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* StructChecker changes. Initial commit. First implementation. Added some tests. * StructChecker: add GoodAtoms and AcidicAtoms. new updates * StructChecker: add new tests * StructChecker: added TransformAugmentedAtoms() * StructCheck: add structCheck to GraphMol. Fix compilation errors. * StructChecker: add stereo verification and some utilities. * StructChecker: function FixDubious3DMolecule was added * StructChecker: checkStereo added. done with stereo. * StructChecker: add StripSmallFragments() * StructChecker: add AtomClash() function. Some cosmetic + tests * StructChecker: checkAtoms() was started * StructChecker: checkAtoms is ready * StructChecker: user RingInfo from RDkit. Start regarge * StructChecker: ReCharge molecule method prototype * StructChecker: updates for ReCharge. Almost finished * StructChecker: all ReCharge is done except external data tables loading * StructChecker: add path tables into API. ReCharge completed * Adds augmented atom data Signed-off-by: Brian Kelley <brian.kelley@novartis.com> * Removes extra files Signed-off-by: Brian Kelley <brian.kelley@novartis.com> * Adds path to test data via RDBASE environment Signed-off-by: Brian Kelley <brian.kelley@novartis.com> * Revert "Struct checker apr15" * StructChecker: add missing tautomer tests * Updates test to use RDBASE * Adds initialization of data from data section * Adds Python API and tests * Fixes namespace for enum * StructChecker: update/imporve strip small fragments * StructChecker: fix acidic atoms (but logic does not work) * StructChecker: fix match issue for CheckAtoms * Adds macro guards * Adds loading API and proper constructor * Fixes tests, adds stereo test * Fixes crash bug, matches[0] was being accessed from an empty match vector * Reverts crash fix - conflicts with previous * Adds the rest of the structure checker options * StructChecker: fix atom matching for aromatic rings * StructChecker: add tautomers checks. Update some tests * StructChecker: stereo fixes. Add some tests * StructChecker: fix check atoms. Start ligand symbol list * StructChecker: fix some check atoms validation. Add Tranform to query lists. Start correct loading augmented atoms * update * another set of fixes * StructChecker: fix loadDefaultAugmentedAtoms. Some changes in CheckAtom + tests + debug conditional breakpoints (TEMP operators) * StructChecker: rewrited RecMatch() to sequential. Changed bond matching algorithm. small bug fixes * Adds better logging of mismatched atoms * Removes duplicated negative charge * Fixes charges * Adds nitro group test * StructChecker: add better logging * remove double logging * Reformats code using RDKit's clang-format style * StructChecker: Fix charge reformat using RDKit format. * StructChecker: compilation restore after merge * restore bond matching * Removes the same fragments that strucheck does in case of ties * Don't resanitize - this adds aromaticity which mucks things up * Adds empty molecule checks * Fixes atom clashes. * Removes debug printing * Removes debug logging info * First pass at stereo fixes * Fixes off by one error for dubious stereo fix * Fixes more off by one errors * Fixes more off by one errors * More off by one fixes. * Another off by one * Fixes chiral flag set in molfile check * Copies chiral flag over to largest fragment if necessary * Poor man’s parity check. * Find unspecified chiral centers ala Avalon. * StructChecker: fix recursive match. Fix transformations * StructChecker: fix transformation for atom list (using query atoms) * Fixes checks && to & * StructChecker: fix carboxylic acids tranform issue. Atom list is changed only if different * StructChecker: documentation was updated * Fixes snprintf and silences some warnings * Adds Get/Set StructCheckerOptions * Adds default AugmentedAtomTransforms
206 lines
2.7 KiB
Plaintext
206 lines
2.7 KiB
Plaintext
# File: struchk.aci
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#
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# Purpose: Contains parameters used to estimate the next
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# position of a molecule to be available for
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# deprotonation. One application is fixing the
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# charges in structures preprocessed by STRUCHK.EXE
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#
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# The parameters are fitted to a set of reference
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# structures taken from the following sources:
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# March, Hollemann/Wiberg, Klumpp, CRC-Handbook
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#
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# augmented atoms considered acidic
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41
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"C"
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"C(-A)"
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"C(-A)(-A)"
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"C(=A)"
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"C(-A)(-A)(-A)"
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"C(=A)(-A)"
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"C(#A)"
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"N"
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"N(-A)"
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"N(=A)"
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"N(-A)(-A)"
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"N+1"
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"N+1(-A)"
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"N+1(-A)(-A)"
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"N+1(-A)(-A)(-A)"
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"N-1(-A)"
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"P"
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"P(-A)"
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"P(-A)(-A)"
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"P(=A)(-A)"
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"P+1"
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"P+1(-A)"
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"P+1(-A)(-A)"
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"O"
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"O(-A)"
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"O+1"
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"O+1(-A)"
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"O+1(-A)(-A)"
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"O+1(=A)"
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"S"
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"S+1"
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"S(-A)"
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"S+1(-A)"
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"Se"
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"Se(-A)"
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"Te"
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"Te(-A)"
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"F"
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"Cl"
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"Br"
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"I"
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# charge increments, hlocal(symbol), halpha(symbol), hbeta(symbol), mult_inc
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2
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O -8.1 -5.9 -2.6 -0.0
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A -8.4 -5.9 -2.6 -1.6
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# element acidity factors, flocal(symbol), falpha(symbol), fbeta(symbol)
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13
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B 18.7 0.7 -0.4
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C 18.7 -0.2 -0.4
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N 16.7 -3.3 -2.6
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O 10.3 -1.3 -2.0
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F 4.7 0.7 -1.4
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P 13.8 -1.7 -0.9
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S 8.8 -0.9 -1.8
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Se 5.1 -0.9 -1.0
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Te 4.4 0.3 -1.0
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Cl -0.2 -2.9 -1.0
