Filters

Atom Filters

/[NO]ATYPE=atype 
/[NO]ATYPE=(atype,atype,...atype)

Selects (/ATYPE=) or excludes (/NOATYPE=) atoms with an atom type field which matches "atype". The atom type field consists of 1- 4 characters, where the first 1-2 characters must be the atom symbol (e.g., "Br"). In specifying the atom symbol, upper and lower case characters are treated equivalently. The wildcard characters "*" (matches any number of characters) and "%" (matches any single character) are not supported for "atype". 

MAINCHAIN
/[NO]MAINCHAIN
Selects (/MAINCHAIN) or excludes (/NOMAINCHAIN) mainchain atoms (N, CA, C, O) in peptides. Note that /NOMAINCHAIN is equivalent to /SIDECHAIN. 

SIDECHAIN
/[NO]SIDECHAIN
Selects (/SIDECHAIN) or excludes (/NOSIDECHAIN) sidechain atoms in peptides. Note that /NOSIDECHAIN is equivalent to /MAINCHAIN. 

HYDROGEN
/[NO]HYDROGEN
Selects (/HYDROGEN) or excludes (/NOHYDROGEN) hydrogen atoms. 

HCARBON
/[NO]HCARBON
Selects (/HCARBON) or excludes (/NOHCARBON) hydrogens on carbon atoms. 

HHETERO
/[NO]HHETERO
Selects (/HHETERO) or excludes (/NOHHETERO) hydrogens on heteroatomic atoms. 

HETERO
/[NO]HETERO
Selects (/HETERO) or excludes (/NOHETERO) heteroatomic atoms (atoms which are neither hydrogen nor carbon). 

DUMMY
/[NO]DUMMY
Selects (/DUMMY) or excludes (/NODUMMY) atoms which are MWS dummy atoms. 

RING
/[NO]RING
Selects (/RING) or excludes (/NORING) atoms which are in rings. 

CHIRAL
/[NO]CHIRAL
Selects (/CHIRAL) or excludes (/NOCHIRAL) atoms which are chiral.

Residue Filters

/[NO]RTYPE=rtype
/[NO]RTYPE=(rtype,rtype,...rtype)
Selects (/RTYPE=) or excludes (/NORTYPE=) residues with residue type "rtype". Residue type "rtype" is a name denoting the particular type of residue (e.g., "ALA", "GLY"). "rtype" is a string of 1-4 characters from the set "A-Z" and "0-9". Provided the input structure adheres to the IUPAC 3-letter naming convention for amino acid residues (e.g., "ALA", "GLY", "LEU", ...), the PSL recognizes the following special "rtype" class names, each of which can optionally be prefixed by "NO" to negate the definition: 

[NO]PHILIC       [no] hydrophilic residues
[NO]PHOBIC       [no] hydrophobic residues
[NO]POLAR        [no] residues with polar sidechains
[NO]CHARGED      [no] residues with charged sidechains
[NO]POSITIVE     [no] residues with positively charged sidechains
[NO]NEGATIVE     [no] residues with negatively charged sidechains
[NO]AROMATIC     [no] residues with aromatic sidechains
[NO]ALIPHATIC    [no] residues with aliphatic sidechains
The definitions of currently defined residue filters are as follows: 

PHILIC
   ARG ASN ASP GLN GLU HIS HID HIE HIP LYS SER THR


PHOBIC
   ALA ILE LEU MET PHE PRO TRP VAL TYR GLY CYS CYX


POLAR
   ARG ASN ASP CYS CYX GLN GLU GLY HIS HID HIE HIP
   LYS SER THR TYR


CHARGED
   ARG ASP GLU HIS HID HIE HIP LYS


POSITIVE
   ARG HIS HID HIE HIP LYS


NEGATIVE
   ASP GLU


AROMATIC
   HIS HID HIE HIP PHE TRP TYR


ALIPHATIC
   ALA ILE LEU LYS PRO VAL

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