def main(pdb):
os.system('cp %s/%s/pdb%s.ent %s.pdb' %(path_pdb,pdb[1:3],pdb,pdb,))
##
## Tommy crystal contacts
##
## create biounit
biounit.biounit().main(pdb, '/data/remediated_pdb/', exclude_ligands = True)
##
## parse header (just use the asu instead!!!)
##
fd = open('%s/%s/pdb%s.ent' %(path_pdb,pdb[1:3],pdb,),'r')
lines = fd.readlines()
fd.close()
for i in range(len(lines)):
line = lines[i]
record = line[:6].strip()
if record in ['MODEL','ATOM',]:
break
lines_header = lines[:i]
##
## parse coordinates
##
fd = open('%s_1.pdb' %(pdb),'r')
lines_biounit = fd.readlines()
fd.close()
fd = open('%s.pdb' %(pdb),'r')
lines_asu = fd.readlines()
fd.close()
## fd = open('C:\Users\Tommy Carstensen\pdb\%s.pdb' %(pdb),'r')
## lines = fd.readlines()
## fd.close()
d_header = parse_pdb.parse_header(lines_header)
d_coordinates_biounit, d_ATOMseq = parse_pdb.parse_coordinates(
lines_biounit,d_header,
parse_atom_seq = False, parse_ligands = False,
)
d_coordinates_asu, d_ATOMseq = parse_pdb.parse_coordinates(
lines_asu,d_header,
parse_atom_seq = False, parse_ligands = False,
)
## set new chain IDs
l_old_chains = d_coordinates_asu['chains'].keys()
l_new_chains = list(
set(s_alphabet)-set(l_old_chains)
)
l_old_chains.sort()
l_new_chains.sort()
d_chains = {}
for i in range(len(l_old_chains)):
d_chains[l_old_chains[i]] = l_new_chains[i]
## a = d_header['CRYST1']['edges'][0]
## b = d_header['CRYST1']['edges'][1]
## c = d_header['CRYST1']['edges'][2]
## alpha = math.pi*d_header['CRYST1']['angles'][0]/180.
## beta = math.pi*d_header['CRYST1']['angles'][1]/180.
## gamma = math.pi*d_header['CRYST1']['angles'][2]/180.
## ## unit cell voumne
## volume = a*b*c*math.sqrt(1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2+2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
## matrix_fractional2cartesian = numpy.array([
## [a, b*math.cos(gamma), c*math.cos(beta),],
## [0, b*math.sin(gamma), c*(math.cos(alpha)-math.cos(beta)*math.cos(gamma))/math.sin(gamma),],
## [0,0,volume/(a*b*math.sin(gamma)),],
## ])
matrix_scale = d_header['SCALE']
matrix_scalei = numpy.linalg.inv(matrix_scale)
## lines = []
l_symop = d_header['REMARK290'].keys()
l_symop.sort()
## l_symop = [1]
for symop in l_symop:
## if symop != 1:
## continue
matrix_symop = d_header['REMARK290'][symop]['4x4matrix']
for i in range(len(l_translations)):
vector_translation = l_translations[i]
## if vector_translation != [-1,0,0]:
## continue
vector_translation = numpy.array([vector_translation[0],vector_translation[1],vector_translation[2],0,])
## if i != 0:
## continue
## if vector_translation[0] != 1:
## continue
## if vector_translation[1] != -1:
## continue
## if vector_translation[2] != -1:
## continue
for chain2 in d_coordinates_asu['chains'].keys():
for res_no2 in d_coordinates_asu['chains'][chain2]['residues'].keys():
## if res_no2 != 1:
## continue
print '%4s %2i/%2i %2i/26 %1s %4i' %(pdb, symop, len(l_symop), i+1, chain2, res_no2)
for iCode2 in d_coordinates_asu['chains'][chain2]['residues'][res_no2]['d_iCodes'].keys():
for chain1 in d_coordinates_biounit['chains'].keys():
for res_no1 in d_coordinates_biounit['chains'][chain1]['residues'].keys():
for iCode1 in d_coordinates_biounit['chains'][chain1]['residues'][res_no1]['d_iCodes'].keys():
for atom_name1 in d_coordinates_biounit['chains'][chain1]['residues'][res_no1]['d_iCodes'][iCode1]['atoms'].keys():
coordinate1 = d_coordinates_biounit['chains'][chain1]['residues'][res_no1]['d_iCodes'][iCode1]['atoms'][atom_name1]['coordinate']
for atom_name2 in d_coordinates_asu['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'].keys():
coordinate2 = d_coordinates_asu['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'][atom_name2]['coordinate']
## coordinate2 = numpy.dot(matrix_symop,coordinate2)+vector_symop
## coordinate2 += numpy.dot(matrix_fractional2cartesian,vector_translation)
## coordinate2[0] = round(coordinate2[0],3)
## coordinate2[1] = round(coordinate2[1],3)
## coordinate2[2] = round(coordinate2[2],3)
## conversion from 3x1 vector to 4x1 vector
coordinate2 = numpy.array([coordinate2[0],coordinate2[1],coordinate2[2],1.,])
## conversion from cartesian to fractional coordinates
coordinate2 = numpy.dot(matrix_scale,coordinate2)
## symmetry operator (before unit cell translation???)
coordinate2 = numpy.dot(matrix_symop,coordinate2)
## unit cell translation
coordinate2 += vector_translation
## conversion from fractional to cartesian coordinates
coordinate2 = numpy.dot(matrix_scalei,coordinate2)
## conversion from 4x1 vector to 3x1 vector
coordinate2 = numpy.array([coordinate2[0],coordinate2[1],coordinate2[2],])
vicinity = False
distant = False
dist = math.sqrt(sum((coordinate2-coordinate1)**2))
if dist < 5:
print vector_translation
print numpy.dot(matrix_fractional2cartesian,vector_translation)
print matrix_fractional2cartesian
print '%2i %2i %.2f %.2f %1s %4i %4s %s %1s %4i %4s %s %s' %(
symop, i, round(dist,2), dist_treshold,
chain2, res_no2, atom_name2, coordinate2,
chain1, res_no1, atom_name1, coordinate1,
d_coordinates_asu['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'][atom_name2]['coordinate'],
)
## break atom_name2 loop
if dist > 80.:
distant = True
break
dist = 0 ## tmp!!! temp!!! get *all* translations
dist_treshold = d_radii_vdw[atom_name1[0]]+d_radii_vdw[atom_name2[0]]+.25
## break atom_name2 loop
if dist < dist_treshold:
vicinity = True
break
## break atom_name1 loop (append line and check next iCode1)
if vicinity == True:
for atom_name3 in d_coordinates_asu['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'].keys():
coordinate3 = d_coordinates_asu['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'][atom_name3]['coordinate']
## conversion from 3x1 vector to 4x1 vector
coordinate3 = numpy.array([coordinate3[0],coordinate3[1],coordinate3[2],1.,])
## conversion from cartesian to fractional coordinates
coordinate3 = numpy.dot(matrix_scale,coordinate3)
## symmetry operator (before unit cell translation???)
coordinate3 = numpy.dot(matrix_symop,coordinate3)
## unit cell translation
coordinate3 += vector_translation
## conversion from fractional to cartesian coordinates
coordinate3 = numpy.dot(matrix_scalei,coordinate3)
## conversion from 4x1 vector to 3x1 vector
coordinate3 = numpy.array([coordinate3[0],coordinate3[1],coordinate3[2],])
line = build_line(
atom_name3,d_coordinates_asu,coordinate3,
chain2,res_no2,iCode2,
d_chains,
)
lines += [line]
break
## break atom_name1 loop (check next iCode1)
if distant == True:
break
## break iCode1 loop (check next iCode2)
if vicinity == True:
break
if distant == True:
break
## break resno1 loop (check next iCode2)
if vicinity == True:
break
if distant == True:
break
## break chain1 loop (check next iCode2)
if vicinity == True:
break
if distant == True:
break
fd = open('%s_biou_cc.pdb' %(pdb),'w')
fd.writelines(lines)
fd.close()
return
def main():
import os, numpy, math
import sys
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import parse_pdb
path = '/oxygenase_local/data/pdb/'
dirs = os.listdir(path)
dirs.sort()
for dir in dirs:
if dir < sys.argv[1][1:3]:
continue
print dir
ents = os.listdir('%s%s' % (path, dir))
ents.sort()
for ent in ents:
pdb = ent[3:7]
if dir == sys.argv[-1][1:3] and pdb < sys.argv[-1]:
continue
print pdb
if pdb in [
'1a0k', ## 310 helix?
