ' + chains[c]['header'] + '\n'
seq += chains[c]['seq'] + '\n'
return seq.strip()
def get_info_chains(self):
"""return A:3-21 B:22-32
"""
seq = ''
curri = int(self.lines[0][22:26])
seq = self.lines[0][19]
chains = OrderedDict()
curri = -100000000000000 #ugly
chain_prev = None
for l in self.lines:
if l.startswith('ATOM') or l.startswith('HETATM') :
resi = int(l[22:26])
if curri != resi:
resname = l[17:20].strip()
if len(resname) == 'GTP': # DG -> g GTP
resname = 'g'
if len(resname) > 1: # DG -> g GTP
resname = resname[-1].lower()
seq += resname
chain_curr = l[21]
if chain_prev != chain_curr and chain_prev:
chains[chain_prev]['header'] += '-' + str(resi_prev)
if chains.has_key(chain_curr):
chains[chain_curr]['seq'] += resname
else:
chains[chain_curr] = dict()
chains[chain_curr]['header'] = chain_curr + ':' + str(resi)#resi_prev)
chains[chain_curr]['seq'] = resname
resi_prev = resi
chain_prev = chain_curr
curri = resi
chains[chain_prev]['header'] += '-' + str(resi_prev)
seq = ''
for c in chains.keys():
seq += chains[c]['header'] + ' '
return seq.strip()
def detect_file_format(self):
pass
def detect_molecule_type(self):
aa = []
na = []
for r in self.res:
if r in AMINOACID_CODES:
aa.append(r)
if r in RESS:
na.append(r)
aa = float(len(aa)) / len(self.res)
na = float(len(na)) / len(self.res)
if aa == 0 and na == 0:
return 'error'
if aa > na:
return '>protein< vs na', aa, na
else:
return 'protein vs >na<', aa, na
def get_head(self):
return '\n'.join(self.lines[:5])
def get_tail(self):
return '\n'.join(self.lines[-5:])
def get_preview(self):
t = '\n'.join(self.lines[:5])
t += '\n-------------------------------------------------------------------\n'
t += '\n'.join(self.lines[-5:])
return t
def remove_hydrogen(self):
lines = []
for l in self.lines:
if l[77:79].strip() == 'H':
continue
if l[12:16].strip() in HYDROGEN_NAMES:
#if l[12:16].strip().startswith('H'):
continue
else:
#print l[12:16]
lines.append(l)
self.lines = lines
def remove_water(self):
"""Remove HOH and TIP3"""
lines = []
for l in self.lines:
if l[17:21].strip() in ['HOH', 'TIP3', 'WAT']:
continue
else:
lines.append(l)
self.lines = lines
def remove_ion(self):
"""
TER 1025 U A 47
HETATM 1026 MG MG A 101 42.664 34.395 50.249 1.00 70.99 MG
HETATM 1027 MG MG A 201 47.865 33.919 48.090 1.00 67.09 MG
"""
lines = []
for l in self.lines:
element = l[76:78].strip().upper()
element2 = l[17:20].strip().upper()
if element in IONS:
continue
if element2 in IONS:
continue
else:
lines.append(l)
self.lines = lines
def fixU__to__U(self):
lines = []
for l in self.lines:
if l.startswith('ATOM') or l.startswith('HETATM') :
rn = l[17:20]
rn = rn.replace('G ', ' G')
rn = rn.replace('U ', ' U')
rn = rn.replace('C ', ' C')
rn = rn.replace('A ', ' A')
l = l[:16] + ' ' + rn + ' ' + l[21:]
#print l.strip()
#print l2
#l = l.replace(' U ', ' U ')
#l = l.replace(' G ', ' G ')
#l = l.replace(' A ', ' A ')
#l = l.replace(' C ', ' C ')
lines.append(l)
print 'fixU__to__U OK'
self.report.append(' Fix: U__ -> __U')
self.lines = lines
def resn_as_dna(self):
lines = []
for l in self.lines:
if l.startswith('ATOM') or l.startswith('HETATM') :
#print l
nl = l.replace( 'DA5', ' DA') # RA should be the last!!!!
