Residue attributes are defined in the residue attribute space (short name r). Residue attributes may only match residue nodes.

The following residue attributes are available in NSL:

aminoAcid (short name aa)
charge (short name c)
completeAminoAcidBackbone (short name caab)
nucleicAcid (short name na)
pKa1, pKa2, and isoelectricPointPH (short name pI), see Dissociation constants
polarity (short name p)
residueSequenceNumber (short name id)
secondaryStructure (short name ss)
standardResidueName (short name srn)
nonStandardResidueName (short name nsrn)
terminal (short name ter)
type (short name t)

Attribute name	Short name	Possible values	Examples
`aminoAcid`	`aa`		`r.aa`
`charge`	`c`	`negative`, `neutral`, `positive`	`r.c neutral`
`completeAminoAcidBackbone`	`caab`		`r.caab`
`nucleicAcid`	`na`		`r.na`
`pKa1`	`pKa1`		`r.pKa1 < 2.0`
`pKa2`	`pKa2`		`r.pKa2 < 9.0`
`isoelectricPointPH`	`pI`		`r.pI < 6.0`
`polarity`	`p`	`acidicPolar`, `basicPolar`, `nonpolar`, `polar`	`r.p polar`
`residueSequenceNumber`	`id`		`r.id == 42`
`secondaryStructure`	`ss`	`alpha` (`helix`), `beta` (`strand`), `unstructured` (`loop`)	`r.ss alpha`
`standardResidueName`	`srn`		`r.srn`
`nonStandardResidueName`	`nsrn`		`r.nsrn`
`terminal`	`ter`		`r.ter`
`type`	`t`	See residue type	`r.t ALA`

aminoAcid

The residue.aminoAcid attribute (short name r.aa) matches residues that are amino acids.

Possible values: boolean.

Examples:

residue.aminoAcid (short version: r.aa): matches all residues that are amino acids
node.type atom in residue.aminoAcid (short version: n.t a in r.aa): matches atoms in amino acid residues

charge

The residue.charge attribute (short name r.c) matches amino acid residues with specific charge.

Possible values:

negative
neutral
positive

Examples:

residue.charge negative (short version: r.c negative): matches all amino acid residues with negative side chain charge
residue.charge neutral (short version: r.c neutral): matches all amino acid residues with neutral side chain charge
residue.charge positive (short version: r.c positive): matches all amino acid residues with positive side chain charge

completeAminoAcidBackbone

The residue.completeAminoAcidBackbone attribute (short name r.caab) matches residues that have complete amino acid backbones.

Possible values: boolean.

Examples:

residue.completeAminoAcidBackbone (short version: r.hcaab): matches all residues that have complete amino acid backbones

nucleicAcid

The residue.nucleicAcid attribute (short name na) matches residues that are nucleic acids.

Possible values: boolean.

Examples:

residue.nucleicAcid (short version: r.na): matches all residues that are nucleic acids
node.type atom in residue.nucleicAcid (short version: n.t a in r.na): matches atoms in nucleic acid residues

Dissociation constants

The residue.pKa1, residue.pKa2, and residue.isoelectricPointPH (short name r.pI) attributes matches amino acid residues with certain dissociation constants: pKa1 - the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH pKa2 - the negative of the logarithm of the dissociation constant for the amino functional group, -NH3 pI - the pH at the isoelectric point

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

Possible values: floating-point values.

Examples:

residue.pKa1 < 2.0 (short version: r.pKa1 < 2.0): matches amino acid residues with pKa1 values less than 2
residue.pKa2 < 9.5 (short version: r.pKa2 < 9.5): matches amino acid residues with pKa2 values less than 9.5
residue.isoelectricPointPH < 6.0 (short version: r.pI < 6.0): matches amino acid residues with pI values less than 6

polarity

The residue.polarity attribute (short name r.p) matches amino acid residues with specific polarity.

Possible values:

acidicPolar (also acidic)
basicPolar (also basic)
nonpolar
polar

Examples:

residue.polarity acidicPolar (short version: r.p acidic): matches all amino acid residues with an acidic side chain
residue.polarity basicPolar (short version: r.p basic): matches all amino acid residues with a basic side chain
residue.polarity nonpolar (short version: r.p nonpolar): matches all amino acid residues with a nonpolar side chain
residue.polarity polar (short version: r.p polar): matches all amino acid residues with a polar side chain
residue.polarity acidicPolar or residue.polarity basicPolar (short version: r.p acidic or r.p basic): matches all amino acid residues with an acidic or basic side chain

residueSequenceNumber

The residue.residueSequenceNumber attribute (short name r.id) matches residues with specific residue sequence number (structure ID).

Possible values: integers.

Examples:

residue.residueSequenceNumber == 42 (short version: r.id == 42): matches residues with residue sequence number equal to 42
residue.residueSequenceNumber > 1 and residue.residueSequenceNumber < 10 (short version: r.id > 1 and r.id < 10): matches all residues with residue sequence number between 1 and 10

secondaryStructure

The residue.secondaryStructure attribute (short name r.ss) matches residues with specific secondary structures.

Possible values:

alpha (short name a) - alpha helix
beta (short name b) - beta strand
unstructured (short name u) - unstructured region (loop)
helix (short name h) (same matches as alpha) - alpha helix
strand (short name s) (same matches as beta) - beta strand
loop (short name l) (same matches as unstructured) - unstructured region (loop)

Examples:

residue.secondaryStructure helix (short version: r.ss h): matches all residues in alpha helices
residue.secondaryStructure beta or residue.secondaryStructure unstructured (short version: r.ss b or r.ss u): matches all residues in beta sheets and in loops

standardResidueName

The residue.standardResidueName attribute (short name r.srn) matches residues that have the standard PDB residue names.

Possible values: boolean.

Examples:

residue.standardResidueName (short version: r.srn): matches all residues that have the standard PDB residue names

nonStandardResidueName

The residue.nonStandardResidueName attribute (short name r.nsrn) matches residues that do not have the standard PDB residue names.

Possible values: boolean.

Examples:

residue.nonStandardResidueName (short version: r.nsrn): matches all residues that do not have the standard PDB residue names

terminal

The residue.terminal attribute (short name r.ter) matches residues that are terminal.

Possible values: boolean.

Examples:

residue.terminal (short version: r.ter): matches all residues that are terminal
"CA" in residue.terminal (short version: "CA" in r.ter): matches alpha carbons (by name) in all terminal residues

type

The residue.type attribute (short name r.t) matches residues with specific types.

Possible values:

A, C, G, U, I
DA, DC, DG, DT, DI
ALA, ARG, ASP, ASN, VAL, HIS, GLY, GLU, GLN, ILE, LEU, LYS, MET, PRO, SER, TYR, THR, TRP, PHE, CYS, ASX, GLX, XLE, XAA, SEC, PYL

Examples:

residue.type ALA (short version: r.t ALA): matches all alanines
residue.type HIS (short version: r.t HIS): matches all histidines
residue.type LYS or residue.type PRO (short version: r.t LYS or r.t PRO): matches all lysines and prolines
"CA" in residue.type VAL (short version: "CA" in r.t VAL): matches alpha carbons (by name) in all valines