add threeLetter SEQRES

[jamesmkrieger]

fixes #1949

So far this works for pdb headers and atomic object only. I'm still working on the cif header part

What we can do so far is the following:

In [1]: from prody import *

In [2]: polys = parsePDBHeader('1bkv', 'polymers', threeLetter=True)
@> PDB file is found in working directory (1bkv.pdb).

In [3]: for prot in polys:
   ...:     SEQRES=prot.sequence
   ...:     print (SEQRES)
   ...: 
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY

In [4]: ag = parsePDB('1bkv', compressed=False)
@> PDB file is found in working directory (1bkv.pdb).
@> 692 atoms and 1 coordinate set(s) were parsed in 0.01s.

In [5]: for chain in ag.iterChains():
   ...:     print(chain.getSequence(threeLetter=True))
   ...: 
GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY
PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY
PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY

In [6]: ag.ca.getSequence(threeLetter=True)
Out[6]: 'GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY'

[jamesmkrieger]

ok, now the CIF version is working too:

In [1]: from prody import *

In [2]: polys = parseCIFHeader('1bkv', 'polymers', threeLetter=True)
@> CIF file is found in working directory (1bkv.cif).

In [3]: for prot in polys:
   ...:     SEQRES=prot.sequence
   ...:     print (SEQRES)
   ...: 
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY

[jamesmkrieger]

This now works with chain getSequence with allres=True too:

In [1]: from prody import *

In [2]: ag = parsePDB('1bkv', compressed=False)
@> PDB file is found in working directory (1bkv.pdb).
@> 692 atoms and 1 coordinate set(s) were parsed in 0.01s.

In [3]: for chain in ag.iterChains():
   ...:     print(chain.getSequence(threeLetter=True, allres=True))
   ...: 
HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY ACY ACY ACY ACY HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY ACY HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH

[karolamik13]

Works fine. Check.

In [1]: from prody import *

In [2]: ag = parsePDB('1bkv', compressed=False)
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 1bkv downloaded (1bkv.pdb)
@> PDB download via FTP completed (1 downloaded, 0 failed).
@> 692 atoms and 1 coordinate set(s) were parsed in 0.02s.

In [3]: for chain in ag.iterChains():
...: print(chain.getSequence(threeLetter=True, allres=True))
...:
HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY ACY ACY ACY ACY HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY ACY HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH

In [4]: for chain in ag.iterChains():
...: print(chain.getSequence(threeLetter=True))
...:
GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY
PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY
PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY

In [5]: polys = parseCIFHeader('1bkv', 'polymers', threeLetter=True)
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 1bkv downloaded (1bkv.cif)
@> PDB download via FTP completed (1 downloaded, 0 failed).

In [6]: for prot in polys:
...: ...: SEQRES=prot.sequence
...: ...: print (SEQRES)
...:
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY
PRO HYP GLY PRO HYP GLY PRO HYP GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY

In [7]: ag.ca.getSequence(threeLetter=True)
Out[7]: 'GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY PRO GLY ILE THR GLY ALA ARG GLY LEU ALA GLY PRO GLY PRO GLY PRO GLY PRO GLY'

[jamesmkrieger]

Actually, I should probably call it something different and I think I still need to add it to docs and make some tests

It should hopefully work for 4 letter resnames like TIP3 or HISE if we parse them like that, but I need to check

[jamesmkrieger]

ok, this doesn't completely work for 4 characters like HISE, because they don't get selected in chain.calpha

[jamesmkrieger]

ok, this doesn't completely work for 4 characters like HISE, because they don't get selected in chain.calpha

now it works after adding HISE and various others from the InSty list to NONSTANDARD in atomic.flags

In [2]: ag = parsePDB('nvt1_nojump_end.pdb', long_resname=True)

In [3]: ag.getSequence(longSeq=True)[1152:1165]
Out[3]: 'GLU GLU HISE '

In [4]: ag.ca.getSequence(longSeq=True)[60:80]
Out[4]: 'THR VAL GLN GLU HISE'

In [5]: chain = ag['A']

In [6]: chain.getSequence(longSeq=True)[60:80]
Out[6]: 'THR VAL GLN GLU HISE'