HIPPOS Configuration Options¶
There are two kinds of options, essential and optional. When nothing declared it means the option is essential. Some options have default value. Also keep in mind that all file names must never use space! So use underscore instead.
You can also inserting comments at the beginning of the line or after the option-value pair by inserting the #
sign before the comment. Everything inserted after the #
sign will be ignored by the software.
Basic Options¶
- docking_method
value:
vina
orplants
- docking_conf
value:
docking_configuration_file_name
, eg.vina.conf
orplants.conf
- direct_ifp
value:
true
orfalse
, (default:false
)If the value is set to true, it will use Direct IFP method and thus
docking_method
anddocking_conf
will be ignored.
Input Options¶
- residue_name
value:
list of residue_name
, eg.ASP107 SER111 THR112
The list of residue_name, each residue separated by space. It is used in PLANTS post-analysis but not in VINA analysis as pdbqt don’t hold the residue_name-residue_number pair field. However it is highly recommended to define it in VINA post analysis as it will be included in output file, making the results easier to interpret.
- residue_number
value:
list of residue_number
, eg.80 84 85
The list of residue number, each number separated by space. Essential option in VINA post-analysis but optional in PLANTS post-analysis.
- similarity_coef (optional)
value:
list of similarity_coef
, eg.tanimoto
ormcconnaughey
ortanimoto mcconnaughey
If the value is set then full_ref or full_nobb_ref or simplified_ref (depends on output_mode used) must be provided, so interaction fingerprint can be compared against reference.
- full_ref
value:
bitstring1 bitstring2 ... n
At least 1 uniform bitstring must be provided
- full_nobb_ref
value:
bitstring1 bitstring2 ... n
At least 1 uniform bitstring must be provided
- simplified_ref
value:
bitstring1 bitstring2 ... n
At least 1 simplified bitstring must be provided
- protein
value:
protein file name
, eg.protein.pdb
The protein file name that will be used in Direct IFP mode. Format allowed:
pdb
,mol2
,pdbqt
.
- ligand_files
value:
list of ligand name
, eg.3BO.pdb 3BR.pdb 3BS.pdb
The list of ligand name that will be paired with the protein in Direct IFP mode.
- ligand_list
value:
a file containing ligand file names
, eg.ligand_list.txt
The name of the file that contain ligand file names.
- multiple_ligand_list
value:
list of file containing ligand file names
, eg.ligand_list1.txt ligand_list2.txt ligand_list3.txt
The list of file that contain ligand file names.
- complex_list
value:
a filename containing list protein-ligand pair
, eg.complex_list.txt
In Direct IFP mode, if this value is set then
protein
,ligand_list
, andmultiple_ligand_list
will not be required.
Output Options¶
- full_outfile (optional)
value:
full_output_file_name
, default:full_ifp.csv
Only used by
full
output_mode. It is recommended to use the csv extensions for clarity.
- full_nobb_outfile (optional)
value:
full_output_file_name
, default:full_nobb_ifp.csv
Only used by
full_nobb
output_mode. It is recommended to use the csv extensions for clarity.
- simplified_outfile (optional)
value:
simplified_output_file_name
, default:simplified_ifp.csv
Only used by
simplified
output_mode. It is recommended to use the csv extensions for clarity.
- sim_outfile (optional)
value:
similarity_output_file_name
, default:similarity.csv
Only used when the similarity coefficient is calculated.
- logfile (optional)
value:
log_file_name
, default:hippos.log
Advanced Options¶
- output_mode (optional)
value:
list of output_mode
, default:full
, options:full
,full_nobb
, andsimplified
The list of output_mode, at least one value required. When multiple value provided each value must be separated by space. Multiple value can only be used in HIPPOS without reference. When nothing provided output_mode full will be used.
- docking_score (optional)
value:
yes
orno
, default:yes
Extract the docking score of ligand poses from docking results and attach them to output file.
- omit_interaction (optional)
value:
interaction_type
andresidue_name
where
interaction_type
is one of the following value:hydrophobic
orHPB
aromatic
orARM
h_bond
orHBD
electrostatic
orELE
h_bond_donor
orHBD_DON
h_bond_acceptor
orHBD_ACC
electrostatic_positive
orELE_POS
electrostatic_negative
orELE_NEG
aromatic_facetoface
orARM_F2F
aromatic_edgetoface
orARM_E2F
While
residue_name
specify which residue will be omitted. Usage example:omit_interaction hydrophobic ARG223