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Descriptors Used in Water Solubility Prediction Study

This document provides a detailed list of all descriptors used in the water solubility prediction study. Each descriptor is briefly described to give context on its relevance and role in the model.

Table of Contents

  1. Basic Descriptors
  2. Functional Group Descriptors
  3. Feature-Engineered Descriptors
  4. Descriptors Used by Sorkun

Basic Descriptors

  1. MaxAbsEStateIndex: The maximum absolute value of the E-state index, a measure of electron distribution.
  2. MaxEStateIndex: The maximum E-state index in the molecule.
  3. MinAbsEStateIndex: The minimum absolute value of the E-state index.
  4. MinEStateIndex: The minimum E-state index in the molecule.
  5. qed: Quantitative estimate of drug-likeness, a metric used to assess the drug-likeness of a molecule.
  6. SPS: Synthetic Accessibility Score, predicting the ease of synthesis for a compound.
  7. MolWt: Molecular Weight, the total mass of the molecule.
  8. HeavyAtomMolWt: The molecular weight of heavy atoms (non-hydrogen atoms).
  9. ExactMolWt: The exact molecular weight considering isotopic distribution.
  10. NumValenceElectrons: Total number of valence electrons in the molecule.
  11. NumRadicalElectrons: Number of radical electrons in the molecule.
  12. MaxPartialCharge: Maximum partial charge on any atom in the molecule.
  13. MinPartialCharge: Minimum partial charge on any atom in the molecule.
  14. MaxAbsPartialCharge: Maximum absolute value of the partial charge on any atom.
  15. MinAbsPartialCharge: Minimum absolute value of the partial charge on any atom.
  16. FpDensityMorgan1: Morgan fingerprint density with radius 1, a circular fingerprint used to encode molecular structure.
  17. FpDensityMorgan2: Morgan fingerprint density with radius 2.
  18. FpDensityMorgan3: Morgan fingerprint density with radius 3.
  19. BCUT2D_MWHI: BCUT metric using molecular weight as the property.
  20. BCUT2D_MWLOW: BCUT metric for low molecular weight property.
  21. BCUT2D_CHGHI: BCUT metric using high charge as the property.
  22. BCUT2D_CHGLO: BCUT metric for low charge property.
  23. BCUT2D_LOGPHI: BCUT metric using high LogP as the property.
  24. BCUT2D_LOGPLOW: BCUT metric for low LogP property.
  25. BCUT2D_MRHI: BCUT metric using high molar refractivity as the property.
  26. BCUT2D_MRLOW: BCUT metric for low molar refractivity property.
  27. AvgIpc: Average Information Content (Ipc) of the molecule.
  28. BalabanJ: Balaban’s J index, a topological descriptor.
  29. BertzCT: Bertz complexity index, a measure of molecular complexity.
  30. Chi0: The first-order connectivity index.
  31. Chi0n: The first-order connectivity index with nitrogen.
  32. Chi0v: The first-order valence connectivity index.
  33. Chi1: The second-order connectivity index.
  34. Chi1n: The second-order connectivity index with nitrogen.
  35. Chi1v: The second-order valence connectivity index.
  36. Chi2n: The third-order connectivity index with nitrogen.
  37. Chi2v: The third-order valence connectivity index.
  38. Chi3n: The fourth-order connectivity index with nitrogen.
  39. Chi3v: The fourth-order valence connectivity index.
  40. Chi4n: The fifth-order connectivity index with nitrogen.
  41. Chi4v: The fifth-order valence connectivity index.
  42. HallKierAlpha: Hall-Kier alpha modification of the shape index.
  43. Ipc: Information content index, a molecular descriptor.
  44. Kappa1: First Kappa shape index.
  45. Kappa2: Second Kappa shape index.
  46. Kappa3: Third Kappa shape index.
  47. LabuteASA: Labute’s approximation to molecular surface area.
  48. PEOE_VSA1: PEOE charge on molecular surface area, bin 1.
  49. PEOE_VSA10: PEOE charge on molecular surface area, bin 10.
  50. PEOE_VSA11: PEOE charge on molecular surface area, bin 11.
  51. PEOE_VSA12: PEOE charge on molecular surface area, bin 12.
