404 lines
11 KiB
Python
Executable File
404 lines
11 KiB
Python
Executable File
#!/usr/bin/python
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import sys, Source.calculations
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from Source.vector_algebra import *
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all_sybyl_types = [
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'C.3', # carbon sp3
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'H', # hydrogen
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'C.2', # carbon sp2
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'H.spc', # hydrogen in Single Point Charge (SPC) water model
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'C.1', # carbon sp
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'H.t3p', # hydrogen in Transferable intermolecular Potential (TIP3P) water model
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'C.ar', # carbon aromatic
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'LP', # lone pair
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'C.cat', # carbocation (C+) used only in a guadinium group
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'Du', # dummy atom
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'N.3', # nitrogen sp3
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'Du.C', # dummy carbon
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'N.2', # nitrogen sp2
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'Any', # any atom
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'N.1', # nitrogen sp
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'Hal', # halogen
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'N.ar', # nitrogen aromatic
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'Het', # heteroatom = N, O, S, P
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'N.am', # nitrogen amide
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'Hev', # heavy atom (non hydrogen)
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'N.pl3', # nitrogen trigonal planar
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'Li', # lithium
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'N.4', # nitrogen sp3 positively charged
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'Na', # sodium
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'O.3', # oxygen sp3
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'Mg', # magnesium
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'O.2', # oxygen sp2
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'Al', # aluminum
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'O.co2', # oxygen in carboxylate and phosphate groups
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'Si', # silicon
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'O.spc', # oxygen in Single Point Charge (SPC) water model
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'K', # potassium
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'O.t3p', # oxygen in Transferable Intermolecular Potential (TIP3P) water model
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'Ca', # calcium
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'S.3', # sulfur sp3
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'Cr.th', # chromium (tetrahedral)
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'S.2', # sulfur sp2
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'Cr.oh', # chromium (octahedral)
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'S.O', # sulfoxide sulfur
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'Mn', # manganese
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'S.O2', # sulfone sulfur
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'Fe', # iron
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'P.3', # phosphorous sp3
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'Co.oh', # cobalt (octahedral)
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'F', # fluorine
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'Cu', # copper
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'Cl', # chlorine
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'Zn', # zinc
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'Br', # bromine
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'Se', # selenium
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'I', # iodine
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'Mo', # molybdenum
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'Sn'] # tin
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#propka_input_types = ['1P','1N','2P','2N']
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#for type in all_sybyl_types:
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# temp = type.replace('.','')
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# if len(temp)>3:
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# temp = temp[0:3]
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# propka_input_types.append(temp)
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#
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#for t in propka_input_types:
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# print (t)
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propka_input_types = [
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'1P',
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'1N',
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'2P',
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'2N',
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'C3',
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'H',
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'C2',
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'Hsp',
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'C1',
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'Ht3',
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'Car',
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'LP',
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'Cca',
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'Du',
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'N3',
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'DuC',
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'N2',
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'Any',
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'N1',
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'Hal',
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'Nar',
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'Het',
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'Nam',
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'Hev',
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'Npl',
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'Li',
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'N4',
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'Na',
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'O3',
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'Mg',
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'O2',
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'Al',
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'Oco',
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'Si',
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'Osp',
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'K',
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'Ot3',
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'Ca',
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'S3',
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'Crt',
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'S2',
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'Cro',
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'SO',
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'Mn',
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'SO2',
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'Fe',
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'P3',
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'Coo',
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'F',
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'Cu',
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'Cl',
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'Zn',
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'Br',
