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8609cd4883
* 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
150 lines
11 KiB
Plaintext
150 lines
11 KiB
Plaintext
145 ! T92 , 29.6.99: transform O-1(-I) --> O(-I) included.
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/*A000*/ "Li,Na,K,Rb,Cs,Fr" --> "Li,Na,K,Rb,Cs,Fr+1" SAF metal
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/*A010*/ "Be,Mg,Ca,Sr,Ba,Ra" --> "Be,Mg,Ca,Sr,Ba,Ra+2" SAF metal
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/*A020*/ "Al,Ga,In,Tl" --> "Al,Ga,In,Tl+3" SAF metal
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/*A030*/ "Sb,Bi" --> "Sb,Bi+3" SAF metal
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/*A040*/ "Sn,Pb" --> "Sn,Pb+2" SAF metal
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/*A080*/ "Sc,Y,La,Ce,Pr,Nd,Pm,Sm" --> "Sc,Y,La,Ce,Pr,Nd,Pm,Sm+3" SAF metal
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/*A090*/ "Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu" --> "Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu+3" SAF metal
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/*A100*/ "N,O,S,F,Cl,Br,I-1" --> "N,O,S,F,Cl,Br,I" SAF anion
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/*A110*/ "N+1" --> "N" SAF ammonium
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/*A201*/ "Li,Na,K(-N,O,S,Se,F,Cl,Br,I)" --> "Li,Na,K+1(?N,O,S,Se,F,Cl,Br,I)" SAF
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/*A211*/ "Cs,Rb(-N,O,S,Se,F,Cl,Br,I)" --> "Cs,Rb+1(?N,O,S,Se,F,Cl,Br,I)" SAF
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/*A302*/ "Be,Mg,Ca(-F,Cl,Br,I)(-F,Cl,Br,I)" --> "Be,Mg,Ca+2(?F,Cl,Br,I)(?F,Cl,Br,I)"
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/*A312*/ "Sr,Ba(-F,Cl,Br,I)(-F,Cl,Br,I)" --> "Sr,Ba+2(?F,Cl,Br,I)(?F,Cl,Br,I)"
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/*A322*/ "Pb(-F,Cl,Br,I)(-F,Cl,Br,I)" --> "Pb+2(?F,Cl,Br,I)(?F,Cl,Br,I)" SAF
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/*A403*/ "Al,Ga(-F,Cl,Br,I)(-F,Cl,Br,I)(-F,Cl,Br,I)" --> "Al,Ga+3(?F,Cl,Br,I)(?F,Cl,Br,I)(?F,Cl,Br,I)"
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/*A413*/ "In,Tl(-F,Cl,Br,I)(-F,Cl,Br,I)(-F,Cl,Br,I)" --> "In,Tl+3(?F,Cl,Br,I)(?F,Cl,Br,I)(?F,Cl,Br,I)"
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/*A701*/ "Cu,Ag,Au,Hg(-N,O,S,Cl,Br,I)" --> "Cu,Ag,Au,Hg+1(?N,O,S,Cl,Br,I)" SAF
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/*A702*/ "Zn(-N+1)(-N+1)" --> "Zn+2(?N)(?N)" SAF
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/*A703*/ "Au(-F,Cl,Br,I)(-F,Cl,Br,I)(-F,Cl,Br,I)" --> "Au+3(?F,Cl,Br,I)(?F,Cl,Br,I)(?F,Cl,Br,I)"
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/*A803*/ "Sc,Y,La,Ce,Pr,Nd,Pm,Sm(-O)(-O)(-O)" --> "Sc,Y,La,Ce,Pr,Nd,Pm,Sm+3(?O)(?O)(?O)"
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/*A813*/ "Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu(-O)(-O)(-O)" --> "Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu+3(?O)(?O)(?O)"
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/*AA04*/ "N(=C)(-C)(-C)(-F,Cl,Br,I)" --> "N+1(=C)(-C)(-C)(?F,Cl,Br,I)"
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/*AA05*/ "N(-C)(-C)(-C)(-C)(-F,Cl,Br,I)" --> "N+1(-C)(-C)(-C)(-C)(?F,Cl,Br,I)"
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/*AX02*/ "O+1(=C)(-B-1)" --> "O(=C)(?B)" bor addukt
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/*B101*/ "N+1(-C,N,O)" --> "N(-C,N,O)" onium
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/*B112*/ "N(-C+1)(-C,N)" --> "N(=C)(-C,N)" onium
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/*B121*/ "N(-C+1)" --> "N(=C)" onium
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/*B131*/ "N+1(=C,N)" --> "N(=C,N)" onium
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/*B302*/ "N+1(-C)(-C,N)" --> "N(-C)(-C,N)" onium
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/*B312*/ "N+1(=C)(-C,N)" --> "N(=C)(-C,N)" onium
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/*b322*/ "N+1(=C)(-B-1)" --> "N(=C)(-B-1)" MAAG N4B
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/*B503*/ "N+1(-C)(-C,N)(-C,N)" --> "N(-C)(-C,N)(-C,N)" onium
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/*C002*/ "I+1(-C,O-1)(-C)" --> "I(=C,O)(-C)" ylid pos.