  52. PEOE_VSA13: PEOE charge on molecular surface area, bin 13.
  53. PEOE_VSA14: PEOE charge on molecular surface area, bin 14.
  54. PEOE_VSA2: PEOE charge on molecular surface area, bin 2.
  55. PEOE_VSA3: PEOE charge on molecular surface area, bin 3.
  56. PEOE_VSA4: PEOE charge on molecular surface area, bin 4.
  57. PEOE_VSA5: PEOE charge on molecular surface area, bin 5.
  58. PEOE_VSA6: PEOE charge on molecular surface area, bin 6.
  59. PEOE_VSA7: PEOE charge on molecular surface area, bin 7.
  60. PEOE_VSA8: PEOE charge on molecular surface area, bin 8.
  61. PEOE_VSA9: PEOE charge on molecular surface area, bin 9.
  62. SMR_VSA1: SMR surface area, bin 1.
  63. SMR_VSA10: SMR surface area, bin 10.
  64. SMR_VSA2: SMR surface area, bin 2.
  65. SMR_VSA3: SMR surface area, bin 3.
  66. SMR_VSA4: SMR surface area, bin 4.
  67. SMR_VSA5: SMR surface area, bin 5.
  68. SMR_VSA6: SMR surface area, bin 6.
  69. SMR_VSA7: SMR surface area, bin 7.
  70. SMR_VSA8: SMR surface area, bin 8.
  71. SMR_VSA9: SMR surface area, bin 9.
  72. SlogP_VSA1: SlogP surface area, bin 1.
  73. SlogP_VSA10: SlogP surface area, bin 10.
  74. SlogP_VSA11: SlogP surface area, bin 11.
  75. SlogP_VSA12: SlogP surface area, bin 12.
  76. SlogP_VSA2: SlogP surface area, bin 2.
  77. SlogP_VSA3: SlogP surface area, bin 3.
  78. SlogP_VSA4: SlogP surface area, bin 4.
  79. SlogP_VSA5: SlogP surface area, bin 5.
  80. SlogP_VSA6: SlogP surface area, bin 6.
  81. SlogP_VSA7: SlogP surface area, bin 7.
  82. SlogP_VSA8: SlogP surface area, bin 8.
  83. SlogP_VSA9: SlogP surface area, bin 9.
  84. TPSA: Topological polar surface area, a predictor of drug absorption.
  85. EState_VSA1: E-state surface area, bin 1.
  86. EState_VSA10: E-state surface area, bin 10.
  87. EState_VSA11: E-state surface area, bin 11.
  88. EState_VSA2: E-state surface area, bin 2.
  89. EState_VSA3: E-state surface area, bin 3.
  90. EState_VSA4: E-state surface area, bin 4.
  91. EState_VSA5: E-state surface area, bin 5.
  92. EState_VSA6: E-state surface area, bin 6.
  93. EState_VSA7: E-state surface area, bin 7.
  94. EState_VSA8: E-state surface area, bin 8.
  95. EState_VSA9: E-state surface area, bin 9.
  96. VSA_EState1: VSA_E-state, bin 1.
  97. VSA_EState10: VSA_E-state, bin 10.
  98. VSA_EState2: VSA_E-state, bin 2.
  99. VSA_EState3: VSA_E-state, bin 3.
  100. VSA_EState4: VSA_E-state, bin 4.
  101. VSA_EState5: VSA_E-state, bin 5.
  102. VSA_EState6: VSA_E-state, bin 6.
  103. VSA_EState7: VSA_E-state, bin 7.
  104. VSA_EState8: VSA_E-state, bin 8.
  105. VSA_EState9: VSA_E-state, bin 9.
  106. FractionCSP3: Fraction of carbon atoms that are sp3 hybridized.
  107. HeavyAtomCount: The number of heavy atoms (non-hydrogen atoms).
  108. NHOHCount: The number of -OH and -NH groups.
  109. NOCount: The number of nitrogen and oxygen atoms.
  110. NumAliphaticCarbocycles: The number of aliphatic carbocycles.
  111. NumAliphaticHeterocycles: The number of aliphatic heterocycles.
  112. NumAliphaticRings: The number of aliphatic rings.
  113. NumAromaticCarbocycles: The number of aromatic carbocycles.
  114. NumAromaticHeterocycles: The number of aromatic heterocycles.
  115. NumAromaticRings: The number of aromatic rings.
  116. NumHAcceptors: The number of hydrogen bond acceptors.
  117. NumHDonors: The number of hydrogen bond donors.
  118. NumHeteroatoms: The number of heteroatoms (non-carbon and non-hydrogen atoms).
  119. NumRotatableBonds: The number of rotatable bonds.
  120. NumSaturatedCarbocycles: The number of saturated carbocycles.
  121. NumSaturatedHeterocycles: The number of saturated heterocycles.
  122. NumSaturatedRings: The number of saturated rings.
  123. RingCount: The total number of rings in the molecule.
  124. MolLogP: The logarithm of the partition coefficient (LogP) of the molecule.
  125. MolMR: The molar refractivity of the molecule.

