read in mol2 file

[Sirilou]

I'm trying to use the bio3d package to read in my .mol2 file. I have it stored on the desktop so I tried

mol <- read.mol2(C:/Users/Siri/Desktop/6T0C/test.mol2)

but no mol2 file is found. The example from the help file

mol <- read.mol2(system.file("test", package="bio3d"))

works just fine. How can I read in my own mol2 file ?

[nirgrahamuk]

you want to pass a string to read.mol2 , so that would require some quote marks, whether single or double.

mol <- read.mol2("C:/Users/Siri/Desktop/6T0C/test.mol2")

[Sirilou]

That's right! I still get the error "error in mol.info[,3]: subscribt out of bounds.

my mol2 file is quite large (when I read it in with read_csv I get almost 100'000 obersvations of 1 variable). Could this maybe cause problems?

[Charli]

@Sirilou

'm trying to use the bio3d package to read in my .mol2 file. I have it stored on the desktop so I tried

mol <- read.mol2(C:/Users/Siri/Desktop/6T0C/test.mol2)

but no mol2 file is found. The example from the help file

mol <- read.mol2(system.file("test", package="bio3d"))

works just fine. How can I read in my own mol2 file ?

If there are no errors, your file has been imported. To read it, you have to use

view ("mol2")

[AlexisW]

Could you share the first few lines of your mol2 file? They should look like that (from the aspirin example):

@<TRIPOS>MOLECULE
ZINC00000053
   20    20     0     0     0

If I understand the error message correctly, one of the molecules in your file looks like that:

@<TRIPOS>MOLECULE
ZINC00000053
   20    20 

so the third field (substructure) is missing. If that is indeed the case, I suspect you have not installed the latest version of bio3d, which automatically fills in the missing fields. The one on CRAN should do it, try running update.packages("bio3d").

@Sirilou

my mol2 file is quite large (when I read it in with read_csv I get almost 100'000 obersvations of 1 variable). Could this maybe cause problems?

You could try with the option maxlines if this worries you. Check your file first to avoid cutting in the middle of a molecule.