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/*C012*/ "N+1(-O-1)(-N)" --> "N(=O)(-N)" ylid pos.
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/*C103*/ "S+1(-C,O-1)(-C)(-C)" --> "S(=C,O)(-C)(-C)" ylid pos.
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/*C204*/ "P+1(-C-1)(-C)(-C)(-C)" --> "P(=C)(-C)(-C)(-C)" ylid pos.
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/*C214*/ "P+1(-O-1)(-N)(-N)(-N)" --> "P(=O)(-N)(-N)(-N)" ylid pos.
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/*C224*/ "S+1(=O)(-C-1)(-C)(-C)" --> "S(=O)(=C)(-C)(-C)" ylid pos.
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/*C301*/ "O-1(-P,S,I+1)" --> "O(=P,S,I)" ylid neg.
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/*C402*/ "C-1(-P,S+1)(-C)" --> "C(=P,S)(-C)" ylid neg.
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/*C503*/ "C-1(-S+1)(-C)(-C)" --> "C(=S)(-C)(-C)" ylid neg.
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/*C513*/ "S-1(-C+1)(-C)(-C)" --> "S(=C)(-C)(-C)" ylid neg.
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/*C601*/ "O(-I+1)" --> "O(=I)" ylid spez.
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/*C702*/ "S(-C+1)(-C)" --> "S+1(=C)(-C)" ylid spez.
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/*C803*/ "S(=O)(=O)(-C,N,O,F,Cl,Br,I)" --> "S(=O)(-O)(-C,N,O,F,Cl,Br,I)" R-SO-OH,O-SO-OH
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/*C804*/ "P,As,Sb(~O)(~O)(~O)(~O)" --> "P,As,Sb(=O)(-O)(-O)(-O)" phosphate
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/*C901*/ "N+1(=N-1)" --> "N-1(=N+1)" diazo
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/*D004*/ "B(-O)(-O)(-O)(-O)" --> "B-1(-O)(-O)(-O)(-O)" complex ion
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/*D104*/ "B+3(-O-1)(-O-1)(-O-1)(-O-1)" --> "B-1(-O)(-O)(-O)(-O)" complex ion
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/*D306*/ "Si.(-F-1)(-F-1)(-F-1)(-F-1)(-F-1)(-F-1)" --> "Si(-F)(-F)(-F)(-F)(-F)(-F)"
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/*D402*/ "Au(=P)(-O,S,F,Cl,Br,I)" --> "Au(-P+1)(-O,S,F,Cl,Br,I)" coord.comp.
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/*D414*/ "Fe,Co,Ni(=P)(=P)(-F,Cl,Br,I)(-F,Cl,Br,I)" --> "Fe,Co,Ni(-P+1)(-P+1)(-F,Cl,Br,I)(-F,Cl,Br,I)" coord.comp.
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/*D424*/ "Hg+2(-N)(-N)(-S-1)(-S-1)" -> "Hg(-N)(-N)(-S)(-S)" coord.comp.
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/*D504*/ "P(=Cu,Ag,Au,Zn,Cd,Hg)(-C)(-C)(-C)" --> "P+1(-Cu,Ag,Au,Zn,Cd,Hg)(-C)(-C)(-C)" coord.comp.