nl = nl.replace('DA3', ' DA')
nl = nl.replace(' DA', ' DA')
nl = nl.replace(' rA', ' DA')
nl = nl.replace('DC5', ' DC')
nl = nl.replace('DC3', ' DC')
nl = nl.replace(' DC', ' DC')
nl = nl.replace(' rC', ' DC')
nl = nl.replace('DG5', ' DG')
nl = nl.replace('DG3', ' DG')
nl = nl.replace(' DG', ' DG')
nl = nl.replace(' rG', ' DG')
nl = nl.replace('DU5', ' DU')
nl = nl.replace('DU3', ' DU')
nl = nl.replace(' DU', ' DU')
nl = nl.replace(' rU', ' DU')
nl = nl.replace('DT5', ' DT')
nl = nl.replace('DT3', ' DT')
nl = nl.replace(' DT', ' DT')
nl = nl.replace(' rT', ' DT')
nl = nl.replace('C5M', 'C7 ')
if l[17:20].strip() == 'G':
nl = nl[:17] + ' DG' + nl[20:]
if l[17:20].strip() == 'C':
nl = nl[:17] + ' DC' + nl[20:]
if l[17:20].strip() == 'T':
nl = nl[:17] + ' DT' + nl[20:]
if l[17:20].strip() == 'U':
nl = nl[:17] + ' DU' + nl[20:]
if l[17:20].strip() == 'A':
nl = nl[:17] + ' DA' + nl[20:]
lines.append(nl)
if l.startswith("END") or l.startswith("TER"):
lines.append(l)
print 'resn_as_dna'
self.report.append(' resn_as_dna')
self.lines = lines
def fix_O_in_UC(self):
""".. warning: remove RU names before using this function"""
lines = []
for l in self.lines:
#if l[12:16].strip() in
#if l[12:16].strip().startswith('H'):
nl = l.replace('O U',
'O2 U')
nl =nl.replace('O C',
'O2 C')
lines.append(nl)
self.lines = lines
def fix_op_atoms(self):
lines = []
for l in self.lines:
nl = l.replace('*', '\'')
nl = nl.replace('O1P', 'OP1')
nl = nl.replace('O2P', 'OP2')
nl = nl.replace('O3P', 'OP3')
lines.append(nl)
self.lines = lines
def get_report(self):
return '\n'.join(self.report)
def is_rna(self):
wrong = []
for r in self.res:
if r.upper().strip() in ['RC', 'RU', 'RA', 'RG', 'RT']:
if r not in wrong_res:
wrong_res.append(r)
return wrong_res
def check_res_if_std_dna(self):
wrong_res = []
for r in self.res:
if r.upper().strip() in ['A', 'T', 'C', 'G']:
if r not in wrong_res:
wrong_res.append(r)
return wrong_res
def check_res_if_supid_rna(self):
wrong_res = []
for r in self.res:
if r.upper().strip() in ['RC', 'RU', 'RA', 'RG', 'RT']:
if r not in wrong_res:
wrong_res.append(r)
return wrong_res
def is_rna(self):
for r in self.res:
if r.upper().strip() in ['RC', 'RU', 'RA', 'RG', 'RT']:
if r not in wrong_res:
wrong_res.append(r)
return wrong_res
def renum_atoms(self):
"""Renum atoms, from 1 to X for line; ATOM/HETATM"""
lines = []
c = 1
for l in self.lines:
l = l[:6] + str(c).rjust(5) + l[11:]
c += 1
lines.append(l)
self.lines = lines
def fix_resn(self):
lines = []
for l in self.lines:
nl = l.replace( 'RA5', ' A') # RA should be the last!!!!