'2aeb', ## helix kink
'2aoc',
'2aod',
'2aog', ## some error...
'2c03',
'2c04',
'3bxd', ## bent helix
'4fbp',
'5fbp', ## pro residue in i+6 position
'1a2f',
'1a2g', ## gly residue in i+1,i+3 position (310 helix?)
]:
continue
if pdb in [ ## from phipsiparseall
## std_res_name in neither REMARK465 nor SEQRES (large peptide length)
'1a3q',
'1c3w',
'1c3x',
'1ad5',
## hetID in SEQRES and HETATM but not MODRES
'2b2u',
'2a2x',
'2b7f',
'2c2k',
'2c2m',
'2c2o',
'2c2z',
'2aal',
'1bdu',
'2ag3',
'2age',
'2agg',
'1an5',
'2ci1',
'2ank',
## ## hetID in SEQRES and REMARK465 but not MODRES
## '1aco','7acn','8acn','2aig','3aig','1g1f','1g1s','2f4i',
## hetID in MODRES but not SEQRES
'2a4o',
'3bbd',
'1orw',
## std_res in REMARK465 but not SEQRES
'2uva',
'2uva',
'2uvc',
## hetID in SEQRES but not REMARK465,ATOM
'2vhn',
## REMARK465 records missing
'1c04',
'3b9v',
'1fka',
'1deq',
'2jcc',
'2jj4',
'1i3q',
'1i50',
'1i6h',
'1iw7',
'1p0t',
'1smy',
'1uf2',
'2v0z',
'2v7n',
'2vs4',
'1zbb',
'1zlv',
## remark470 records missing (alpha carbon only in most cases)
'1cc0',
'1f1o',
'1ffk',
'3b5d',
'3b5w',
'3b5x',
'3b5y',
'3b5z',
'3b61',
'3b62',
'1bdx',
'1d3l',
'1gix',
'1e8s',
'1j5a',
'4cro',
'1i9w',
'1giy',
'2v9l',
## SEQRES/ATOM conflict (incorrect res_name)
'2c38',
'2j01',
'2j03',
'4icd',
'2aew',
'2plv',
'1d2q',
## remark465 initiation line missing
'2iwq',
'2v07',
## incorrect residue numbers (N-terminal)
'1ef0',
'2ji5',
'1eu3',
## incorrect residue numbers (reversed)
'9lpr',
## incorrect residue numbers (insertion)
'1a4k',
'2ged',
'1cj0',
## incorrect residue numbers (altloc)
'2bb3',
## incorrect residue numbers (C-terminal)
'1a7l',
'1ce0',
'2ci0',
'2cib',
'1f32',
## inccorect residue numbers (type error)
'1f7o',
'1f7p',
'1ke8',
'1kj4',
'1n3f',
'1nlq',
'1nv8',
'1nv9',
'1pxx',
'2by6',
'1ll0',
'2bfk',
'2gnk',
'1e5r',
'1lox',
'1ca8',
'1x11',
## incorrect residue numbers (REMARK465)
'1jn6',
## incorrect residue numbers (ATOM)
'2qqh',
## incorrect residue numbers ("reset"/"broken"... 28,29,30,1,2,3)
'1jpl',
'1juq',
'1k4j',
'1q6j',
'1q6m',
'2oxg',
'2oxr',
'2qzl',
'1swf',
'1swg',
'2z5s',
'1yr6',
'1yr7',
'1yr8',
'1yr9',
## incorrect residue numbers (iCodes)
'1iao',
'2iad',
'1dki',
'1es0',
'7pck',
'1pfz',
'1qdm',
'1ygp',
'2qri',
'2qrs',
'2qrt',
'3dgv',
## incorrect residue numbers (none)
'2om7',
## incorrect chain ID (ATOM)
'1bml',
'1h74',
'1jwt',
## incorrect iCode (ATOM)
'2ius',
## incorrect SEQRES sequence
'1clw',
## identical ATOM/HETATM IDs (coordinate section)
'1h9h',
'427d',
'2olb',
'11gs',
'121p',
'12gs',
'13gs',
'16gs',
'16pk',
'17gs',
'185d',
'18gs',
'193d',
'19gs',
'1a05',
'1a0i',
'1a25',
'1a3l',
'1a44',
'1a48',
'1a4a',
'1a4b',
'1a4c',
'1a4f',
'1a4g',
'1a4k',
'1a4q',
'1a52',
'1a5a',
'1a5b',
'1a5z',
'1a65',
'1a69',
'1a6g',
'1a6m',
'1a6q',
'1a71',
'1a78',
'1a79',
'1a8i',
'1a8s',
'1a8u',
'1a9c',
'1a9m',
'1a9x',
'1a9y',
'1a9z',
'1aal',
'1aax',
'1aaz',
'1aba',
'1abw',
'1aby',
'1ad8',
'1ad9',
'1adb',
'1adc',
'1adf',
'1adg',
'1adj',
'1aec',
'1af6',
'1afa',
'1afb',
'1ag0',
'1ah8',
'1ahe',
'1ahf',
'1ahx',
'1ahy',
'1ai4',
'1ai5',
'1ai6',
'1ai7',
'1ai8',
'1aix',
'1aj6',
'1aj9',
'1ajn',
'1ajp',
'1ajq',
'1aku',
'1akv',
'1all',
'1ami',
'1ao5',
'1aok',
'1aor',
'1apm',
'1aq1',
'1aq6',
'1aq7',
'1ar1',
'1ari',
'1art',
'1arx',
'1asm',
'1asn',
'1aso',
'1asp',
'1asq',
'1at1',
'1atg',
'1atl',
'1atn',
'1atp',
'1au1',
'1aua',
'1auj',
'1aus',
'1av4',
'1av6',
'1avb',
'1avf',
'1avq',
'1awb',
'1axa',
'1axd',
'1axs',
'1aya',
'1ayo',
'1ayr',
'1azr',
'1azs',
'1b08',
'1b0m',
'1b25',
'1b4k',
'1b4n',
'1b55',
'1b6h',
'1b8t',
'1b92',
'1b9f',
'1bb1',
'1bch',
'1bcj',
'1bcr',
'1bcs',
'1bd0',
'1be3',
'1beh',
'1ben',
'1bfn',
'1bgy',
'1bh3',
'1bij',
'1biq',
'1biz',
'1bj3',
'1bja',
'1bk5',
'1bks',
'1bnl',
'1bow',
'1bps',
'1bqa',
'1bqd',
'1bqh',
'1brh',
'1brk',
'1brt',
'1bsk',
'1btc',
'1bvc',
'1bvd',
'1bwn',
'1bwo',
'1cdk',
'1cdm',
'1cel',
'1ces',
'1cf5',
'1cgk',
'1ch0',
'1ch4',
'1cls',
'1cml',
'1cnt',
'1coh',
'1con',
'1cow',
'1cpc',
'1cpq',
'1cpr',
'1crx',
'1ctf',
'1ctp',
'1cxe',
'1cxf',
'1cxh',
'1czf',
'1d33',
'1d35',
'1d39',
'1d40',
'1d61',
'1d8h',
'1daj',
'1dan',
'1dbj',
'1dbk',
'1dbp',
'1dbr',
'1dff',
'1dhy',
'1dif',
'1djc',
'1dkk',
'1dl4',
'1dlr',
'1dls',
'1dmr',
'1dms',
'1dpe',
'1dpm',
'1drf',
'1drj',
'1drk',
'1dut',
'1eas',
'1ecc',
'1ecg',
'1efg',
'1eg6',
'1elp',
'1ent',