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'Se',
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'I',
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'Mo',
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'Sn']
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max_C_double_bond = 1.3
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max_C_triple_bond = 1.2
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max_C_double_bond_squared = max_C_double_bond*max_C_double_bond
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max_C_triple_bond_squared = max_C_triple_bond*max_C_triple_bond
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def assign_sybyl_type(atom):
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# check if we already have assigned a name to this atom
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if atom.sybyl_assigned:
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#print(atom.name,'already assigned')
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return
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# find some properties of the atom
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ring_atoms = is_ring_member(atom)
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aromatic = is_aromatic_ring(ring_atoms)
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planar = is_planar(atom)
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bonded_elements = {}
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for i in range(len(atom.bonded_atoms)):
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bonded_elements[i]=atom.bonded_atoms[i].element
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# Aromatic carbon/nitrogen
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if aromatic:
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for ra in ring_atoms:
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if ra.element in ['C','N']:
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set_type(ra, ra.element+'.ar')
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return
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# check for amide
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if atom.element in ['O','N','C']:
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O=None
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N=None
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C=None
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# oxygen, nitrogen
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if atom.element in ['O','N']:
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for b in atom.get_bonded_elements('C'):
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for bb in b.bonded_atoms:
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if (bb.element =='N' and atom.element == 'O'):
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O=atom
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C=b
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N=bb
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elif (bb.element =='O' and atom.element == 'N'):
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N=atom
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C=b
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O=bb
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# carbon
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if atom.element == 'C':
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nitrogens = atom.get_bonded_elements('N')
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oxygens = atom.get_bonded_elements('O')
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if len(nitrogens)==1 and len(oxygens)==1:
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C = atom
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N = nitrogens[0]
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O = oxygens[0]
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if C and N and O:
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# make sure that the Nitrogen is not aromatic and that it has two heavy atom bonds
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if not is_aromatic_ring(is_ring_member(N)) and len(N.get_bonded_heavy_atoms())==2:
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set_type(N,'N.am')
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set_type(C,'C.2')
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set_type(O,'O.2')
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return
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if atom.element=='C':
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# check for carboxyl
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if len(atom.bonded_atoms)==3 and list(bonded_elements.values()).count('O')==2:
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i1 = list(bonded_elements.values()).index('O')
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i2 = list(bonded_elements.values()).index('O',i1+1)
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if len(atom.bonded_atoms[i1].bonded_atoms)==1 and len(atom.bonded_atoms[i2].bonded_atoms)==1:
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set_type(atom.bonded_atoms[i1],'O.co2-')
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set_type(atom.bonded_atoms[i2],'O.co2')
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set_type(atom,'C.2')
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return
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# sp carbon
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if len(atom.bonded_atoms)<=2:
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for b in atom.bonded_atoms:
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if Source.calculations.squared_distance(atom, b) < max_C_triple_bond_squared:
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set_type(atom,'C.1')
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set_type(b,b.element+'.1')
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if atom.sybyl_assigned:
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return
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# sp2 carbon
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if planar:
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set_type(atom,'C.2')
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# check for N.pl3
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for b in atom.bonded_atoms:
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if b.element=='N':
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if len(b.bonded_atoms)<3 or is_planar(b):
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set_type(b,'N.pl3')
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return
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# sp3 carbon
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set_type(atom, 'C.3')
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return
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# Nitrogen
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if atom.element == 'N':
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# check for planar N
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if len(atom.bonded_atoms)==1:
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if is_planar(atom.bonded_atoms[0]):
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set_type(atom,'N.pl3')
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return
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if planar:
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set_type(atom,'N.pl3')
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return
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set_type(atom,'N.3')
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return
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# Oxygen
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if atom.element == 'O':
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set_type(atom,'O.3')
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if len(atom.bonded_atoms) == 1:
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# check for carboxyl
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if atom.bonded_atoms[0].element == 'C':
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the_carbon = atom.bonded_atoms[0]
