Molecule.pm Show Source

The Molecule package manages all-atom protein structures. Methods are available to read and write structures from and to different formats and to do some simple manipulations.
This is one of the most fundamental packages since all other packages dealing with all-atom structures use Molecule objects. 

new([PDBfile])
creates a new Molecule object and reads a PDB structures if a file name is given
 
newInherit([PDBfile])
creates a new Molecule object and reads a PDB structures if a file name is given (this form can act as a base class for derived classes) 
readPDB(file[,translate[,ignoreseg]])
reads a protein structures from a PDB file. translate may be set to CHARMM19 for proper recognition of histidine residues. If ignoreseg is set segment IDs from the PDB are not read.
 
readCRD(file)
reads a protein structures from a CHARMM CRD file.
 
readMol2(file)
reads a molecular structure from a MOL2 file
 
readPSF(file)
reads a molecular structure from a CHARMM PSF file.
 
writePDB(file[,translate=>format, longaux2=>1, ssbond=>0, cleanaux=>0])
writes out the current structure in PDB format the output format may be specified through translate. Possible formats are CHARMM19, CHARMM22, AMBER, and GENERIC. A segment ID as required by CHARMM may be given as the third argument
 
readAmber(partopfile,coorfile)
reads protein structure from Amber topology and coordinate files
 
readAmber(partopfile,coorfile)
reads protein structure from Amber topology and coordinate files Amber6
 
readAmber(partopfile,coorfile)
reads protein structure from Amber topology and coordinate files Amber7
 
writeAmber(file)
writes Amber coordinate file
 
slist = generateSegNames(segname)
generates segment names for the current structure from the template given as the argument. It returns a list of generated segment names.
 
slist = generateSplitSegNames()
generates segment names, splitting where chain breaks are found. Names go AA00-ZZ00. Returns a list of generated segment names.
 
slist = getSegNames()
generates and returns segment name list for the current structure
 
copySegNames(mol)
sets the segment names from another Molecule object
 
getChain([chainid])
returns chain for given ID or first chain if no argument is given
 
activeChains([chainid])
returns a list of active chains
 
selectChain(chainid)
set a chain to be used as default
 
numberAtoms()
numbers all atoms continously across chain/segment boundaries
 
removeChain()
 
removeHetero()
if there's a heteroatom chain, remove it
 
countInterfaceContacts([distCut][,chainA][,chainB][,CACBonly])
Count the number of atomic contacts across an interface Operates on all pairs of chains if no chain IDs are specified Operates on all partners for given chain if one chain ID is specified Operates only on one pair if two chain IDs are specified Returns an array of hashes with {AAcontacts}, {cidA}, {cidB}
 
setValidSequence(sequencestring)
sets the valid flag to 1 for residues that match the given sequence string this method recognizes a previous residue subselection
 
setValidChain(chain[,exclude])
sets the valid flag to 1 for all residues in the given chain
 
setValidResidues(fraglist)
sets the valid flag to 1 for residues in the fragment list and to 0 for residues outside the list
 
setValidSegment(segname[,exclmode])
sets the valid flag to 1 for residues with the given segment name
 
markClashes()
finds and marks atom-atom clashes
 
resetValidResidues([value])
sets the valid flag of all residues to the given value (default: 1)
 
$list = listFromValid(force)
returns a list of residues from the residues previously set with setValidResidues.
 
zapCoordinates([chain])
sets all coordinates in the current structure to zero
 
fillCoorFromPDB(file)
updates only coordinates from a PDB file
 
merge(refmol)
merges the current structure with the structure in refmol on a per residue basis
 
$mol = clone([valid])
generates a copy of the current molecule and returns it. If the valid flag is set, only valid residues are copied
 
translate(mode)
translates the current structure according to the mode argument. As with writePDB the following modes are recognized: CHARMM19, CHARMM22, AMBER, and GENERIC.
 
