Usage: APROPOS parameter_file
Each line in the parameter file has the form
parameter value_of_the_parameter
The following parameter are available:
OUTPUT (char [15]) name of the output file, should be set.
default: OUTPUT Output
PDBLISTE (char [15]) list of molecules.
default: PDBLISTE Pdbliste
ALPHA_COMPARE (float) alpha-shape for the describtion of the global form
of the molecule
default: ALPHA_COMPARE 20.0
ALPHA_1 (float), ALPHA_FAMILY (int), ALPHA_STEP (float) describe the family of
alpha-shapes which will be compared with the global form;
family is given by the shape with
alpha = ALPHA_1 - ALPHA_FAMILY*ALPHA_STEP,
alpha = ALPHA_1 - ALPHA_FAMILY*ALPHA_STEP + 1, ...,
alpha = ALPHA_1 + ALPHA_FAMILY*ALPHA_STEP
default: ALPHA_1 4.0, ALPHA_FAMILY 5, ALPHA_STEP 0.1
SELECT_MAX (float) determines the level for the selecting of the
deepest atoms (part 0 of the pockets)
atom deepness > SELECT_MAX*(maximal deepness of all surface
atoms),
default: SELECT_MAX 0.7
SELECT_MIN (float) determines level for selecting highest atoms
atom deepness < SELECT_MIN
With this parameter you can try to find something
like "hills" on the molecule surface.
It works only if SELECT_MAX is set to a value >= 1,
default: SELECT_MIN 0.5
CUT_OFF (float) cut_off for the clustering of the selected atoms
default: CUT_OFF 11.5
POCKET (int) determines of far APROPOS extends the initial set of
atoms (part 0 of the pocket)
default: POCKET 2
ALLCLUSTERS (int) switch for the form of the output of the
pockets
ALLCLUSTERS 1: output of all pockets,
ALLCLUSTERS 0: output of only those pockets with >=
(2*ALPHA_FAMILY+1)*(POCKET+1) atoms over all
default ALLCLUSTERS 1
ALLHETEROS (int) switch for the output of the hetero atoms
ALLHETEROS 1: output of all hetero atoms,
ALLHETEROS 0: output of only those hetero atoms with
more than 5 atoms,
default: ALLHETEROS 1
ATOMOUTPUT (int) switch for the form of the output of the atoms of the pockets
ATOMOUTPUT 1: output of the atoms forming the pocket
ATOMOUTPUT 0: output of only the aminoacids the atoms of the pocket
belonging to
default: ATOMOUTPUT 1
PARAMETER (int) switch for the output of the most important parameters.
PARAMETER 1: output of values for PDBLISTE, ALPHA_1,
ALPHA_FAMILY, SELECT_MAX, SELECT_MIN, CUT_OFF, POCKET,
PARAMETER 0: not parameter output
default:PARAMETER 1
ONLYCNN (int) switch for the generation of only a list of coordinates
ONLYCNN 1: only list of coordinates
ONLYCNN 0: normal work,
default: ONLYCNN 0
VERSION (int) determines which version of alpha-shapes APROPOS uses
VERSION < 3: unweighted alpha_shapes (dlecx is called detri),
VERSION >= 3: weighted alpha_shapes (taking into account the atoms radii),
default: VERSION 3
DELETE (int) determines which of the generated files should be removed
after calculation:
a=1/0: the list of coordinates yes/no
b=1/0: Delaunay triangulation and alpha-shape family yes/no
c=1/0: face lists (*.fl),
DELETE = 4*c + 2*b + a
default: DELETE 3 (delete list of coordinates, Delaunay triangulation
and alpha-shape family)
SURFACE (float) output of atoms belonging to specified alpha-shape
as PDB file in standard output
SURFACE 0.0: no output
default SURFACE 0.0
Format of the list of molecules
-------------------------------
The list of molecules has the form
path_to_the_molecule describtion_of_the_chains_to_read
First of all APROPOS never reads the atoms belonging to a hetero atoms
(indicated by HETATM in the PDB file) and APROPOS only reads the atoms
with the element types C,N,S,O,A,Q (never hydrogene atoms).
Then the describtion of the chains to read can be
emty, i.e. APROPOS reads all atoms or
or
consist of one ore more chain idicators separated by commata.
Each chain indicator can be followed by
-NUMBER or +NUMBER.
If -NUMBER follows APROPOS reads all atoms of amino acid with a
number <= NUMBER, if +NUMBER follows APROPOS reads all atoms of amino acids
with number >= NUMBER. If only the chain indicator is written APROPOS
read all atoms of this chain.
Example:
/PDB/pdb1ace.ent read all atoms
/PDB/pdb7aat.ent A read only chain A
/PDB/pdb1lts.ent D,E,F,G,H read chains D,E,F,G and H
/PDB/pdb1mda.ent H+25,L,A read from chain H atoms with
amino acid number >= 25 and
all atoms from chains L and A
/PDB/pdb1ncc.ent L-107,H-112,N read from chain L all amino acids
with number <= 107, from chain H
all amino acid with number <= 112
and all atoms of chain N.
Dr. Klaus Peters, April 1996