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if len(the_carbon.bonded_atoms)==3 and the_carbon.count_bonded_elements('O')==2:
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[O1,O2] = the_carbon.get_bonded_elements('O')
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if len(O1.bonded_atoms)==1 and len(O2.bonded_atoms)==1:
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set_type(O1,'O.co2-')
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set_type(O2,'O.co2')
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set_type(the_carbon,'C.2')
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return
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# check for X=O
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if Source.calculations.squared_distance(atom, atom.bonded_atoms[0]) < max_C_double_bond_squared:
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set_type(atom,'O.2')
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if atom.bonded_atoms[0].element=='C':
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set_type(atom.bonded_atoms[0],'C.2')
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return
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# Sulphur
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if atom.element == 'S':
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# check for SO2
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if list(bonded_elements.values()).count('O')==2:
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i1 = list(bonded_elements.values()).index('O')
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i2 = list(bonded_elements.values()).index('O',i1+1)
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set_type(atom.bonded_atoms[i1],'O.2')
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set_type(atom.bonded_atoms[i2],'O.2')
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set_type(atom,'S.o2')
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return
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# check for SO4
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if list(bonded_elements.values()).count('O')==4:
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no_O2 = 0
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for i in range(len(atom.bonded_atoms)):
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if len(atom.bonded_atoms[i].bonded_atoms)==1 and no_O2<2:
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set_type(atom.bonded_atoms[i],'O.2')
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no_O2+=1
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else:
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set_type(atom.bonded_atoms[i],'O.3')
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set_type(atom,'S.3')
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return
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# Phosphorus
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if atom.element == 'P':
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set_type(atom,'P.3')
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# check for phosphate group
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bonded_oxygens = atom.get_bonded_elements('O')
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for o in bonded_oxygens: set_type(o,'O.3')
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# if len(bonded_oxygens)>=3:
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# # find oxygens only bonded to current phosphorus
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# bonded_oxygens_1 = [o for o in bonded_oxygens if len(o.get_bonded_heavy_atoms())==1]
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# # find the closest oxygen ...
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# closest_oxygen = min(bonded_oxygens_1,
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# key= lambda o:Source.calculations.squared_distance(atom,o))
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# # ... and set it to O.2
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# set_type(closest_oxygen,'O.2')
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return
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element = atom.element.capitalize()
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set_type(atom,element)
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# print('Using element as type for %s'%atom.element)
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return
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def is_ring_member(atom):
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return identify_ring(atom,atom,0,[])
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def identify_ring(this_atom, original_atom, number, past_atoms):
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number+=1
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past_atoms=past_atoms+[this_atom]
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return_atoms = []
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if number > 10:
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return return_atoms
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for atom in this_atom.get_bonded_heavy_atoms():
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if atom == original_atom and number>2:
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return past_atoms
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if atom not in past_atoms:
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these_return_atoms = identify_ring(atom, original_atom, number, past_atoms)
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if len(these_return_atoms) > 0:
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if len(return_atoms)>len(these_return_atoms) or len(return_atoms)==0:
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return_atoms = these_return_atoms
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return return_atoms
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def set_type(atom,type):
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#print(atom, '->',type)
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atom.sybyl_type = type
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atom.sybyl_assigned=True
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return
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def is_planar(atom):
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""" Finds out if atom forms a plane together with its bonded atoms"""
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atoms = [atom]+atom.bonded_atoms
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return are_atoms_planar(atoms)
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def are_atoms_planar(atoms):
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if len(atoms)==0:
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return False
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if len(atoms)<4:
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return False
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v1 = vector(atom1=atoms[0], atom2=atoms[1])
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v2 = vector(atom1=atoms[0], atom2=atoms[2])
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n = (v1**v2).rescale(1.0)
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margin = 0.20
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for b in atoms[3:]:
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v = vector(atom1=atoms[0], atom2=b).rescale(1.0)
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#print(atoms[0],abs(v*n) )
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if abs(v*n)>margin:
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return False
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return True
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def is_aromatic_ring(atoms):
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if len(atoms)<5:
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return False
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for i in range(len(atoms)):
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if not are_atoms_planar(atoms[i:]+atoms[:i]):
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return False
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return True
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