IDATM provides a method for automatically typing atoms in a molecule based on geometric information. When run, it can apply atom types and, in combination with molefacture, properly add hydrogens when necessary. IDATM is based on the algorithm presented by Meng and Lewis (JCC 12(7):891-898), with a few minor modifications.
Usage
IDATM can be used directly from the command line, or accessed through the Molefacture GUI. To use IDATM from the command line, use the commands
package require IDATM
runtyping SELECTION
Where SELECTION is the selection to be typed. Proper atoms types will be applied, and proper bond orders set, for all atoms in SELECTION.
By default, IDATM uses the atom types listed below. The builtin type names can be overloaded with the command
read_idatm_types FILE
Here FILE contains a set of type definitions, one per line, where the first entry is the builtin IDATM name for a type, and the second entry is the new type name. For example, to type all IDATM C3 atoms as C.3 (useful, for example, for SYBYL-compatible mol2 files), one would use a file including the line
C3 C.3
A sample conversion file to map between IDATM types and SYBIL types is shown here.
Builtin atom types
The following atom type definitions are included in IDATM (mostly taken from Meng and Lewis, 1991):
C3 - sp3 carbon
C2 - sp2 carbon
C1 - sp carbon
Cac - carboxylate carbon
N3p - Quaternary amine nitrogen
N3 - Uncharged sp3 nitrogen
Npl - sp2 nitrogen
N1 - sp nitrogen
Nox - Nitrogen bound to oxygen
Ntr - NO2 nitrogen
Ngp - guanidinium nitrogen
O3 - sp3 oxygen
O2 - sp2 oxygen
Om - carboxylate or nitro oxygen
S3p - Positively charged sulfur
S3 - sp3 sulfur
S2 - sp2 sulfur
Sac - Sulfate sulfur
Sox - Sulfoxide sulfur
S - Generic sulfur
Bac - Borate boron
Box - Oxidized boron
B - Boron
Pac - Phosphate phosphorus
Pox - P-oxide phosphorus
P3p - Positively charged sp3 phosphorus
P - Other phosphorus
HC - Hydrogen bonded to carbon
H - Other hydrogen
DC - Deuterium bonded to carbon
D - Other deuterium