$map = renumber([map|startindex][,chain])
renumbers the residues either according to a map given as an argument or continuously beginning from a start index. The method returns the translation map which may be applied to other structures or used to revert the residue numbering to its original form using numberReset
 
renumberWaterSegments()
renumber water segments to range from 1-10000 and avoid overflow water segments are identifed by WT* labels
 
numberReset(map[,chain])
applies the reverse translation from the one given in the map argument
 
shiftResNumber(add[,chain])
shifts all residue numbers by a constant. A chain ID may be given to shift residues in that chain
 
($cx,$cy,$cz) = centerOfMass()
calculates the center of mass for the current structure
 
center()
centers the current structure by subtracting the center of mass from all coordinates
 
move(dx,dy,dz,chain)
shifts the current structure by the given distances in x/y/z direction
 
add (mol)
adds $cmp (a vector in the form of a pdb object) to mol (similar to but simpler than "displace")
 
subtract(mol)
calculates the difference vector with respect to given molecule
 
scale(factor,[chain])
scales all coordinates by given factor
 
displace(vectorarr,amplitude,massweighting)
displaces atoms along given vectors with amplitude mass weighting is done if flag is set
 
rotate(m11,m12,m13,m21,m22,m23,m31,m32,m33,chain)
rotates the current structure according to the given rotation matrix
 
matrixOperation(A,B,C,D,E,F,G,H,I [,chain])
apply the matrix operator: A B C D E F G H I
 
resetResidueName(resname,resnum[,chain])
sets the residue name for a given residue number
 
fromSequence(inx,atomname,sequence)
generates a molecule structure from a list of amino acids
 
rebuildFromSICHO(sequence,chain[,fraglistoption,refPDB])
fromSICHO(sequence,chain)
rebuilds an all-atom structure from a SICHO chain and sequence file. For loop modeling loop/fragment residues and a protein template in PDB form may be given as generates a molecule structure from a SICHO chain file
 
fromXYZ(xyz,atomname)
generates a molecule structure from a list of XYZ coordinates
 
rebuildFromSICHO(sequence,chain[,fraglistoption,refPDB])
rebuilds an all-atom structure from a SICHO chain and sequence file. For loop modeling loop/fragment residues and a protein template in PDB form may be given as extra arguments
 
completeWater()
adds water hydrogens
 
completeResidue()
completes missing peptide backbone and side chain atoms
 
fixCOO()
corrects the position of OT2/OXT if necessary
 
solvate([cutoff,[shape]])
solvates a PDB from a pre-equilibrated water box returns error output from solvate program
 
replaceIons(list)
replaces water molecules randomly with ions
 
changeResName(list)
changes the residue names according to the list
 
fixHistidine(hsdlist,hselist,hsplist)
changes the residue names to HSD and HSE respectively according to the lists of residues given as arguments
 
setChain(chainid)
sets the chain ID for the current structure
 
match(refMolecule)
matches residues between two structures with different residue numbering and/or missing residues. This method changes the residue numbering of the current structure to match the reference structure given as the argument
 
$index = getResidue(resnum[,chain])
returns the residue index for a residue number. A chain ID may be given as additional argument for multi-domain structures
 
$index = getResidueInChain(resnum[,chain])
returns the residue index for a residue number. A reference to a chain structure may be given as additional argument for multi-domain structures
 
$atom = getAtomInResidue(residue,name,chain)
returns the atom index for an atom name
 
$distance = minDistance(ir,jr)
returns the minimum distance between heavy atoms of residue structures ir and jr.
 
number = firstResNum([chain])
returns the number of the first residue. If a chain reference is given as argument it returns the number of the first residue of that chain
 
number = lastResNum([chain])
returns the number of the last residue. If a chain reference is given as argument it returns the number of the last residue of that chain.
 
ret = empty()
returns 1 or 0 whether the current molecule is empty
 
setValidSelection(selection)
sets the valid flag to 1 for residues/atoms according to the given selection 
$mol = genPRIMO()
generate reduced PRIMO (protein intermediate model) representation from all-atom structure
 
$sel = parseSelection($selection)
parses selection data structure and returns results in hash data structure with the following elements: chain, segment, residue, atom, mode, resrange 
chain[] -> { id atom[] res[] resinx[]
             xcoor[] ycoor[] zcoor[] }
  atom[] -> { atominx atomname resname resnum
              chain xcoor ycoor zcoor hyd seg aux1 aux2 hetero }
  res[]  -> { name num start end seg valid chain hetero }
molecule information with substructures containing atom and residue information as well as a residue lookup table and coordinate cache arrays.
 
chainlookup -> { chainid ... }
lookup hash table for multiple chains
 
defchain
currently selected default chain
 
segmentlist[] -> { name first last }
list of segment IDs
 
ssbond[] -> { chain1 resnum1 chain2 resnum2 }
disulfide bonds
 
havesegments
GenUtil.pm  Sequence.pm  SICHO.pm  Analyze.pm
Michael Feig, Brooks group, TSRI