Functional Group Descriptors

Polar Functional Groups

  1. Hydroxyl Group ('[OH]'): Indicates the presence of a hydroxyl group (-OH) in the molecule.
  2. Carbonyl Group ('C=O'): Indicates the presence of a carbonyl group (C=O) in the molecule.
  3. Amide Group ('C(=O)N'): Indicates the presence of an amide group (-C(=O)N-) in the molecule.
  4. Carboxyl Group ('C(=O)[OH]'): Indicates the presence of a carboxyl group (-COOH) in the molecule.

Non-Polar Functional Groups

  1. Alkyl ('[R]'): Indicates the presence of an alkyl group (R-) in the molecule.
  2. Aromatic Rings ('c'): Indicates the presence of aromatic rings in the molecule.
  3. Alkene ('C=C'): Indicates the presence of an alkene group (C=C) in the molecule.

Feature-Engineered Descriptors

  1. charge: The total charge of the molecule.
  2. many_double_bonds: The count of double bonds in the molecule.
  3. atoms_degree_0: Number of atoms with zero degree (not connected to other atoms).
  4. atoms_degree_1: Number of atoms with one connection.
  5. atoms_degree_2: Number of atoms with two connections.
  6. atoms_degree_3: Number of atoms with three connections.
  7. atoms_degree_4: Number of atoms with four connections.
  8. atoms_degree_5: Number of atoms with five connections.
  9. atoms_degree_6: Number of atoms with six connections.
  10. atoms_valence_0: Number of atoms with zero valence electrons.
  11. atoms_valence_1: Number of atoms with one valence electron.
  12. atoms_valence_2: Number of atoms with two valence electrons.
  13. atoms_valence_3: Number of atoms with three valence electrons.
  14. atoms_valence_4: Number of atoms with four valence electrons.
  15. atoms_valence_5: Number of atoms with five valence electrons.
  16. atoms_valence_6: Number of atoms with six valence electrons.
  17. atom_hybridization_S: Number of atoms with S orbital hybridization.
  18. atom_hybridization_SP: Number of atoms with SP orbital hybridization.
  19. atom_hybridization_SP2: Number of atoms with SP2 orbital hybridization.
  20. atom_hybridization_SP3: Number of atoms with SP3 orbital hybridization.
  21. atom_hybridization_SP3D: Number of atoms with SP3D orbital hybridization.
  22. atom_hybridization_SP3D2: Number of atoms with SP3D2 orbital hybridization.
  23. atom_hybridization_UNSPECIFIED: Number of atoms with unspecified hybridization.
  24. aromatic_atoms: Number of aromatic atoms in the molecule.
  25. single_bonds: Number of single bonds in the molecule.
  26. double_bonds: Number of double bonds in the molecule.
  27. triple_bonds: Number of triple bonds in the molecule.
  28. aromatic_bonds: Number of aromatic bonds in the molecule.
  29. zero_bonds: Number of atoms with zero bonds.
  30. conjugated_bonds: Number of conjugated bonds in the molecule.
  31. bonds_in_ring: Number of bonds present in a ring structure.
  32. chirality_none: Number of atoms without chirality.
  33. chirality_any: Number of atoms with any chirality.
  34. chirality_z: Number of atoms with Z chirality.
  35. chirality_e: Number of atoms with E chirality.
  36. n_atoms: Total number of atoms in the molecule.
  37. n_bonds: Total number of bonds in the molecule.
  38. n_rings: Total number of rings in the molecule.