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/*D514*/ "P(=Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt)(-C)(-C)(-C)" --> "P+1(-Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt)(-C)(-C)(-C)" coord.comp.
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/*D522*/ "O(=C)(-Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn)" --> "O+1(=C)(-Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn)" coord.comp.
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/*D523*/ "N(=C,N)(-Al,Ge,V,Cr,Mn,Fe,Co,Ni,Cu,Zn)(-C,N,O)" --> "N+1(=C,N)(-Al,Ge,V,Cr,Mn,Fe,Co,Ni,Cu,Zn)(-C,N,O)" coord.comp.
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/*D533*/ "O(-C)(-C)(-Cr,Mn,Fe,Co,Ni,Cu,Zn)" --> "O+1(-C)(-C)(-Cr,Mn,Fe,Co,Ni,Cu,Zn)" coord.comp.
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/*E003*/ "N(=C)(=C)(-C)" --> "N+1(=C)(-C-1)(-C)" quart. N
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/*E013*/ "N(=C)(=N,O)(-C,N,O)" --> "N+1(=C)(-N,O-1)(-C,N,O)" quart. N
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/*E023*/ "N(=N)(=N,O)(-C)" --> "N+1(=N)(-N,O-1)(-C)" quart. N
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/*E033*/ "N(=O)(=O)(-C,N,O)" --> "N+1(=O)(-O-1)(-C,N,O)" quart. N
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/*E104*/ "N(=C,O,S)(-C)(-C,N)(-C,N,O)" --> "N+1(-C,O,S-1)(-C)(-C,N)(-C,N,O)" quart. N
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/*E203*/ "N(=C,O)(=O)(-O-1)" --> "N+1(=C,O)(-O-1)(-O)" quart. N spez.
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/*E302*/ "N(#C)(=O,S)" --> "N+1(#C)(-O,S-1)" quart. N
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/*E402*/ "N(#N)(=C)" --> "N+1(=N-1)(=C)" quart. N
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/*E502*/ "N+1(#N)(-C,N-1)" --> "N+1(=N-1)(=C,N)" quart. N
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/*E601*/ "N(#N)" --> "N-1(=N+1)" quart. N allg.
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/*F001*/ "C-1(#N)" --> "C(#N)" prot.
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/*F002*/ "C(#N)(-C,O,S-1)" --> "C(#N)(-C,O,S)" prot.
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/*F011*/ "C(-N,P,O,S-1)" --> "C(-N,P,O,S)" prot.
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/*F012*/ "C(-C,N,O)(-N,P,O,S-1)" --> "C(-C,N,O)(-N,P,O,S)" prot.
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/*F022*/ "C(=C)(-N,O-1)" --> "C(-C)(=N,O)" prot. enol
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/*F032*/ "C(=C)(=N-1)" --> "C(-C)(#N)" prot. spez.
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/*F042*/ "C(=O,S)(-O,S-1)" --> "C(=O,S)(-O,S)" prot.
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/*F052*/ "N+1(=N-1)(=N-1)" --> "N+1(=N-1)(=N)" MAAG N3
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/*F113*/ "C(-C)(-N,O,S-1)(-C,N,O)" --> "C(-C)(-N,O,S)(-C,N,O)" prot.
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/*F123*/ "C(-C)(-O-1)(-N+1)" --> "C(-C)(-O)(-N+1)" prot.
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/*F203*/ "C(=C)(-N-1)(-C,N)" --> "C(=C)(-N)(-C,N)" prot.
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/*F213*/ "C(=C)(-O,S-1)(-C)" --> "C(=C)(-O,S)(-C)" prot. enol C
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/*F223*/ "!@C(=C)(-O-1)(-N,O,S)" --> "C(-C)(=O)(-N,O,S)" prot. enol Het.
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/*F233*/ "C(=C)(-S-1)(-N,S)" --> "C(-C)(=S)(-N,S)" prot. enol
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/*F243*/ "C(=C)(-O-1)(-N+1)" --> "C(-C)(=O)(-N+1)" prot. enol
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/*F303*/ "C(=N)(-C,N,O,S-1)(-C,N,O,S)" --> "C(=N)(-C,N,O,S)(-C,N,O,S)" prot.