'1epm',
'1epn',
'1epp',
'1epq',
'1eta',
'1etb',
'1eth',
'1etj',
'1fax',
'1fbt',
'1fdh',
'1fgh',
'1fgj',
'1fig',
'1fiv',
'1fkb',
'1fki',
'1fn1',
'1fpc',
'1fpi',
'1fpj',
'1fpl',
'1fsa',
'1fui',
'1fuo',
'1fup',
'1fuq',
'1fur',
'1fv7',
'1fyl',
'1g5l',
'1gac',
'1gaf',
'1gan',
'1gbu',
'1gdi',
'1gic',
'1gj2',
'1glc',
'1gld',
'1gle',
'1gli',
'1gmk',
'1gmp',
'1gmr',
'1gnm',
'1gnn',
'1gno',
'1gnw',
'1gpa',
'1gpd',
'1gqh',
'1gsu',
'1gsy',
'1gti',
'1gtm',
'1gtp',
'1hab',
'1hac',
'1hah',
'1hbg',
'1hbi',
'1hbs',
'1hbt',
'1hcn',
'1hcs',
'1hct',
'1hds',
'1hdt',
'1hfp',
'1hfq',
'1hfr',
'1hga',
'1hgb',
'1hgc',
'1hgt',
'1hho',
'1hih',
'1hii',
'1hiv',
'1hmd',
'1hmo',
'1hpc',
'1hr3',
'1hro',
'1hrp',
'1htp',
'1huj',
'1huk',
'1hur',
'1hvq',
'1hvr',
'1hxp',
'1hya',
'1i3t',
'1i47',
'1i7v',
'1iak',
'1ibg',
'1icj',
'1idc',
'1ide',
'1iea',
'1ieb',
'1igt',
'1igy',
'1ils',
'1ilu',
'1imc',
'1imd',
'1ipw',
'1irn',
'1iro',
'1ith',
'1ixx',
'1izb',
'1j8l',
'1jaw',
'1jdb',
'1jfd',
'1jka',
'1jkb',
'1jkc',
'1jkd',
'1jlx',
'1jpc',
'1jsa',
'1jst',
'1jsu',
'1kao',
'1kpe',
'1kr7',
'1krb',
'1krc',
'1krn',
'1ksa',
'1kvq',
'1kvr',
'1kvs',
'1kvt',
'1kvu',
'1lam',
'1lcj',
'1lck',
'1lcp',
'1ldp',
'1len',
'1lia',
'1lkk',
'1lkl',
'1llo',
'1lml',
'1loa',
'1lob',
'1lpa',
'1lpb',
'1lth',
'1ltr',
'1lu2',
'1lya',
'1lyb',
'1lyw',
'1m5k',
'1mae',
'1maf',
'1mbd',
'1mfr',
'1mhe',
'1mhk',
'1mmb',
'1mmo',
'1mmp',
'1mmq',
'1mmr',
'1mpa',
'1mpg',
'1mpq',
'1mpr',
'1mwe',
'1myf',
'1myh',
'1myj',
'1nah',
'1nai',
'1nas',
'1nbb',
'1nbc',
'1nbe',
'1nci',
'1nco',
'1nec',
'1nfd',
'1nfp',
'1nlk',
'1nn2',
'1nnc',
'1np1',
'1nrs',
'1nsa',
'1nsc',
'1nsd',
'1nzr',
'1oaa',
'1oat',
'1ohj',
'1olc',
'1ord',
'1otg',
'1ouu',
'1ova',
'1ovw',
'1p35',
'1pag',
'1pam',
'1pbo',
'1pea',
'1pgt',
'1php',
'1ply',
'1pnk',
'1pnl',
'1pnm',
'1poi',
'1ppm',
'1ppr',
'1psc',
'1psh',
'1ptv',
'1pty',
'1pyt',
'1qbi',
'1qd6',
'1qdc',
'1qf8',
'1qge',
'1qha',
'1qhf',
'1qpr',
'1qrd',
'1qs8',
'1qsg',
'1raa',
'1rab',
'1rac',
'1rad',
'1rae',
'1raf',
'1rag',
'1rah',
'1rai',
'1rbl',
'1rcm',
'1rcp',
'1rdg',
'1rdi',
'1rdj',
'1rdk',
'1rdl',
'1rdm',
'1rdn',
'1rdv',
'1rdx',
'1rdy',
'1rdz',
'1rem',
'1rge',
'1rgf',
'1rgg',
'1rgh',
'1rn1',
'1rnc',
'1rsy',
'1rtf',
'1rth',
'1rti',
'1rtj',
'1rtm',
'1rvw',
'1sac',
'1scu',
'1sda',
'1sdk',
'1sdl',
'1sep',
'1sfi',
'1sft',
'1sgc',
'1shb',
'1shd',
'1skj',
'1sky',
'1slb',
'1slc',
'1sli',
'1slt',
'1slu',
'1smp',
'1sps',
'1stc',
'1sty',
'1swd',
'1swe',
'1swn',
'1swp',
'1swr',
'1taq',
'1tar',
'1tat',
'1taw',
'1tcb',
'1tcf',
'1tco',
'1tei',
'1tet',
'1thb',
'1ths',
'1tlc',
'1tlg',
'1tli',
'1tlp',
'1tmb',
'1tmn',
'1tmu',
'1tn4',
'1tpf',
'1tpk',
'1try',
'1trz',
'1tsd',
'1ttp',
'1ttq',
'1tub',
'1tyl',
'1tym',
'1tyu',
'1tyw',
'1tyx',
'1udg',
'1udh',
'1uma',
'1uz8',
'1vdr',
'1vrt',
'1vru',
'1vwt',
'1wav',
'1wgi',
'1wgj',
'1whs',
'1wht',
'1wyk',
'1xel',
'1xgm',
'1xgn',
'1xgs',
'1xik',
'1xso',
'1yag',
'1yec',
'1yef',
'1yeg',
'1yeh',
'1yrq',
'1zeg',
'1zeh',
'1zni',
'1znj',
'20gs',
'211d',
'219d',
'21gs',
'221p',
'22gs',
'253d',
'256b',
'258d',
'25c8',
'277d',
'2a3h',
'2aaa',
'2aac',
'2aae',
'2ahj',
'2arc',
'2at1',
'2atc',
'2ay1',
'2ay2',
'2ay3',
'2ay4',
'2ay5',
'2ay6',
'2ay7',
'2ay8',
'2ay9',
'2azu',
'2btf',
'2bvw',
'2c7e',
'2cah',
'2cht',
'2cmm',
'2cpk',
'2cst',
'2d34',
'2d95',
'2da8',
'2dhb',
'2dhn',
'2dmr',
'2dri',
'2ecp',
'2fbj',
'2fus',
'2gli',
'2glr',
'2gls',
'2gsa',
'2gss',
'2hck',
'2hhb',
'2hhd',
'2hk6',
'2hmq',
'2hmz',
'2hr7',
'2iep',
'2kau',
'2lal',
'2lhb',
'2mas',
'2mcp',
'2mhb',
'2mpa',
'2mpr',
'2msb',
'2nac',
'2np1',
'2otc',
'2ovw',
'2oxi',
'2pax',
'2pcp',
'2pfl',
'2pgh',
'2pgt',
'2phk',
'2pk4',
'2pld',
'2ple',
'2prc',
'2prg',
'2q41',
'2qwa',
'2qwb',
'2qwc',
'2qwd',
'2qwe',
'2qwf',
'2qwg',
'2qwh',
'2qwi',
'2qwj',
'2qwk',
'2r2f',
'2ran',
'2rkm',
'2rus',
'2scp',
'2sec',
'2shk',
'2sli',
'2sn3',
'2sni',
'2sod',
'2taa',
'2tgd',
'2tli',
'2tmn',
'2tn4',
'2trc',
'2tsc',
'2wea',
'2web',
'2wec',
'308d',
'367d',
'380d',
'381d',
'382d',
'3a3h',
'3at1',
'3azu',
'3chb',
'3cyt',
'3dmr',
'3eng',
'3fru',
'3fx2',
'3grs',
'3gss',
'3gst',
'3hat',
'3hhb',
'3ljr',
'3lkf',
'3np1',
'3p2p',
'3pax',
'3pca',
'3pcb',
'3pcc',
'3pcd',
'3pce',
'3pcf',
'3pcg',
'3pch',
'3pci',
'3pcj',
'3pck',
'3pcn',
'3pmg',
'3prc',
'3prn',
'3pro',
'3sc2',
'3sli',
'3sqc',
'3tli',
'3tmn',
'421p',
'455d',
'456c',
'4a3h',
'4at1',
'4cts',
