Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
YingyingJin`ProteinLigandInteractionAnalysis`
ParsePDBAtoms  |
|
| | ||||
Details and Options
Examples
(1)
Basic Examples
(1)
In[1]:=
examplePDB="/tmp/example.pdb";Export[examplePDB,{"ATOM 1 N VAL A 1 10.111 11.222 12.333 1.00 20.00 N","ATOM 2 CA VAL A 1 10.444 11.555 12.666 1.00 20.00 C","ATOM 3 C VAL A 1 10.777 11.888 12.999 1.00 20.00 C","HETATM 4001 C1 ZINC A 401 15.123 16.234 17.345 1.00 30.00 C","HETATM 4002 O1 ZINC A 401 15.456 16.567 17.678 1.00 30.00 O"},"Text"]
Out[1]=
/tmp/example.pdb
In[2]:=
Import[examplePDB,"Text"]//Print
ATOM 1 N VAL A 1 10.111 11.222 12.333 1.00 20.00 NATOM 2 CA VAL A 1 10.444 11.555 12.666 1.00 20.00 CATOM 3 C VAL A 1 10.777 11.888 12.999 1.00 20.00 CHETATM 4001 C1 ZINC A 401 15.123 16.234 17.345 1.00 30.00 CHETATM 4002 O1 ZINC A 401 15.456 16.567 17.678 1.00 30.00 O
In[3]:=
parsed=ParsePDBAtoms[examplePDB]
Out[3]=
{RecordNameATOM,AtomSerialNumber1,AtomNameN,ResidueNameVAL,ChainIDA,ResidueSequenceNumber1,AtomCoordinates{10.111,11.222,12.333},Occupancy1.,TempFactor20.,ElementN,Charge,RecordNameATOM,AtomSerialNumber2,AtomNameCA,ResidueNameVAL,ChainIDA,ResidueSequenceNumber1,AtomCoordinates{10.444,11.555,12.666},Occupancy1.,TempFactor20.,ElementC,Charge,RecordNameATOM,AtomSerialNumber3,AtomNameC,ResidueNameVAL,ChainIDA,ResidueSequenceNumber1,AtomCoordinates{10.777,11.888,12.999},Occupancy1.,TempFactor20.,ElementC,Charge,RecordNameHETATM,AtomSerialNumber4001,AtomNameC1,ResidueNameZIN,ChainID,ResidueSequenceNumber40A,AtomCoordinates{15.12,48.69,69.36},Occupancy5.,TempFactor0.,Element,Charge,RecordNameHETATM,AtomSerialNumber4002,AtomNameO1,ResidueNameZIN,ChainID,ResidueSequenceNumber40A,AtomCoordinates{15.45,99.36,123.69},Occupancy8.,TempFactor0.,Element,Charge}
 |
|
""