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/*F313*/ "C(=N)(-N-1)(-C,N)" --> "C(=N)(-N)(-C,N)" prot.
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/*F323*/ "C(=N)(-N,O,S-1)(-N,P+1)" --> "C(=N)(-N,O,S)(-N,P+1)" prot.
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/*F333*/ "C(=N+1)(-O,S-1)(-C,N)" --> "C(=N+1)(-O,S)(-C,N)" prot.
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/*F343*/ "C(=N+1)(-N-1)(-S)" --> "C(=N+1)(-N)(-S)" prot.
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/*F403*/ "C(=O)(-C,N,P,O,S-1)(-C,N,P,O,S)" --> "C(=O)(-C,N,P,O,S)(-C,N,P,O,S)" prot.
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/*F413*/ "C(=S)(-C,N,O,S-1)(-N,P,O,S)" --> "C(=S)(-C,N,O,S)(-N,P,O,S)" prot.
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/*F423*/ "C(=O)(-O,S-1)(-N+1)" --> "C(=O)(-O,S)(-N+1)" prot.
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/*F503*/ "N(-N,O-1)(-C)(-C)" --> "N(-N,O)(-C)(-C)" prot.
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/*F513*/ "N+1(-O-1)(-C)(-C)" --> "N(-O)(-C)(-C)" prot.
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/*F523*/ "N+1(=C,O)(-O-1)(-O-1)" --> "N+1(=C,O)(-O-1)(-O)" prot.
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/*F603*/ "P(=O)(-O-1)(-C,O)" --> "P(=O)(-O)(-C,O)" prot.
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/*F703*/ "S,Se(=O)(-O-1)(-C,O)" --> "S,Se(=O)(-O)(-C,O)" prot.
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/*F804*/ "C(-C)(-O-1)(-N)(-O)" --> "C(-C)(-O)(-N)(-O)" prot.
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/*F904*/ "P,As(=O)(-O,S-1)(-C,N,O,S)(-C,N,O,S)" --> "P,As(=O)(-O,S)(-C,N,O,S)(-C,N,O,S)"
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/*F914*/ "P(=S)(-O,S-1)(-C,N,O,S)(-C,N,O,S)" --> "P(=S)(-O,S)(-C,N,O,S)(-C,N,O,S)"
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/*FA04*/ "S(=N)(=O)(-N,O-1)(-C,N,O,S)" --> "S(=N)(=O)(-N,O)(-C,N,O,S)" prot.
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/*FA14*/ "S(=O)(=O)(-N,O-1)(-C,N,O,S)" --> "S(=O)(=O)(-N,O)(-C,N,O,S)" prot.
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/*FA24*/ "S(=O)(=O)(-N,O-1)(-N+1)" --> "S(=O)(=O)(-N,O)(-N+1)" prot.
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/*G003*/ "C(=N,O)(-N,P,O,S-1)(-N,P,O,S-1)" --> "C(=N,O)(-N,P,O,S)(-N,P,O,S)" prot.2x
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/*G104*/ "P,As(=O)(-C,N,O)(-O-1)(-O-1)" --> "P,As(=O)(-C,N,O)(-O)(-O)" prot.2x
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/*G204*/ "S(=O)(=O)(-O-1)(-O-1)" --> "S(=O)(=O)(-O)(-O)" prot. 2x
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/*H003*/ "V(=O)(=O)(-O-1)" --> "V(=O)(=O)(-O)" prot. trans.met.
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/*I001*/ "O-1(-B,N,P,As,O,Se,Cl,I)" --> "O(-B,N,P,As,O,Se,Cl,I)" prot. allg.
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/*I011*/ "S-1(-S)" --> "S(-S)" prot. allg.
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/*I021*/ "O-1(-V)" --> "O(-V)" prot. allg.
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/*I101*/ "N-1(=C,N)" --> "N(=C,N)" prot. allg.
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/*I202*/ "C-1(-C)(-C,N)" --> "C(-C)(-C,N)" prot. allg.