'4dfr',
'4dmr',
'4eng',
'4fx2',
'4gr1',
'4gsa',
'4gss',
'4hhb',
'4hmg',
'4mdh',
'4np1',
'4ovw',
'4pax',
'4rub',
'4sli',
'4tgl',
'4tmn',
'5at1',
'5bir',
'5dnb',
'5fx2',
'5gss',
'5hmg',
'5mdh',
'5prn',
'5tmn',
'621p',
'6abp',
'6adh',
'6at1',
'6gsp',
'6gss',
'6gsu',
'6gsv',
'6gsw',
'6gsx',
'6ins',
'6prn',
'6tmn',
'721p',
'7aat',
'7abp',
'7at1',
'7gss',
'7odc',
'7prn',
'7taa',
'830c',
'8aat',
'8abp',
'8at1',
'8gss',
'8prn',
'966c',
'9gss',
'9pap',
'9rub',
'2q44',
## identical IDs in REMARK465 and ATOM records
'3c9u',
## altloc not in MODRES records
'354d',
]:
continue
file = '%s%s/%s' % (path, dir, ent)
fd = open(file, 'r')
lines = fd.readlines()
fd.close()
##
## parse header
##
d_header = parse_pdb.parse_header(lines)
if not 'HELIX' in d_header.keys():
continue
if d_header['EXPDTA'] != 'X-RAY':
continue
##
## parse coordinates
##
d_coordinates, d_ATOMseq = parse_pdb.parse_coordinates(
lines,
d_header,
)
for chain in d_header['SEQRES']['chains']:
if chain not in d_header['HELIX'].keys():
continue
for helix_no in d_header['HELIX'][chain].keys():
res_no = d_header['HELIX'][chain][helix_no]['res_no']
iCode = d_header['HELIX'][chain][helix_no]['iCode']
helix_len = d_header['HELIX'][chain][helix_no]['len']
if not res_no in d_coordinates['chains'][chain][
'residues'].keys():
continue
seq_no = d_coordinates['chains'][chain]['residues'][
res_no]['d_iCodes'][iCode]['seq_no']
if seq_no == -1:
continue ## hoeker-loesning
if seq_no >= len(d_ATOMseq[chain]['res_nos']):
continue ## hoeker-loesning
if d_ATOMseq[chain]['res_nos'][seq_no] != res_no:
stop
if d_ATOMseq[chain]['iCodes'][seq_no] != iCode:
stop
## if d_ATOMseq[chain]['altlocs'][seq_no] != ' ':
## stop
if helix_len < 11:
continue
l_angles = []
for i in range(
seq_no + 1,
min(seq_no + helix_len,
len(d_ATOMseq[chain]['res_nos'])) - 4 - 1):
res_no1 = d_ATOMseq[chain]['res_nos'][i]
res_no2 = d_ATOMseq[chain]['res_nos'][i + 4]
iCode1 = d_ATOMseq[chain]['iCodes'][i]
iCode2 = d_ATOMseq[chain]['iCodes'][i + 4]
record1 = d_ATOMseq[chain]['records'][i]
record2 = d_ATOMseq[chain]['records'][i + 4]
if not res_no1 in d_coordinates['chains'][chain][
'residues'].keys() and record1 == 'REMARK465':
continue
if not res_no2 in d_coordinates['chains'][chain][
'residues'].keys() and record2 == 'REMARK465':
continue
res_name1 = d_coordinates['chains'][chain]['residues'][
res_no1]['d_iCodes'][iCode1]['res_name']
if not 'O' in d_coordinates['chains'][chain][
'residues'][res_no1]['d_iCodes'][iCode1][
'atoms'].keys():
continue
if not 'H' in d_coordinates['chains'][chain][
'residues'][res_no2]['d_iCodes'][iCode2][
'atoms'].keys():
continue
O = d_coordinates['chains'][chain]['residues'][
res_no1]['d_iCodes'][iCode1]['atoms']['O'][
'coordinate']
N = d_coordinates['chains'][chain]['residues'][
res_no2]['d_iCodes'][iCode2]['atoms']['N'][
'coordinate']
H = d_coordinates['chains'][chain]['residues'][
res_no2]['d_iCodes'][iCode2]['atoms']['H'][
'coordinate']
vNH = N - H
vOH = O - H
angle = (180 / math.pi) * math.acos(
numpy.dot(vNH, vOH) /
math.sqrt(sum(vNH**2) * sum(vOH**2)))
print pdb, chain, res_no1, res_no2, angle
if res_name1 != 'GLY' and angle < 78: ## 113
print res_name1
stop1
if res_name1 == 'GLY' and angle < 101:
stop1
l_angles += [angle]
if len(l_angles) > 0:
print helix_len, sum(l_angles) / len(l_angles)
if sum(l_angles) / len(l_angles) > 171:
stop3
if sum(l_angles) / len(l_angles) < 149:
stop4
def main():
for pdb in [
## '2hhb',
## '1hho',
## '1hv4',
'2lzm',
## '2lzt',
## '1c76',
## '1c77',
## '1c78',
]:
## os.system('cp /local/data/pdb/%s/pdb%s.ent %s.pdb' %(pdb[1:3],pdb,pdb,))
##
#### biounit.biounit().main(pdb, '/data/remediated_pdb/', exclude_ligands = True)
####
#### os.system('cp %s_1.pdb %s.pdb' %(pdb,pdb,))
##
## fd = open('%s.pdb' %(pdb),'r')
## lines = fd.readlines()
## fd.close()
fd = open('C:\Users\Tommy Carstensen\pdb\%s.pdb' % (pdb), 'r')
lines = fd.readlines()
fd.close()
d_header = parse_pdb.parse_header(lines)
d_coordinates, d_ATOMseq = parse_pdb.parse_coordinates(
lines,
d_header,
)
l_coordinates = []
a = d_header['CRYST1']['edges'][0]
b = d_header['CRYST1']['edges'][1]
c = d_header['CRYST1']['edges'][2]
alpha = math.pi * d_header['CRYST1']['angles'][0] / 180.
beta = math.pi * d_header['CRYST1']['angles'][1] / 180.
gamma = math.pi * d_header['CRYST1']['angles'][2] / 180.