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Br -0.3 0.0 -1.0
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I -0.4 2.5 -1.0
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A 8.0 0.5 -1.0
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# alpha condictivities, galpha(path)
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8
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"B(-B,C,N,O,F)" 0.8
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"C(-B,C,N,O,F)" 0.8
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"N(-B,C,N,O,F)" 0.5
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"O(-B,C,N,O,F)" 0.1
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"A(-B,C,N,O,F)" 0.9
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"A(-A)" 0.6
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"A(=A)" 0.8
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"A(#A)" 1.9
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# beta conductivities, gbeta(path)
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10
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"A(-B,C,N,O)(-A)" 0.3
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"O(-A)(-A)" 0.5
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"A(-A)(-A)" 1.5
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"A(-B,C,N,O)(=A)" 2.0
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"O(-A)(=A)" 1.7
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"A(-A)(=A)" 0.8
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"A(-A)(#A)" 1.6
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"A(=A)(-A)" 0.0
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"A(=A)(=A)" 1.3
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"A(#A)(-A)" 1.6
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# transformation polynom coefficient.
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# transformation is pKa = 7+(x-7)*beta+((x-7)*alpha)^3
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# alpha beta
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0.2452 1.6358
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# electronegativity used for relaxation process
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# The carbon entry must!! be the first one.
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103
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C 2.55
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N 3.04
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O 3.44
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F 3.98
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P 2.19
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S 2.58
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Cl 3.16
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As 2.18
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Se 2.55
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Br 2.96
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Sb 2.05
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Te 2.10
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I 2.66
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Si 1.90
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H 2.20
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He 0.00
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Li 0.98
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Be 1.57
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B 2.04
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Ne 0.00
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Na 0.93
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Mg 1.31
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Al 1.61
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Ar 0.00
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K 0.82
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Ca 1.00
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Sc 1.36
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Ti 1.54
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V 1.63
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Cr 1.66
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Mn 1.55
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Fe 1.83
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Co 1.88
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Ni 1.91
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Cu 1.90
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Zn 1.65
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Ga 1.81
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Ge 2.01
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Kr 0.00
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Rb 0.82
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Sr 0.95
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Y 1.22
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Zr 1.33
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Nb 1.60
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Mo 2.16
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Tc 1.90
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Ru 2.20
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Rh 2.28
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Pd 2.20
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Ag 1.93
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Cd 1.69
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In 1.78
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Sn 1.96
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Xe 0.00
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Cs 0.79
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Ba 0.89
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La 1.10
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Ce 1.12
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Pr 1.13
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Nd 1.14
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Pm 1.20
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Sm 1.17
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Eu 1.20
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Gd 1.20
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Tb 1.20
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Dy 1.22
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Ho 1.23
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Er 1.24
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Tm 1.25
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Yb 1.10
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Lu 1.27
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Hf 1.30
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Ta 1.50
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W 2.36
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Re 1.90
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Os 2.20
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Ir 2.20
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Pt 2.28
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Au 2.54
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Hg 2.00
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Tl 2.04
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Pb 2.33
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Bi 2.02
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Po 2.00
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At 2.20
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Rn 0.00
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Fr 0.70
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Ra 0.90
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Ac 1.10
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Th 1.30
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Pa 1.50
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U 1.38
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Np 1.36
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Pu 1.28
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Am 1.30
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Cm 1.30
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Bk 1.30
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Cf 1.30
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Es 1.30
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Fm 1.30
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Md 0.00
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No 0.00
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Lr 0.00
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