Commit bcb91326 authored by jdurrant's avatar jdurrant
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Moved COMMAND_LINE_USE.md

parent e3f65fbb
......@@ -19,7 +19,7 @@ The BINANA Git repository is hosted at
## Command-Line Use
See `./COMMAND_LINE_USE.md` in the Git repository for detailed instructions.
See `./python/COMMAND_LINE_USE.md` in the Git repository for detailed instructions.
Here is a simple example:
```bash
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......@@ -197,10 +197,10 @@ are implemented in order to accommodate low-resolution crystal structures. A
hydrogen bond is identified if the hydrogen-bond donor comes within
`hydrogen_bond_dist_cutoff` angstroms of the hydrogen-bond acceptor, and the
angle formed between the donor, the hydrogen atom, and the acceptor is no
greater than `hydrogen_halogen_bond_angle_cutoff` degrees. BINANA tallies the number of
hydrogen bonds according to the secondary structure of the receptor atom, the
side-chain/backbone status of the receptor atom, and the location (ligand or
receptor) of the hydrogen bond donor. Thus there are twelve possible
greater than `hydrogen_halogen_bond_angle_cutoff` degrees. BINANA tallies the
number of hydrogen bonds according to the secondary structure of the receptor
atom, the side-chain/backbone status of the receptor atom, and the location
(ligand or receptor) of the hydrogen bond donor. Thus there are twelve possible
categorizations: alpha-sidechain-ligand, alpha-backbone-ligand, beta-sidechain-
ligand, beta-backbone-ligand, other-sidechain-ligand, other-backbone-ligand,
alpha-sidechain-receptor, alpha-backbone-receptor, beta-sidechain-receptor,
......@@ -318,6 +318,6 @@ aromatic ring or charged functional group: alpha helix, beta sheet, or other.
Ligand Atom Types and Rotatable Bonds
=====================================
BINANA also tallies the number of atoms of each AutoDock type present in the
BINANA also tallies the number of atoms of each AutoDock type present in the
ligand as well as the number of ligand rotatable bonds identified by the
AutoDockTools scripts used to generate the input PDBQT files.
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