nl = nl.replace('RA3', ' A')
nl = nl.replace('ADE', ' A')
nl = nl.replace(' RA', ' A')
nl = nl.replace(' rA', ' A')
nl = nl.replace('RC5', ' C')
nl = nl.replace('RC3', ' C')
nl = nl.replace('CYT', ' C')
nl = nl.replace(' RC', ' C')
nl = nl.replace(' rC', ' C')
nl = nl.replace('RG5', ' G')
nl = nl.replace('RG3', ' G')
nl = nl.replace('GUA', ' G')
nl = nl.replace(' RG', ' G')
nl = nl.replace(' rG', ' G')
nl = nl.replace('RU5', ' U')
nl = nl.replace('RU3', ' U')
nl = nl.replace('URA', ' U')
nl = nl.replace(' RU', ' U')
nl = nl.replace(' rU', ' U')
nl = nl.replace('RT5', ' T')
nl = nl.replace('RT3', ' T')
nl = nl.replace('THY', ' T')
nl = nl.replace(' RT', ' T')
nl = nl.replace(' rT', ' T')
lines.append(nl)
self.lines = lines
def check_res_if_std_prot(self):
wrong = []
for r in self.res:
if r not in AMINOACID_CODES:
wrong.append(r)
return wrong
def write(self, outfn,v=True):
"""Write ```self.lines``` to a file (and END file")"""
f = open(outfn, 'w')
for l in self.lines:
f.write(l + '\n')
if not l.startswith('END'):
f.write('END')
f.close()
if v:
print 'Write %s' % outfn
def get_atom_num(self,line):
"""Extract atom number from a line of PDB file
Arguments:
* line = ATOM line from a PDB file
Output:
* atom number as an integer
"""
return int(''.join(filter(lambda x: x.isdigit(), line[6:11])))
def get_res_num(self,line):
"""Extract residue number from a line of PDB file
Arguments:
* line = ATOM line from a PDB file
Output:
* residue number as an integer
"""
return int(''.join(filter(lambda x: x.isdigit(), line[22:27])))
def get_res_code(self,line):
"""Get residue code from a line of a PDB file
"""
if not line.startswith('ATOM'):
return None
return line[17:20]
def get_atom_code(self,line):
"""Get atom code from a line of a PDB file
"""
if not line.startswith('ATOM'):
return None
return line[13:16].replace(' ', '')
def get_atom_coords(self,line):
"""Get atom coordinates from a line of a PDB file
"""
if not line.startswith('ATOM'):
return None
return tuple(map(float, line[31:54].split()))
def set_line_bfactor(self,line, bfactor):
if not line.startswith('ATOM'):
return None
return line[:60] + (" %5.2f" % bfactor) + line[66:]
def set_atom_code(self,line, code):
return line[:13] + code + ' ' * (3 - len(code)) + line[16:]
def set_res_code(self,line, code):
return line[:17] + code.rjust(3) + line[21:]
def get_chain_id(self,line):
return line[21:22]
def get_atom_index(self,line):
try:
return int(line[6:11])
except:
return None
def set_atom_index(self,line,index):
return line[:7] + str(index).rjust(4) + line[11:]
def get_res_index(self,line):
return int(line[22:26])
def set_res_index(self,line, index):
return line[:23] + str(index).rjust(3) + line[26:]
def set_chain_id(self,line, chain_id):
return line[:21] + chain_id + line[22:]
def get_rnapuzzle_ready(self, renumber_residues=True):
"""Get rnapuzzle ready structure.
