There are a large number of physical property
limits. They occur as three fields on a line. For example:
MIN_HETEROATOMS 2 "Minimum number of heteroatoms"
The first field is the property keyword, the second field is the value assigned
to that keyword, and the third field is a brief informational message. There
are a fixed number of physical property keywords. No additional physical
property keywords can be added by the user. The current keywords and a brief
definitions of each are included below.
- Molecular Weight
- Isotopic molecular weight
MIN_MOLWT
MAX_MOLWT
- Heavy Atom Count
- Number of non-hydrogen atoms
MIN_NUM_HVY
MAX_NUM_HVY
- Carbon Count
- Number of carbons
MIN_CARBONS
MAX_CARBONS
- Hetero-Count
- Number of non-carbon and non-hydrogen atoms
MIN_HETEROATOMS
MAX_HETEROATOMS
- Hetero-Atom to Carbon Ratio
- Hetero Count/Carbon Count
MIN_Het_C_Ratio
MAX_Het_C_Ratio
- Chiral Count
- Number of chiral atoms
MIN_CHIRAL_CENTERS
MAX_CHIRAL_CENTERS
- Hydrogen-bond Acceptors
- Sum of a) degree 2, aromatic, non-positive
nitrogens, b) electron rich or negative, valence less than 4,
non-aromatic nitrogens, c) negatively charged or not electron withdrawn and
neutral oxygens, and d) degree 1, double bonded, electron rich sulfur.
MIN_HBOND_ACCEPTORS
MAX_HBOND_ACCEPTORS
- Hydrogen-bond Donors
- Sum of hydrogen atoms on Nitrogen, Oxygen and
Sulfur atoms.
MIN_HBOND_DONORS
MAX_HBOND_DONORS
- Lipinski Acceptors
- Number of Nitrogens + Oxygens
MIN_LIPINSKI_ACCEPTORS
MAX_LIPINSKI_ACCEPTORS
- Lipinski Donors
- Number of Hydrogens attached to Nitrogen or Oxygen
MIN_LIPINSKI_DONORS
MAX_LIPINSKI_DONORS
- Halide Fraction
- Percent of molecular weight from halides
MIN_HALIDE_FRACTION
MAX_HALIDE_FRACTION
- Formal Count
- Number of atoms with a formal charge (excludes dative)
MIN_COUNT_FORMAL_CRG
MAX_COUNT_FORMAL_CRG
- Formal Sum
- Sum of formal charges
MIN_SUM_FORMAL_CRG
MAX_SUM_FORMAL_CRG
- Connected Non-Ring
- Considers sets of contiguous (bonded) non-ring atoms
MIN_CON_NON_RING
MAX_CON_NON_RING
- Unbranched Chains
- The size of unbranched non-ring chains
MIN_UNBRANCHED
MAX_UNBRANCHED
- Total Functional Group Count
- Total number of functional groups (not just
those recognized by filter patterns). Does not count any ring-systems as
functional groups. Degree 1 atoms heteroatoms, particularly those with double
bonds or dative bonds are considered part of ring systems and do not count
as a functional group.
MIN_FCNGRP
MAX_FCNGRP
- Ring Systems
- Number of ring systems (contiguous systems of ring atoms and
bonds)
MIN_RING_SYS
MAX_RING_SYS
- Ring Size
- Maximum size of any single ring system
MIN_RING_SIZE
MAX_RING_SIZE
- Rotor Count
- Number of rotatable bonds. Allows optional adjustment for aliphatic rings following the method of Oprea [4].
MIN_ROT_BONDS
MAX_ROT_BONDS
ADJUST_ROT_FOR_RING
- Rigid Count
- Number of rigid bonds
MIN_RIGID_BONDS
MAX_RIGID_BONDS