Descriptors Used by Sorkun

  1. nX: Number of halogen atoms in the molecule.
  2. nHeavyAtom: Number of non-hydrogen atoms in the molecule.
  3. nAromAtom: Number of aromatic atoms in the molecule.
  4. nHBAcc: Number of hydrogen bond acceptors.
  5. nHBDon: Number of hydrogen bond donors.
  6. nRot: Number of rotatable bonds.
  7. nBonds: Total number of bonds in the molecule.
  8. nAromBond: Number of aromatic bonds in the molecule.
  9. nBondsO: Number of bonds to oxygen atoms.
  10. nBondsS: Number of bonds to sulfur atoms.
  11. nBondsD: Number of double bonds in the molecule.
  12. nBondsT: Number of triple bonds in the molecule.
  13. VMcGowan: McGowan volume, a descriptor related to molecular size.
  14. TopoPSA(NO): Topological polar surface area, calculated considering only oxygen and nitrogen atoms.
  15. TopoPSA: Topological polar surface area, considering all polar atoms.
  16. LabuteASA: Labute’s Approximation to Molecular Surface Area.
  17. apol: Sum of atomic polarizabilities (including implicit hydrogens).
  18. bpol: Sum of atomic polarizabilities (excluding hydrogens).
  19. nAcid: Number of acidic groups in the molecule.
  20. nBase: Number of basic groups in the molecule.
  21. ECIndex: Eccentric connectivity index, a topological descriptor.
  22. GGI1: Gutman Molecular Topological Index.
  23. JGI1: Topological charge index of the first order.
  24. SLogP: Logarithm of the partition coefficient (SLogP).
  25. SMR: Sum of atomic molar refractivity values.
  26. BertzCT: Bertz complexity index, related to the molecular complexity.
  27. BalabanJ: Balaban’s J index, a topological descriptor.
  28. WPol: Weighted path order 3.
  29. Zagreb1: First Zagreb index, a topological descriptor.
  30. ABC: Aromatic bond count.
  31. ABCGG: Generalized graph approach to aromatic bond count.
  32. nRing: Number of rings in the molecule.
  33. nHRing: Number of rings with hydrogen atoms.
  34. naRing: Number of aromatic rings in the molecule.
  35. naHRing: Number of aromatic rings with hydrogen atoms.
  36. nARing: Number of rings with atoms other than carbon.
  37. nFRing: Number of fused rings in the molecule.
  38. NsCH3: Number of sulfur-carbon single bonds where carbon is connected to three other atoms.
  39. NdCH2: Number of carbon atoms doubly bonded to another atom and singly bonded to two other atoms.
  40. NssCH2: Number of carbon atoms singly bonded to a sulfur atom and two other atoms.
  41. NtCH: Number of carbon atoms triply bonded to another atom and singly bonded to one other atom.
  42. NdsCH: Number of carbon atoms doubly bonded to a sulfur atom and singly bonded to one other atom.
  43. NaaCH: Number of carbon atoms singly bonded to two other atoms and a sulfur atom.
  44. NsssCH: Number of carbon atoms singly bonded to three other atoms and a sulfur atom.
  45. NddC: Number of carbon atoms doubly bonded to two other atoms.
  46. NtsC: Number of carbon atoms triply bonded to another atom and singly bonded to one other atom.
  47. NdssC: Number of carbon atoms doubly bonded to a sulfur atom and singly bonded to one other atom.
  48. NaasC: Number of carbon atoms singly bonded to a sulfur atom and one other atom.
  49. NaaaC: Number of carbon atoms singly bonded to three other atoms.
  50. NssssC: Number of carbon atoms singly bonded to four other atoms.
  51. NsNH2: Number of nitrogen atoms singly bonded to one other atom and two hydrogens.
  52. NssNH: Number of nitrogen atoms singly bonded to two other atoms and one hydrogen.
  53. NaaNH: Number of nitrogen atoms singly bonded to two other atoms and one hydrogen.
  54. NtN: Number of nitrogen atoms triply bonded to another atom.
  55. NdsN: Number of nitrogen atoms doubly bonded to another atom and singly bonded to one other atom.
  56. NaaN: Number of nitrogen atoms singly bonded to two other atoms.
  57. NsssN: Number of nitrogen atoms singly bonded to three other atoms.
  58. NaasN: Number of nitrogen atoms singly bonded to two other atoms.
  59. NsOH: Number of oxygen atoms singly bonded to one other atom and one hydrogen.
  60. NdO: Number of oxygen atoms doubly bonded to another atom.
  61. NssO: Number of oxygen atoms singly bonded to two other atoms.
  62. NaaO: Number of oxygen atoms singly bonded to two other atoms.