Submission format @http://ahsoka.u-strasbg.fr/rnapuzzles/
Does:
- keep only given atoms,
- renumber residues from 1, if renumber_residues=True (by default)
"""
try:
from Bio import PDB
from Bio.PDB import PDBIO
except:
sys.exit('Error: Install biopython to use this function (pip biopython)')
import copy
G_ATOMS = ['P', 'OP1', 'OP2', 'O5\'', 'C5\'', 'C4\'', 'O4\'', 'C3\'', 'O3\'', 'C2\'', 'O2\'', 'C1\'', 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4']
A_ATOMS = "P OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N9 C8 N7 C5 C6 N6 N1 C2 N3 C4".split()
U_ATOMS = "P OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N1 C2 O2 N3 C4 O4 C5 C6".split()
C_ATOMS = "P OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N1 C2 O2 N3 C4 N4 C5 C6".split()
ftmp = '/tmp/out.pdb'
self.write(ftmp,v=False)
parser = PDB.PDBParser()
struct = parser.get_structure('', ftmp)
model = struct[0]
s2 = PDB.Structure.Structure(struct.id)
m2 = PDB.Model.Model(model.id)
chains2 = []
missing = []
for chain in model.get_list():
res = []
for r in chain:
res.append(r)
res = copy.copy(res)
c2 = PDB.Chain.Chain(chain.id)
c = 1 # new chain, goes from 1 !!!
for r in res:
# hack for amber/qrna
r.resname = r.resname.strip()
if r.resname == 'RC3': r.resname = 'C'
if r.resname == 'RU3': r.resname = 'U'
if r.resname == 'RG3': r.resname = 'G'
if r.resname == 'RA3': r.resname = 'A'
if r.resname == 'C3': r.resname = 'C'
if r.resname == 'U3': r.resname = 'U'
if r.resname == 'G3': r.resname = 'G'
if r.resname == 'A3': r.resname = 'A'
if r.resname == 'RC5': r.resname = 'C'
if r.resname == 'RU5': r.resname = 'U'
if r.resname == 'RG5': r.resname = 'G'
if r.resname == 'RA5': r.resname = 'A'
if r.resname == 'C5': r.resname = 'C'
if r.resname == 'U5': r.resname = 'U'
if r.resname == 'G5': r.resname = 'G'
if r.resname == 'A5': r.resname = 'A'
if r.resname.strip() == 'RC': r.resname = 'C'
if r.resname.strip() == 'RU': r.resname = 'U'
if r.resname.strip() == 'RG': r.resname = 'G'
if r.resname.strip() == 'RA': r.resname = 'A'
r2 = PDB.Residue.Residue(r.id, r.resname.strip(), r.segid)
if renumber_residues:
r2.id = (r2.id[0], c, r2.id[2]) ## renumber residues
if str(r.get_resname()).strip() == "G":
for an in G_ATOMS:
try:
r2.add(r[an])
except KeyError:
#print 'Missing:', an, r, ' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
elif str(r.get_resname()).strip() == "A":
for an in A_ATOMS:
try:
r2.add(r[an])
except KeyError:
#print 'Missing:', an, r, ' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
elif str(r.get_resname()).strip() == "C":
for an in C_ATOMS:
try:
r2.add(r[an])
except:
#print 'Missing:', an, r, ' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
elif str(r.get_resname()).strip() == "U":
for an in U_ATOMS:
try:
r2.add(r[an])
except KeyError:
#print 'Missing:', an, r,' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
c += 1
chains2.append(c2)
io = PDBIO()
s2.add(m2)
for chain2 in chains2:
m2.add(chain2)
#print c2
#print m2
io.set_structure(s2)
#fout = fn.replace('.pdb', '_fx.pdb')
fout = '/tmp/outout.pdb' # hack
io.save(fout)
if missing:
print 'REMARK 000 Missing atoms:'
for i in missing:
print 'REMARK 000 +', i[0], i[1], i[2], 'residue #', i[3]
#raise Exception('Missing atoms in %s' % self.fn)
#
# fix ter 'TER' -> TER 1528 G A 71
#
s = StrucFile(fout)
self.lines = s.lines
c = 0
#ATOM 1527 C4 G A 71 0.000 0.000 0.000 1.00 0.00 C
nlines = []
no_ters = 0
for l in self.lines:
if l.startswith('TER'):
atom_l = self.lines[c-1]
#print 'TER 1528 G A 71 <<<'
new_l = 'TER'.ljust(80)
new_l = self.set_atom_index(new_l, str(self.get_atom_index(atom_l)+1 + no_ters))
new_l = self.set_res_code(new_l, self.get_res_code(atom_l))
new_l = self.set_chain_id(new_l, self.get_chain_id(atom_l))
new_l = self.set_res_index(new_l, self.get_res_index(atom_l))
#print new_l
nlines.append(new_l)
no_ters += 1
else:
if self.get_atom_index(l):
l = self.set_atom_index(l, self.get_atom_index(l) + no_ters) # 1 ter +1 2 ters +2 etc
nlines.append(l)
c += 1
self.lines = nlines
def get_simrna_ready(self, renumber_residues=True):
"""Get simrna_ready ..