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/*I212*/ "N-1(-C,N)(-C,N,S)" --> "N(-C,N)(-C,N,S)" prot. allg.
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/*I303*/ "C-1(-C)(-C)(-C,N)" --> "C(-C)(-C)(-C,N)" prot. allg.
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/*K002*/ "S(-C+1)(-S)" --> "S(-C)(=S+1)" MAAG special
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/*K006*/ "Si-2(-F)(-F)(-F)(-F)(-F)(-F)" --> "Si(-F)(-F)(-F)(-F)(-F)(-F)" MAAG special
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/*L000*/ "P,Sb-3" --> "P,Sb"
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/*L000*/ "S-2" --> "S"
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/*L100*/ "Ca+1(-O)" --> "Ca+2(?O)"
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/*L100*/ "O-1(-O-1)" --> "O(=O)"
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/*L200*/ "C(#N)(-Na)" --> "C(#N)(?Na+1)"
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/*L200*/ "Ca(-O)(-S,Cl)" --> "Ca+2(?O)(?S,Cl)"
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/*L200*/ "O(=C)(-Cr)" --> "O+1(=C)(-Cr)"
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/*L300*/ "N(=O)(=O)(-N+1)" --> "N+1(=O)(-O-1)(-N+1)"
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/*L300*/ "N(=C)(-C)(-Co,Ni,Cu)" --> "N+1(=C)(-C)(-Co,Ni,Cu)"
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/*L400*/ "Al(-O)(-O)(-O)(-O)" --> "Al-1(-O)(-O)(-O)(-O)"
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/*L200*/ "Ca,Ba,Mg(-O)(-O)" --> "Ca,Ba,Mg+2(?O)(?O)"
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/*L100*/ "C+2(=O)" --> "C-1(#O+1)"
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/*L400*/ "N+1(-H)(-H)(-H)(-O)" --> "N(-H)(-H)(-H)(?O)"
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/*L400*/ "N(-O,Cl,Br)(-H)(-H)(-H)" --> "N(?O,Cl,Br)(-H)(-H)(-H)"
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/*L500*/ "N+1(-Br-1)(-C)(-C)(-C)(-C)" --> "N+1(?Br)(-C)(-C)(-C)(-C)"
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/*L100*/ "Ca(-O)" --> "Ca+2(?O)"
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/*L200*/ "N(=N+3)(-C)" --> "N+1(#N)(-C)"
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/*L200*/ "N+1(-C)(-H)" --> "N(-C)(-H)"
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/*L200*/ "N+1(=N-1)(=O)" --> "N+1(#N)(-O-1)"
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/*L200*/ "N+1(=O-1)(=O)" --> "N.(=O)(=O)"
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/*L200*/ "O(=C)(-C)" --> "O+1(=C)(-C)"
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/*L200*/ "O-1(-N+1)(-Na)" --> "O-1(-N+1)(?Na+1)"
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/*L300*/ "Bi(-O)(-O)(-O)" --> "Bi+3(?O)(?O)(?O)"
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/*L300*/ "Zn(-Cl)(-Cl)(-Cl)" --> "Zn-1(-Cl)(-Cl)(-Cl)"
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/*L300*/ "N+1(=O)(=O)(-O)" --> "N+1(=O)(-O-1)(-O)"
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/*L400*/ "S(=O)(=O)(=O)(-C,O)" --> "S(=O)(=O)(-O)(-C,O)"
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/*L400*/ "Cr+1(-O)(-O)(-O)(-O)" --> "Cr-1(-O)(-O)(-O)(-O)"
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/*L400*/ "Cr+2(-O)(-O)(-O)(-O)" --> "Cr-1(-O)(-O)(-O)(-O)"
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/*L400*/ "Cr-3(-O)(-O)(-O)(-O)" --> "Cr-1(-O)(-O)(-O)(-O)"
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/*L100*/ "H(-H)" --> "Hyd(-Hyd)"
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/*====================================================================*/
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/*B202*/ "I+1(-C)(-C)" --> "I(-C)(-C)" onium
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/*F253*/ "C(=C)(-N+1)(-S-1)" --> "C(=C)(-N+1)(-S)" MAAG SH+Noxid
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