## unit cell voumne
volume = a * b * c * math.sqrt(
1 - math.cos(alpha)**2 - math.cos(beta)**2 - math.cos(gamma)**2 +
2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)))
matrix_fractional2cartesian = numpy.array([
[
a,
b * math.cos(gamma),
c * math.cos(beta),
],
[
0,
b * math.sin(gamma),
c * (math.cos(alpha) - math.cos(beta) * math.cos(gamma)) /
math.sin(gamma),
],
[
0,
0,
volume / (a * b * math.sin(gamma)),
],
])
## lines = []
for symop in d_header['REMARK290'].keys():
print 'symop', symop
matrix_symop = d_header['REMARK290'][symop]['matrix']
vector_symop = d_header['REMARK290'][symop]['vector']
for i_translation in range(len(l_translations)):
print 'symop', symop, 'translation', i_translation
vector_translation = l_translations[i_translation]
for chain2 in d_coordinates['chains'].keys():
for res_no2 in d_coordinates['chains'][chain2][
'residues'].keys():
## print symop, i, chain2, res_no2
for iCode2 in d_coordinates['chains'][chain2][
'residues'][res_no2]['d_iCodes'].keys():
for chain1 in d_coordinates['chains'].keys():
for res_no1 in d_coordinates['chains'][chain1][
'residues'].keys():
## if res_no2 != 75:
## continue
for iCode1 in d_coordinates['chains'][
chain1]['residues'][res_no1][
'd_iCodes'].keys():
for atom_name1 in d_coordinates[
'chains'][chain1]['residues'][
res_no1]['d_iCodes'][
iCode1]['atoms'].keys(
):
coordinate1 = d_coordinates[
'chains'][chain1]['residues'][
res_no1]['d_iCodes'][
iCode1]['atoms'][
atom_name1][
'coordinate']
for atom_name2 in d_coordinates[
'chains'][chain2][
'residues'][res_no2][
'd_iCodes'][iCode2][
'atoms'].keys(
):
coordinate2 = d_coordinates[
'chains'][chain2]['residues'][
res_no2]['d_iCodes'][
iCode2]['atoms'][
atom_name2][
'coordinate']
coordinate2 = numpy.dot(
matrix_symop,
coordinate2) + vector_symop
coordinate2 += numpy.dot(
matrix_fractional2cartesian,
vector_translation)
coordinate2[0] = round(
coordinate2[0], 3)
coordinate2[1] = round(
coordinate2[1], 3)
coordinate2[2] = round(
coordinate2[2], 3)
vicinity = False
distant = False
dist = math.sqrt(
sum((coordinate2 -
coordinate1)**2))
dist = 0
## if dist < 5:
## print '%2i %.2f %.2f %4i %4s %s %4i %4s %s ' %(
## i, round(dist,2), dist_treshold,
## res_no2, atom_name2, coordinate2, res_no1, atom_name1, coordinate1
## )
dist_treshold = d_radii_vdw[
atom_name1[
0]] + d_radii_vdw[
atom_name2[
0]] + 0.25
## break atom_name2 loop
if dist < dist_treshold:
vicinity = True
break
## break atom_name2 loop
if dist > 10.: ## length of lysine is 7-8Angstrom
distant = True
break
## break atom_name1 loop (append line and check next iCode1)
if vicinity == True:
for atom_name3 in d_coordinates[
'chains'][chain2][
'residues'][res_no2][
'd_iCodes'][
iCode2][
'atoms'].keys(
):
coordinate3 = d_coordinates[
'chains'][chain2]['residues'][
res_no2]['d_iCodes'][
iCode2]['atoms'][
atom_name3][
'coordinate']
coordinate3 = numpy.dot(
matrix_symop,
coordinate3,
) + vector_symop
coordinate3 += numpy.dot(
matrix_fractional2cartesian,
vector_translation,
)
line = build_line(
atom_name3,
d_coordinates,
coordinate3,
chain2,
res_no2,
iCode2,
symop,
i_translation,
)
lines += [line]
break
## break atom_name1 loop (check next iCode1)
if distant == True:
break
## break iCode1 loop (check next iCode2)
if vicinity == True:
break
## break resno1 loop (check next iCode2)
if vicinity == True:
break
## break chain1 loop (check next iCode2)
if vicinity == True:
break
fd = open('%s_crystalcontacts.pdb' % (pdb), 'w')
fd.writelines(lines)
fd.close()
source = 'whatif.src'
fd = open(source, 'w')
fd.writelines([
'/software/whatif/DO_WHATIF.COM <<EOF\n',
'GETMOL %s.pdb\n' % (pdb, ),
'%s\n' % (pdb, ),
'%DELWAT\n',
'%DELLIG\n',
'%SOUSHL\n', ## crystal contacts
'%MAKMOL\n',
'\n', ## The file header will be copied from a PDB file. Hit return for the default header that has no information in it.
'soushl_%s.pdb\n' % (pdb),
'TOT 0\n',
'\n', ## REMARKS
'STOP\n',
'Y\n',
])
fd.close()
os.system('source %s > whatif_surface/%s.out' % (source, pdb))
os.system(
'rm DRG* DAVADRUG.PDB ALTERR.LOG PDBFILE whatif.src FOR*.DAT WHATIF.FIG'
)
return
def main():
import os, numpy, math
import sys
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import parse_pdb
path = '/oxygenase_local/data/pdb/'
dirs = os.listdir(path)
dirs.sort()
for dir in dirs:
if dir < sys.argv[1][1:3]:
continue
print dir
ents = os.listdir('%s%s' %(path,dir))
ents.sort()
for ent in ents:
pdb = ent[3:7]
if dir == sys.argv[-1][1:3] and pdb < sys.argv[-1]:
continue
print pdb
if pdb in [
'1a0k', ## 310 helix?
'2aeb', ## helix kink
'2aoc','2aod','2aog', ## some error...
'2c03','2c04','3bxd', ## bent helix
'4fbp','5fbp', ## pro residue in i+6 position
'1a2f','1a2g', ## gly residue in i+1,i+3 position (310 helix?)