- take only first model,
- renumber residues if renumber_residues=True
.. warning:: requires: Biopython"""
try:
from Bio import PDB
from Bio.PDB import PDBIO
except:
sys.exit('Error: Install biopython to use this function (pip biopython)')
import warnings
warnings.filterwarnings('ignore', '.*Invalid or missing.*',)
warnings.filterwarnings('ignore', '.*with given element *',)
import copy
G_ATOMS = "P OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N9 C8 N7 C5 C6 O6 N1 C2 N2 N3 C4".split()
A_ATOMS = "P OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N9 C8 N7 C5 C6 N6 N1 C2 N3 C4".split()
U_ATOMS = "P OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N1 C2 O2 N3 C4 O4 C5 C6".split()
C_ATOMS = "P OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N1 C2 O2 N3 C4 N4 C5 C6".split()
ftmp = '/tmp/out.pdb'
self.write(ftmp,v=False)
parser = PDB.PDBParser()
struct = parser.get_structure('', ftmp)
model = struct[0]
s2 = PDB.Structure.Structure(struct.id)
m2 = PDB.Model.Model(model.id)
chains2 = []
missing = []
for chain in model.get_list():
res = []
for r in chain:
res.append(r)
res = copy.copy(res)
c2 = PDB.Chain.Chain(chain.id)
c = 1 # new chain, goes from 1 if renumber True
for r in res:
# hack for amber/qrna
r.resname = r.resname.strip()
if r.resname == 'RC3': r.resname = 'C'
if r.resname == 'RU3': r.resname = 'U'
if r.resname == 'RG3': r.resname = 'G'
if r.resname == 'RA3': r.resname = 'A'
if r.resname == 'C3': r.resname = 'C'
if r.resname == 'U3': r.resname = 'U'
if r.resname == 'G3': r.resname = 'G'
if r.resname == 'A3': r.resname = 'A'
if r.resname == 'RC5': r.resname = 'C'
if r.resname == 'RU5': r.resname = 'U'
if r.resname == 'RG5': r.resname = 'G'
if r.resname == 'RA5': r.resname = 'A'
if r.resname == 'C5': r.resname = 'C'
if r.resname == 'U5': r.resname = 'U'
if r.resname == 'G5': r.resname = 'G'
if r.resname == 'A5': r.resname = 'A'
if r.resname.strip() == 'RC': r.resname = 'C'
if r.resname.strip() == 'RU': r.resname = 'U'
if r.resname.strip() == 'RG': r.resname = 'G'
if r.resname.strip() == 'RA': r.resname = 'A'
r2 = PDB.Residue.Residue(r.id, r.resname.strip(), r.segid)
if renumber_residues:
r2.id = (r2.id[0], c, r2.id[2]) ## renumber residues
if c == 1:
p_missing = True
#if p_missing:
# try:
# x = r["O5'"]
# x.id = ' P'
# x.name = ' P'
# x.fullname = ' P'
# print "REMARK 000 FIX O5' -> P fix in chain ", chain.id
# except:
# pass
for a in r:
if a.id == 'P':
p_missing = False
if p_missing:
currfn = __file__
if currfn == '':
path = '.'
