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CONICA: Largest enclosed cone calculation.
Reference:
Petitjean M.,
A fast algorithm to compute conical pockets in proteins.
Application to the structural characterization of $\gamma$-carbonic anhydrases.
Mol. Inf., 2017, 36 (in press). (DOI 10.1002/minf.201600155)
Mailto: petitjean.chiral@gmail.com
CONICA computes the largest cone of fixed apex enclosed in a set of N atoms
(e.g. inside a protein).
Input data and parameters:
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INPUT FORMAT:
BIO : Biosym (MSI) files
CAS : Reserved for internal purposes
HIN : Hyperchem-type files
ISU : Reserved for internal purposes
MDL : Cambridge Crystallographic Model files
ML2 : SYBYL Mol2 files
PDB : Protein Data Bank or Nucleic Acid Data Bank files
(only HEADER, ATOM, ENDMDL and END records are recognized)
SDF : Symyx Mol/SDF files
(data between 'M END' and '$$$$' are treated as comments)
XYZ : n+2 lines. Line 1: n; line 2: free comment,
Next n lines: label or atomic symbol, x, y, z
(separator: spaces; no tabulation allowed).
INPUT MOLEC FILE NAME: name of the input file containing the set of atoms
(protein or molecule).
Several sets can be concatenated in the file.
EPSTAB:
Generates randomly perturbated cartesian coordinates.
The coordinates are not modified when EPSTAB is negative or null.
Independant random 3-tuples (x,y,z) are added to the spatial atomic positions.
Each random 3-tuple follow an isotropic normal law of std.dev equal to EPSTAB.
with radius equal to EPSTAB and centered on the atomic position.
When needed, most of the time, EPSTAB=1.D-7 is effective.
DELTA:
See below.
APEX:
If a single integer is entered, it is read as the sequential number (from 1 to N)
of the atom set as the apex of the cone.
If three reals are entered, they are read as the x,y,z coordinates of the apex.
If the distance between (x,y,z) and an atom in the set is smaller than DELTA,
the apex is set to this atom.
Output results:
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The axis and the angle of the cone.
The three atoms at the surface of the cone (apex not included).
The location of the point where the axis intersects the convex hull of the N points
(the triangular face of the convex hull where this intersection occurs is output).
The height of the cone: distance from the apex to the the point above.
Remarks:
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The number of atoms is currently limited to 150000 for each set of atoms.
The source has to be recompiled to read larger atomic sets.
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