]:
continue
if pdb in [ ## from phipsiparseall
## std_res_name in neither REMARK465 nor SEQRES (large peptide length)
'1a3q','1c3w','1c3x','1ad5',
## hetID in SEQRES and HETATM but not MODRES
'2b2u','2a2x','2b7f','2c2k','2c2m','2c2o','2c2z','2aal','1bdu',
'2ag3','2age','2agg','1an5','2ci1','2ank',
## ## hetID in SEQRES and REMARK465 but not MODRES
## '1aco','7acn','8acn','2aig','3aig','1g1f','1g1s','2f4i',
## hetID in MODRES but not SEQRES
'2a4o','3bbd','1orw',
## std_res in REMARK465 but not SEQRES
'2uva','2uva','2uvc',
## hetID in SEQRES but not REMARK465,ATOM
'2vhn',
## REMARK465 records missing
'1c04','3b9v','1fka','1deq','2jcc','2jj4','1i3q','1i50','1i6h',
'1iw7','1p0t','1smy','1uf2','2v0z','2v7n','2vs4','1zbb','1zlv',
## remark470 records missing (alpha carbon only in most cases)
'1cc0','1f1o','1ffk','3b5d','3b5w','3b5x','3b5y','3b5z','3b61',
'3b62','1bdx','1d3l','1gix','1e8s','1j5a','4cro','1i9w','1giy',
'2v9l',
## SEQRES/ATOM conflict (incorrect res_name)
'2c38','2j01','2j03','4icd','2aew','2plv','1d2q',
## remark465 initiation line missing
'2iwq','2v07',
## incorrect residue numbers (N-terminal)
'1ef0','2ji5','1eu3',
## incorrect residue numbers (reversed)
'9lpr',
## incorrect residue numbers (insertion)
'1a4k','2ged','1cj0',
## incorrect residue numbers (altloc)
'2bb3',
## incorrect residue numbers (C-terminal)
'1a7l','1ce0','2ci0','2cib','1f32',
## inccorect residue numbers (type error)
'1f7o','1f7p','1ke8','1kj4','1n3f','1nlq','1nv8','1nv9','1pxx',
'2by6','1ll0','2bfk','2gnk','1e5r','1lox','1ca8','1x11',
## incorrect residue numbers (REMARK465)
'1jn6',
## incorrect residue numbers (ATOM)
'2qqh',
## incorrect residue numbers ("reset"/"broken"... 28,29,30,1,2,3)
'1jpl','1juq','1k4j','1q6j','1q6m','2oxg','2oxr','2qzl',
'1swf','1swg','2z5s','1yr6','1yr7','1yr8','1yr9',
## incorrect residue numbers (iCodes)
'1iao','2iad','1dki','1es0','7pck','1pfz','1qdm','1ygp',
'2qri','2qrs','2qrt','3dgv',
## incorrect residue numbers (none)
'2om7',
## incorrect chain ID (ATOM)
'1bml','1h74','1jwt',
## incorrect iCode (ATOM)
'2ius',
## incorrect SEQRES sequence
'1clw',
## identical ATOM/HETATM IDs (coordinate section)
'1h9h','427d','2olb','11gs','121p','12gs','13gs','16gs','16pk','17gs','185d','18gs','193d','19gs','1a05','1a0i','1a25','1a3l','1a44','1a48','1a4a','1a4b','1a4c','1a4f','1a4g','1a4k','1a4q','1a52','1a5a','1a5b','1a5z','1a65','1a69','1a6g','1a6m','1a6q','1a71','1a78','1a79','1a8i', '1a8s', '1a8u', '1a9c', '1a9m', '1a9x', '1a9y', '1a9z', '1aal', '1aax', '1aaz', '1aba', '1abw', '1aby', '1ad8', '1ad9', '1adb', '1adc', '1adf', '1adg', '1adj', '1aec', '1af6', '1afa', '1afb', '1ag0', '1ah8', '1ahe', '1ahf', '1ahx', '1ahy', '1ai4', '1ai5', '1ai6', '1ai7', '1ai8', '1aix', '1aj6', '1aj9', '1ajn', '1ajp', '1ajq', '1aku', '1akv', '1all', '1ami', '1ao5', '1aok', '1aor', '1apm', '1aq1', '1aq6', '1aq7', '1ar1', '1ari', '1art', '1arx', '1asm', '1asn', '1aso', '1asp', '1asq', '1at1', '1atg', '1atl', '1atn', '1atp', '1au1', '1aua', '1auj', '1aus', '1av4', '1av6', '1avb', '1avf', '1avq', '1awb', '1axa', '1axd', '1axs', '1aya', '1ayo', '1ayr', '1azr', '1azs', '1b08', '1b0m', '1b25', '1b4k', '1b4n', '1b55', '1b6h', '1b8t', '1b92', '1b9f', '1bb1', '1bch', '1bcj', '1bcr', '1bcs', '1bd0', '1be3', '1beh', '1ben', '1bfn', '1bgy', '1bh3', '1bij', '1biq', '1biz', '1bj3', '1bja', '1bk5', '1bks', '1bnl', '1bow', '1bps', '1bqa', '1bqd', '1bqh', '1brh', '1brk', '1brt', '1bsk', '1btc', '1bvc', '1bvd', '1bwn', '1bwo', '1cdk', '1cdm', '1cel', '1ces', '1cf5', '1cgk', '1ch0', '1ch4', '1cls', '1cml', '1cnt', '1coh', '1con', '1cow', '1cpc', '1cpq', '1cpr', '1crx', '1ctf', '1ctp', '1cxe', '1cxf', '1cxh', '1czf', '1d33', '1d35', '1d39', '1d40', '1d61', '1d8h', '1daj', '1dan', '1dbj', '1dbk', '1dbp', '1dbr', '1dff', '1dhy', '1dif', '1djc', '1dkk', '1dl4', '1dlr', '1dls', '1dmr', '1dms', '1dpe', '1dpm', '1drf', '1drj', '1drk', '1dut', '1eas', '1ecc', '1ecg', '1efg', '1eg6', '1elp', '1ent', '1epm', '1epn', '1epp', '1epq', '1eta', '1etb', '1eth', '1etj', '1fax', '1fbt', '1fdh', '1fgh', '1fgj', '1fig', '1fiv', '1fkb', '1fki', '1fn1', '1fpc', '1fpi', '1fpj', '1fpl', '1fsa', '1fui', '1fuo', '1fup', '1fuq', '1fur', '1fv7', '1fyl', '1g5l', '1gac', '1gaf', '1gan', '1gbu', '1gdi', '1gic', '1gj2', '1glc', '1gld', '1gle', '1gli', '1gmk', '1gmp', '1gmr', '1gnm', '1gnn', '1gno', '1gnw', '1gpa', '1gpd', '1gqh', '1gsu', '1gsy', '1gti', '1gtm', '1gtp', '1hab', '1hac', '1hah', '1hbg', '1hbi', '1hbs', '1hbt', '1hcn', '1hcs', '1hct', '1hds', '1hdt', '1hfp', '1hfq', '1hfr', '1hga', '1hgb', '1hgc', '1hgt', '1hho', '1hih', '1hii', '1hiv', '1hmd', '1hmo', '1hpc', '1hr3', '1hro', '1hrp', '1htp', '1huj', '1huk', '1hur', '1hvq', '1hvr', '1hxp', '1hya', '1i3t', '1i47', '1i7v', '1iak', '1ibg', '1icj', '1idc', '1ide', '1iea', '1ieb', '1igt', '1igy', '1ils', '1ilu', '1imc', '1imd', '1ipw', '1irn', '1iro', '1ith', '1ixx', '1izb', '1j8l', '1jaw', '1jdb', '1jfd', '1jka', '1jkb', '1jkc', '1jkd', '1jlx', '1jpc', '1jsa', '1jst', '1jsu', '1kao', '1kpe', '1kr7', '1krb', '1krc', '1krn', '1ksa', '1kvq', '1kvr', '1kvs', '1kvt', '1kvu', '1lam', '1lcj', '1lck', '1lcp', '1ldp', '1len', '1lia', '1lkk', '1lkl', '1llo', '1lml', '1loa', '1lob', '1lpa', '1lpb', '1lth', '1ltr', '1lu2', '1lya', '1lyb', '1lyw', '1m5k', '1mae', '1maf', '1mbd', '1mfr', '1mhe', '1mhk', '1mmb', '1mmo', '1mmp', '1mmq', '1mmr', '1mpa', '1mpg', '1mpq', '1mpr', '1mwe', '1myf', '1myh', '1myj', '1nah', '1nai', '1nas', '1nbb', '1nbc', '1nbe', '1nci', '1nco