read.mol2(file, maxlines = -1L)"print"(x, ...)
read.mol2. Read a Tripos MOL2 file
Basic functionality to parse a MOL2 file. The current version reads
and stores ‘@
In the case of a multi-molecule MOL2 file, each molecule will be stored
as an individual ‘mol2’ object in a list. Conversely, if the multi-molecule
MOL2 file contains identical molecules in different conformations
(typically from a docking run), then the output will be one object
with an atom and xyz component (xyz in
matrix representation; row-wise coordinates).
See examples for further details.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
For atom list components the column names can be
used as a convenient means of data access, namely:
Atom serial number “eleno”,
Atom name “elena”,
Orthogonal coordinates “x”,
Orthogonal coordinates “y”,
Orthogonal coordinates “z”,
Reisude number “resno”,
Atom type “elety”,
Residue name “resid”,
Atom charge “charge”,
Status bit “statbit”,
For bond list components the column names are:
Bond identifier “id”,
number of the atom at one end of the bond“origin”,
number of the atom at the other end of the bond “target”,
the SYBYL bond type “type”.
For substructure list components the column names are:
substructure identifier “id”,
substructure name “name”,
the ID number of the substructure's root atom “root_atom”,
the substructure type “subst_type”,
the type of dictionary associated with the substructure “dict_type”,
the chain to which the substructre belongs “chain”,
the subtype of the chain “sub_type”,
the number of inter bonds “inter_bonds”,
status bit “status”.
See examples for further details.
cat("\n")## Read a single entry MOL2 file ## (returns a single object) mol <- read.mol2( system.file("examples/aspirin.mol2", package="bio3d") ) ## Short summary of the molecule print(mol)... Name: ZINC00000053 ... 20 atoms in molecule ... 20 bonds in molecule ... 1 frame(s) stored + attr: atom, bond, substructure, xyz, info, name## ATOM records mol$atomeleno elena x y z elety resno resid charge statbit 1 1 C1 -1.4238 1.4221 1.2577 C.3 1 <0> -0.1370 <NA> 2 2 C2 -1.3441 -0.0813 1.1904 C.2 1 <0> 0.4790 <NA> 3 3 O1 -1.4532 -0.7378 2.1988 O.2 1 <0> -0.5137 <NA> 4 4 O2 -1.1519 -0.6914 0.0093 O.3 1 <0> -0.2785 <NA> 5 5 C3 -0.9822 -2.0375 0.0080 C.ar 1 <0> 0.1140 <NA> 6 6 C4 0.2935 -2.5790 0.0577 C.ar 1 <0> -0.1438 <NA> 7 7 C5 0.4647 -3.9491 0.0557 C.ar 1 <0> -0.1168 <NA> 8 8 C6 -0.6330 -4.7933 0.0047 C.ar 1 <0> -0.1375 <NA> 9 9 C7 -1.9078 -4.2739 -0.0447 C.ar 1 <0> -0.0755 <NA> 10 10 C8 -2.0966 -2.8882 -0.0379 C.ar 1 <0> -0.1363 <NA> 11 11 C9 -3.4564 -2.3257 -0.0844 C.2 1 <0> 0.5228 <NA> 12 12 O3 -4.4256 -3.0711 -0.1243 O.co2 1 <0> -0.6853 <NA> 13 13 O4 -3.6170 -1.1130 -0.0830 O.co2 1 <0> -0.6764 <NA> 14 14 H1 -1.5815 1.7317 2.2908 H 1 <0> 0.0951 <NA> 15 15 H2 -0.4932 1.8522 0.8875 H 1 <0> 0.0914 <NA> 16 16 H3 -2.2544 1.7698 0.6434 H 1 <0> 0.1039 <NA> 17 17 H4 1.1543 -1.9280 0.0976 H 1 <0> 0.1207 <NA> 18 18 H5 1.4605 -4.3654 0.0938 H 1 <0> 0.1210 <NA> 19 19 H6 -0.4882 -5.8635 0.0032 H 1 <0> 0.1200 <NA> 20 20 H7 -2.7604 -4.9357 -0.0844 H 1 <0> 0.1328 <NA>## BOND records mol$bondid origin target type statbit 1 1 1 2 1 <NA> 2 2 1 14 1 <NA> 3 3 1 15 1 <NA> 4 4 1 16 1 <NA> 5 5 2 3 2 <NA> 6 6 2 4 1 <NA> 7 7 4 5 1 <NA> 8 8 5 10 ar <NA> 9 9 5 6 ar <NA> 10 10 6 7 ar <NA> 11 11 6 17 1 <NA> 12 12 7 8 ar <NA> 13 13 7 18 1 <NA> 14 14 8 9 ar <NA> 15 15 8 19 1 <NA> 16 16 9 10 ar <NA> 17 17 9 20 1 <NA> 18 18 10 11 1 <NA> 19 19 11 12 2 <NA> 20 20 11 13 1 <NA>## Print some coordinate data head(mol$atom[, c("x","y","z")])x y z 1 -1.4238 1.4221 1.2577 2 -1.3441 -0.0813 1.1904 3 -1.4532 -0.7378 2.1988 4 -1.1519 -0.6914 0.0093 5 -0.9822 -2.0375 0.0080 6 0.2935 -2.5790 0.0577## Or coordinates as a numeric vector #head(mol$xyz) ## Print atom charges head(mol$atom[, "charge"])[1] -0.1370 0.4790 -0.5137 -0.2785 0.1140 -0.1438## Convert to PDB pdb <- as.pdb(mol)Summary of PDB generation: .. number of atoms in PDB determined by 'xyz' .. 0 atom(s) from 'string' selection .. 0 atom(s) in final combined selection .. number of atoms in PDB: 20 .. number of calphas in PDB: 0 .. number of residues in PDB: 1## Read a multi-molecule MOL2 file ## (returns a list of objects) #multi.mol <- read.mol2("zinc.mol2") ## Number of molecules described in file #length(multi.mol) ## Access ATOM records for the first molecule #multi.mol[[1]]$atom ## Or coordinates for the second molecule #multi.mol[[2]]$xyz ## Process output from docking (e.g. DOCK) ## (typically one molecule with many conformations) ## (returns one object, but xyz in matrix format) #dock <- read.mol2("dock.mol2") ## Reference PDB file (e.g. X-ray structure) #pdb <- read.pdb("dock_ref.pdb") ## Calculate RMSD of docking modes #sele <- atom.select(dock, "noh") #rmsd(pdb$xyz, dock$xyz, b.inds=sele$xyz)