  63. NsF: Number of fluorine atoms singly bonded to one other atom.
  64. NdsssP: Number of phosphorus atoms doubly bonded to another atom and singly bonded to three other atoms.
  65. NdS: Number of sulfur atoms doubly bonded to another atom.
  66. NssS: Number of sulfur atoms singly bonded to two other atoms.
  67. NaaS: Number of sulfur atoms singly bonded to two other atoms.
  68. NdssS: Number of sulfur atoms doubly bonded to another atom and singly bonded to one other atom.
  69. NddssS: Number of sulfur atoms doubly bonded to two other atoms.
  70. NsCl: Number of chlorine atoms singly bonded to one other atom.
  71. NsBr: Number of bromine atoms singly bonded to one other atom.
  72. NsI: Number of iodine atoms singly bonded to one other atom.
  73. SsCH3: Number of carbon atoms singly bonded to one sulfur atom and three other atoms.
  74. SdCH2: Number of carbon atoms doubly bonded to another atom and singly bonded to two other atoms.
  75. SssCH2: Number of carbon atoms singly bonded to two other atoms and one sulfur atom.
  76. StCH: Number of carbon atoms triply bonded to another atom and singly bonded to one other atom.
  77. SdsCH: Number of carbon atoms doubly bonded to a sulfur atom and singly bonded to one other atom.
  78. SaaCH: Number of carbon atoms singly bonded to a sulfur atom and two other atoms.
  79. SsssCH: Number of carbon atoms singly bonded to three other atoms and a sulfur atom.
  80. SddC: Number of carbon atoms doubly bonded to two other atoms.
  81. StsC: Number of carbon atoms triply bonded to another atom and singly bonded to one other atom.
  82. SdssC: Number of carbon atoms doubly bonded to a sulfur atom and singly bonded to one other atom.
  83. SaasC: Number of carbon atoms singly bonded to two other atoms and a sulfur atom.
  84. SaaaC: Number of carbon atoms singly bonded to three other atoms.
  85. SssssC: Number of carbon atoms singly bonded to four other atoms.
  86. SsNH2: Number of nitrogen atoms singly bonded to one other atom and two hydrogens.
  87. SssNH: Number of nitrogen atoms singly bonded to two other atoms and one hydrogen.
  88. SaaNH: Number of nitrogen atoms singly bonded to two other atoms and one hydrogen.
  89. StN: Number of nitrogen atoms triply bonded to another atom.
  90. SdsN: Number of nitrogen atoms doubly bonded to another atom and singly bonded to one other atom.
  91. SaaN: Number of nitrogen atoms singly bonded to two other atoms.
  92. SsssN: Number of nitrogen atoms singly bonded to three other atoms.
  93. SaasN: Number of nitrogen atoms singly bonded to two other atoms.
  94. SsOH: Number of oxygen atoms singly bonded to one other atom and one hydrogen.
  95. SdO: Number of oxygen atoms doubly bonded to another atom.
  96. SssO: Number of oxygen atoms singly bonded to two other atoms.
  97. SaaaO: Number of oxygen atoms singly bonded to two other atoms.
  98. SsF: Number of fluorine atoms singly bonded to one other atom.
  99. SdsssP: Number of phosphorus atoms doubly bonded to another atom and singly bonded to three other atoms.
  100. SdS: Number of sulfur atoms doubly bonded to another atom.
  101. SssS: Number of sulfur atoms singly bonded to two other atoms.
  102. SaaaS: Number of sulfur atoms singly bonded to two other atoms.
  103. SdssS: Number of sulfur atoms doubly bonded to another atom and singly bonded to one other atom.
  104. SddssS: Number of sulfur atoms doubly bonded to two other atoms.
  105. SsCl: Number of chlorine atoms singly bonded to one other atom.
  106. SsBr: Number of bromine atoms singly bonded to one other atom.
  107. SsI: Number of iodine atoms singly bonded to one other atom.
  108. C: Total number of carbon atoms.
  109. H: Total number of hydrogen atoms.
  110. Br: Total number of bromine atoms.
  111. N: Total number of nitrogen atoms.
  112. O: Total number of oxygen atoms.
  113. I: Total number of iodine atoms.
  114. Cl: Total number of chlorine atoms.
  115. S: Total number of sulfur atoms.
  116. F: Total number of fluorine atoms.
  117. P: Total number of phosphorus atoms.
  118. As: Total number of arsenic atoms.
  119. Si: Total number of silicon atoms.
  120. Se: Total number of selenium atoms.
  121. Sn: Total number of tin atoms.
  122. Hg: Total number of mercury atoms.
  123. Ge: Total number of germanium atoms.