', '1nec', '1nfd', '1nfp', '1nlk', '1nn2', '1nnc', '1np1', '1nrs', '1nsa', '1nsc', '1nsd', '1nzr', '1oaa', '1oat', '1ohj', '1olc', '1ord', '1otg', '1ouu', '1ova', '1ovw', '1p35', '1pag', '1pam', '1pbo', '1pea', '1pgt', '1php', '1ply', '1pnk', '1pnl', '1pnm', '1poi', '1ppm', '1ppr', '1psc', '1psh', '1ptv', '1pty', '1pyt', '1qbi', '1qd6', '1qdc', '1qf8', '1qge', '1qha', '1qhf', '1qpr', '1qrd', '1qs8', '1qsg', '1raa', '1rab', '1rac', '1rad', '1rae', '1raf', '1rag', '1rah', '1rai', '1rbl', '1rcm', '1rcp', '1rdg', '1rdi', '1rdj', '1rdk', '1rdl', '1rdm', '1rdn', '1rdv', '1rdx', '1rdy', '1rdz', '1rem', '1rge', '1rgf', '1rgg', '1rgh', '1rn1', '1rnc', '1rsy', '1rtf', '1rth', '1rti', '1rtj', '1rtm', '1rvw', '1sac', '1scu', '1sda', '1sdk', '1sdl', '1sep', '1sfi', '1sft', '1sgc', '1shb', '1shd', '1skj', '1sky', '1slb', '1slc', '1sli', '1slt', '1slu', '1smp', '1sps', '1stc', '1sty', '1swd', '1swe', '1swn', '1swp', '1swr', '1taq', '1tar', '1tat', '1taw', '1tcb', '1tcf', '1tco', '1tei', '1tet', '1thb', '1ths', '1tlc', '1tlg', '1tli', '1tlp', '1tmb', '1tmn', '1tmu', '1tn4', '1tpf', '1tpk', '1try', '1trz', '1tsd', '1ttp', '1ttq', '1tub', '1tyl', '1tym', '1tyu', '1tyw', '1tyx', '1udg', '1udh', '1uma', '1uz8', '1vdr', '1vrt', '1vru', '1vwt', '1wav', '1wgi', '1wgj', '1whs', '1wht', '1wyk', '1xel', '1xgm', '1xgn', '1xgs', '1xik', '1xso', '1yag', '1yec', '1yef', '1yeg', '1yeh', '1yrq', '1zeg', '1zeh', '1zni', '1znj', '20gs', '211d', '219d', '21gs', '221p', '22gs', '253d', '256b', '258d', '25c8', '277d', '2a3h', '2aaa', '2aac', '2aae', '2ahj', '2arc', '2at1', '2atc', '2ay1', '2ay2', '2ay3', '2ay4', '2ay5', '2ay6', '2ay7', '2ay8', '2ay9', '2azu', '2btf', '2bvw', '2c7e', '2cah', '2cht', '2cmm', '2cpk', '2cst', '2d34', '2d95', '2da8', '2dhb', '2dhn', '2dmr', '2dri', '2ecp', '2fbj', '2fus', '2gli', '2glr', '2gls', '2gsa', '2gss', '2hck', '2hhb', '2hhd', '2hk6', '2hmq', '2hmz', '2hr7', '2iep', '2kau', '2lal', '2lhb', '2mas', '2mcp', '2mhb', '2mpa', '2mpr', '2msb', '2nac', '2np1','2otc', '2ovw', '2oxi', '2pax', '2pcp', '2pfl', '2pgh', '2pgt', '2phk', '2pk4', '2pld', '2ple', '2prc', '2prg', '2q41', '2qwa', '2qwb', '2qwc', '2qwd', '2qwe', '2qwf', '2qwg', '2qwh', '2qwi', '2qwj', '2qwk', '2r2f', '2ran', '2rkm', '2rus', '2scp', '2sec', '2shk', '2sli', '2sn3', '2sni', '2sod', '2taa', '2tgd', '2tli', '2tmn', '2tn4', '2trc', '2tsc', '2wea', '2web', '2wec', '308d', '367d', '380d', '381d', '382d', '3a3h', '3at1', '3azu', '3chb', '3cyt', '3dmr', '3eng', '3fru', '3fx2', '3grs', '3gss', '3gst', '3hat', '3hhb', '3ljr', '3lkf', '3np1', '3p2p', '3pax', '3pca', '3pcb', '3pcc', '3pcd', '3pce', '3pcf', '3pcg', '3pch', '3pci', '3pcj', '3pck', '3pcn', '3pmg', '3prc', '3prn', '3pro', '3sc2', '3sli', '3sqc', '3tli', '3tmn', '421p', '455d', '456c', '4a3h', '4at1', '4cts', '4dfr', '4dmr', '4eng', '4fx2', '4gr1', '4gsa', '4gss', '4hhb', '4hmg', '4mdh', '4np1', '4ovw', '4pax', '4rub', '4sli', '4tgl', '4tmn', '5at1', '5bir', '5dnb', '5fx2', '5gss', '5hmg', '5mdh', '5prn', '5tmn', '621p', '6abp', '6adh', '6at1', '6gsp', '6gss', '6gsu', '6gsv', '6gsw', '6gsx', '6ins', '6prn', '6tmn', '721p', '7aat', '7abp', '7at1', '7gss', '7odc', '7prn', '7taa', '830c', '8aat', '8abp', '8at1', '8gss', '8prn', '966c', '9gss', '9pap', '9rub','2q44',
## identical IDs in REMARK465 and ATOM records
'3c9u',
## altloc not in MODRES records
'354d',
]:
continue
file = '%s%s/%s' %(path,dir,ent)
fd = open(file,'r')
lines = fd.readlines()
fd.close()
##
## parse header
##
d_header = parse_pdb.parse_header(lines)
if not 'HELIX' in d_header.keys():
continue
if d_header['EXPDTA'] != 'X-RAY':
continue
##
## parse coordinates
##
d_coordinates, d_ATOMseq = parse_pdb.parse_coordinates(lines, d_header,)
for chain in d_header['SEQRES']['chains']:
if chain not in d_header['HELIX'].keys():
continue
for helix_no in d_header['HELIX'][chain].keys():
res_no = d_header['HELIX'][chain][helix_no]['res_no']
iCode = d_header['HELIX'][chain][helix_no]['iCode']
helix_len = d_header['HELIX'][chain][helix_no]['len']
if not res_no in d_coordinates['chains'][chain]['residues'].keys():
continue
seq_no = d_coordinates['chains'][chain]['residues'][res_no]['d_iCodes'][iCode]['seq_no']
if seq_no == -1:
continue ## hoeker-loesning
if seq_no >= len(d_ATOMseq[chain]['res_nos']):
continue ## hoeker-loesning
if d_ATOMseq[chain]['res_nos'][seq_no] != res_no:
stop
if d_ATOMseq[chain]['iCodes'][seq_no] != iCode:
stop
## if d_ATOMseq[chain]['altlocs'][seq_no] != ' ':
## stop
if helix_len < 11:
continue
l_angles = []
for i in range(seq_no+1,min(seq_no+helix_len,len(d_ATOMseq[chain]['res_nos']))-4-1):
res_no1 = d_ATOMseq[chain]['res_nos'][i]
res_no2 = d_ATOMseq[chain]['res_nos'][i+4]
iCode1 = d_ATOMseq[chain]['iCodes'][i]
iCode2 = d_ATOMseq[chain]['iCodes'][i+4]
record1 = d_ATOMseq[chain]['records'][i]
record2 = d_ATOMseq[chain]['records'][i+4]
if not res_no1 in d_coordinates['chains'][chain]['residues'].keys() and record1 == 'REMARK465':
continue
if not res_no2 in d_coordinates['chains'][chain]['residues'].keys() and record2 == 'REMARK465':
continue
res_name1 = d_coordinates['chains'][chain]['residues'][res_no1]['d_iCodes'][iCode1]['res_name']
if not 'O' in d_coordinates['chains'][chain]['residues'][res_no1]['d_iCodes'][iCode1]['atoms'].keys():
continue
if not 'H' in d_coordinates['chains'][chain]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'].keys():
continue
O = d_coordinates['chains'][chain]['residues'][res_no1]['d_iCodes'][iCode1]['atoms']['O']['coordinate']