else:
path = os.path.dirname(currfn)
if os.path.islink(currfn):#path + os.sep + os.path.basename(__file__)):
path = os.path.dirname(os.readlink(path + os.sep + os.path.basename(currfn)))
po3_struc = PDB.PDBParser().get_structure('', path + '/data/PO3_inner.pdb')
po3 = [po3_atom for po3_atom in po3_struc[0].get_residues()][0]
r_atoms = [r["O4'"], r["C4'"], r["C3'"]]
po3_atoms = [po3["O4'"], po3["C4'"], po3["C3'"]]
sup = PDB.Superimposer()
sup.set_atoms(r_atoms, po3_atoms)
rms = round(sup.rms, 3)
sup.apply( po3_struc.get_atoms() ) # to all atoms of po3
r.add( po3['P'])
r.add( po3['OP1'])
r.add( po3['OP2'])
try:
r.add( po3["O5'"])
except:
del r["O5'"]
r.add( po3["O5'"])
p_missing = False # off this function
# save it
#io = PDB.PDBIO()
#io.set_structure( po3_struc )
#io.save("po3.pdb")
if str(r.get_resname()).strip() == "G":
for an in G_ATOMS:
if c == 1 and ignore_op3:
if an in ['P', 'OP1', 'OP2']:
continue
try:
if c == 1 and an == "O5'" and p_missing:
r2.add(x)
else:
r2.add(r[an])
except KeyError:
#print 'Missing:', an, r, ' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
elif str(r.get_resname()).strip() == "A":
for an in A_ATOMS:
if c == 1 and ignore_op3:
if an in ['P', 'OP1', 'OP2']:
continue
try:
if c == 1 and an == "O5'" and p_missing:
r2.add(x)
else:
r2.add(r[an])
except KeyError:
#print 'Missing:', an, r, ' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
elif str(r.get_resname()).strip() == "C":
for an in C_ATOMS:
if c == 1 and ignore_op3:
if an in ['P', 'OP1', 'OP2']:
continue
try:
if c == 1 and an == "O5'" and p_missing:
r2.add(x)
else:
r2.add(r[an])
except:
#print 'Missing:', an, r, ' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
elif str(r.get_resname()).strip() == "U":
for an in U_ATOMS:
if c == 1 and ignore_op3:
if an in ['P', 'OP1', 'OP2']:
continue
try:
if c == 1 and an == "O5'" and p_missing:
r2.add(x)
else:
r2.add(r[an])
except KeyError:
#print 'Missing:', an, r,' new resi', c
missing.append([an, chain.id, r, c])
c2.add(r2)
c += 1
chains2.append(c2)
io = PDBIO()
s2.add(m2)
for chain2 in chains2:
m2.add(chain2)
#print c2
#print m2
io.set_structure(s2)
#fout = fn.replace('.pdb', '_fx.pdb')
fout = '/tmp/outout.pdb' # hack
io.save(fout)
if missing:
print 'REMARK 000 Missing atoms:'
for i in missing:
print 'REMARK 000 +', i[0], i[1], i[2], 'residue #', i[3]
#raise Exception('Missing atoms in %s' % self.fn)
s = StrucFile(fout)
self.lines = s.lines
def edit_occupancy_of_pdb(txt, pdb, pdb_out,v=False):
"""Make all atoms 1 (flexi) and then set occupancy 0 for seletected atoms.
Return False if error. True if OK
"""
struc = PDB.PDBParser().get_structure('struc', pdb)
txt = txt.replace(' ','')
if v:print txt
l = re.split('[,:;]', txt)
if v:print l
for s in struc:
for c in s:
for r in c:
for a in r:
a.set_occupancy(1) # make it flaxi
for i in l: # ['A', '1-10', '15', '25-30', 'B', '1-10']
if i in string.ascii_letters:
if v:print 'chain', i
chain_curr = i
continue