ShaEP

Change log

Improved robustness in creating field graph vertices for amide nitrogens.
Fix memory address based logic in field graph vertex coordinate calculation. This led to small non-deterministic variance in field graph vertex locations and therefore in ESP similarity index values.
Added guard against non-finite atomic coordinates, which could lead to infinite loop.

Report supported file formats and their attributes in help listing.
Added reading of predefined electrostatic potential (ESP) field graphs from input files.
The vertices of a field graph are encoded as helium atoms with isotope value 5. The electrostatic potential value [V] is stored as partial atomic charge. These special He⁵ atoms are omitted from steric (shape) terms. Instead of creating the field graph on-the-fly, ShaEP uses the predefined field graph in superimposition and similarity value calculations. This allows ShaEP to use ESP field graphs calculated with external software.
Added writing of field graphs to structure files. Option '--exportFieldgraphs' omits screening and only writes the query structures with their ESP field graphs as special He⁵ atoms into a structure file. That file can be subsequently used as input to screening as query or target. Use Mol2 or VBF file format that preserve the ESP potential values.

Added exclusion volume option '--exclusion' that takes a molecule structure file as a parameter. The atoms of the first structure in that file are used as repulsive Gaussian functions in the optimization of superimpositions. They do not affect similarity value calculations. The exclusion volume Gaussians are added to all query structures. This means all query structures and the exclusion volume atoms should be in the same coordinate space (frame of reference).

Changed the default value of parameter 'transformDistance' from 2.0 to 1.9. The old default value caused too aggressive pruning of the list of candidate transform used as initial overlays for optimization in some cases.

Fixed bug in parsing isotope (mass difference flag) in SDF file.
Update element symbols to include the new IUPAC approved names for elements 113, 115, 117, and 118.
Parse SDF files with truncated bond line (missing bond stereo flag and all remaining flags on the line).
Fixed a bug in calculating screw parameters from a dual quaternion.
Dropped support for 32-bit binaries, old Linux (kernel < 2.6.18), and FreeBSD. (Please let me know if you absolutely need a binary for those platforms.)

Improved detection of formal charges from MOL2 (and PDB and Gaussian log) files.

Changed parsing of bond stereo flags from SDF files to have effect only on the pointed atom of the wedge/hash bond. Previously a wedge/hash bond was considered to affect both atoms of the bond, but that was against the common "tip only" practise of parsing SDF.
Added output of hash/wedge bond flags for tetrahedral chiral atoms in SDF format.

Added support for radicals.
Added option '--outputAllOverlays', which will write each input conformation superimposed with each query structure into a separate output file in SDF file format.

Fixed a bug in parsing continued lines in V3000 molfiles (SDF)
Minor improvements in parsing MOL2 file format - now isotope information is parsed from UNITY atom attribute record.

Added command-line option 'noconfs', which causes all input structures to be considered as separate molecules. The default is to detect (based on molecule names) whether successive structures are conformers of the same molecule.
Revised graph matching algorithm.

Recompiled targeting Mac OS X 10.5. The previous version did not run on OS X 10.5 as intended.

Atoms within a molecule are now written into output file in the same order as they are in the input file in SDF and MOL2 formats.
As a result of code refactorization, removed "substructure" handling from MOL2 file format.

Added command-line option 'nStructures', which controls the output of alternative superimpositions per molecule.

Added command-line option 'noOptimization', which skips the optimization of superimposition and computes the similarity index for the structures in the input orientation. This can be used for rescoring docking poses, for example.
Added support for Visipoint Binary File (VBF) input file format, which can store partial atomic charges (and other meta-data), but is more compact than MOL2 format. Balloon can write conformers in VBF format. Please contact us if you are interested in the details of VBF.
Code clean-up, small performance fixes.

Fixed a bug that may have caused errors in the shape-based similarity index value. According to our tests the effect was minor, in the second or third decimal place.
Fixed a bug in writing stereo parity flag values in sdf V3000.
Removed unnecessary linefeeds from the file output.

First release.