N = d_coordinates['chains'][chain]['residues'][res_no2]['d_iCodes'][iCode2]['atoms']['N']['coordinate']
H = d_coordinates['chains'][chain]['residues'][res_no2]['d_iCodes'][iCode2]['atoms']['H']['coordinate']
vNH = N-H
vOH = O-H
angle = (180/math.pi)*math.acos(
numpy.dot(vNH,vOH)/math.sqrt(
sum(vNH**2)*sum(vOH**2)
)
)
print pdb, chain, res_no1, res_no2, angle
if res_name1 != 'GLY' and angle < 78: ## 113
print res_name1
stop1
if res_name1 == 'GLY' and angle < 101:
stop1
l_angles += [angle]
if len(l_angles) > 0:
print helix_len, sum(l_angles)/len(l_angles)
if sum(l_angles)/len(l_angles) > 171:
stop3
if sum(l_angles)/len(l_angles) < 149:
stop4
def main():
for pdb in [
## '2hhb',
## '1hho',
## '1hv4',
'2lzm',
## '2lzt',
## '1c76',
## '1c77',
## '1c78',
]:
## os.system('cp /local/data/pdb/%s/pdb%s.ent %s.pdb' %(pdb[1:3],pdb,pdb,))
##
#### biounit.biounit().main(pdb, '/data/remediated_pdb/', exclude_ligands = True)
####
#### os.system('cp %s_1.pdb %s.pdb' %(pdb,pdb,))
##
## fd = open('%s.pdb' %(pdb),'r')
## lines = fd.readlines()
## fd.close()
fd = open('C:\Users\Tommy Carstensen\pdb\%s.pdb' %(pdb),'r')
lines = fd.readlines()
fd.close()
d_header = parse_pdb.parse_header(lines)
d_coordinates, d_ATOMseq = parse_pdb.parse_coordinates(lines,d_header,)
l_coordinates = []
a = d_header['CRYST1']['edges'][0]
b = d_header['CRYST1']['edges'][1]
c = d_header['CRYST1']['edges'][2]
alpha = math.pi*d_header['CRYST1']['angles'][0]/180.
beta = math.pi*d_header['CRYST1']['angles'][1]/180.
gamma = math.pi*d_header['CRYST1']['angles'][2]/180.
## unit cell voumne
volume = a*b*c*math.sqrt(1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2+2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma)))
matrix_fractional2cartesian = numpy.array([
[a, b*math.cos(gamma), c*math.cos(beta),],
[0, b*math.sin(gamma), c*(math.cos(alpha)-math.cos(beta)*math.cos(gamma))/math.sin(gamma),],
[0,0,volume/(a*b*math.sin(gamma)),],
])
## lines = []
for symop in d_header['REMARK290'].keys():
print 'symop', symop
matrix_symop = d_header['REMARK290'][symop]['matrix']
vector_symop = d_header['REMARK290'][symop]['vector']
for i_translation in range(len(l_translations)):
print 'symop', symop, 'translation', i_translation
vector_translation = l_translations[i_translation]
for chain2 in d_coordinates['chains'].keys():
for res_no2 in d_coordinates['chains'][chain2]['residues'].keys():
## print symop, i, chain2, res_no2
for iCode2 in d_coordinates['chains'][chain2]['residues'][res_no2]['d_iCodes'].keys():
for chain1 in d_coordinates['chains'].keys():
for res_no1 in d_coordinates['chains'][chain1]['residues'].keys():
## if res_no2 != 75:
## continue
for iCode1 in d_coordinates['chains'][chain1]['residues'][res_no1]['d_iCodes'].keys():
for atom_name1 in d_coordinates['chains'][chain1]['residues'][res_no1]['d_iCodes'][iCode1]['atoms'].keys():
coordinate1 = d_coordinates['chains'][chain1]['residues'][res_no1]['d_iCodes'][iCode1]['atoms'][atom_name1]['coordinate']
for atom_name2 in d_coordinates['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'].keys():
coordinate2 = d_coordinates['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'][atom_name2]['coordinate']
coordinate2 = numpy.dot(matrix_symop,coordinate2)+vector_symop
coordinate2 += numpy.dot(matrix_fractional2cartesian,vector_translation)
coordinate2[0] = round(coordinate2[0],3)
coordinate2[1] = round(coordinate2[1],3)
coordinate2[2] = round(coordinate2[2],3)
vicinity = False
distant = False
dist = math.sqrt(sum((coordinate2-coordinate1)**2))
dist = 0
## if dist < 5:
## print '%2i %.2f %.2f %4i %4s %s %4i %4s %s ' %(
## i, round(dist,2), dist_treshold,
## res_no2, atom_name2, coordinate2, res_no1, atom_name1, coordinate1
## )
dist_treshold = d_radii_vdw[atom_name1[0]]+d_radii_vdw[atom_name2[0]]+0.25
## break atom_name2 loop
if dist < dist_treshold:
vicinity = True
break
## break atom_name2 loop
if dist > 10.: ## length of lysine is 7-8Angstrom
distant = True
break
## break atom_name1 loop (append line and check next iCode1)
if vicinity == True:
for atom_name3 in d_coordinates['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'].keys():
coordinate3 = d_coordinates['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2]['atoms'][atom_name3]['coordinate']
coordinate3 = numpy.dot(matrix_symop,coordinate3,)+vector_symop
coordinate3 += numpy.dot(matrix_fractional2cartesian,vector_translation,)
line = build_line(
atom_name3,d_coordinates,coordinate3,
chain2,res_no2,iCode2,
symop, i_translation,
)
lines += [line]
break
## break atom_name1 loop (check next iCode1)
if distant == True:
break
## break iCode1 loop (check next iCode2)
if vicinity == True:
break
## break resno1 loop (check next iCode2)
if vicinity == True:
break
## break chain1 loop (check next iCode2)
if vicinity == True:
break
fd = open('%s_crystalcontacts.pdb' %(pdb),'w')
fd.writelines(lines)
fd.close()
source = 'whatif.src'
fd = open(source,'w')
fd.writelines([
'/software/whatif/DO_WHATIF.COM <<EOF\n',
'GETMOL %s.pdb\n' %(pdb,),
'%s\n' %(pdb,),
'%DELWAT\n',
'%DELLIG\n',
'%SOUSHL\n', ## crystal contacts
'%MAKMOL\n',
'\n', ## The file header will be copied from a PDB file. Hit return for the default header that has no information in it.
'soushl_%s.pdb\n' %(pdb),
'TOT 0\n',
'\n', ## REMARKS
'STOP\n',
'Y\n',
])
fd.close()
os.system('source %s > whatif_surface/%s.out' %(source, pdb))
os.system('rm DRG* DAVADRUG.PDB ALTERR.LOG PDBFILE whatif.src FOR*.DAT WHATIF.FIG')
return